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Editing others comments

I though editing others comments was a no go? Doc James (talk · contribs · email) (if I write on your page reply on mine) 09:06, 2 January 2013 (UTC)

A barnstar for you!

The Editor's Barnstar
Thank you for taking the time merging Xenobiotic metabolism and Drug metabolism with a high catalytic turnover without any toxic side-effects. Squidonius (talk) 01:05, 4 January 2013 (UTC)
Thanks for pointing out the problem. Those two articles were begging to be merged. No one has so far complained, so it appears any toxicity was minimal ;-) Boghog (talk) 21:05, 6 January 2013 (UTC)

Thanks for fixing my edits

Hi Boghog. I just wanted to thank you for fixing my edits. I was not sure how to merge the references. 132.216.227.218 (talk) 20:49, 6 January 2013 (UTC)

No problem. And thank you for your contributions. Cheers. Boghog (talk) 21:10, 6 January 2013 (UTC)

Wikipedia Ambassadors update

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the updated hCG diet

I dont consider Mayoclinic an unreliable source, by "spammy content" I was referring to the website of an hCG clinic. However, I again must insist that the statement from the American Society of Bariatric Physicians be edited, as this is an OBVIOUS CONFLICT OF INTEREST. Also, the comment that implies the prisoners in Auschwitz had it better than people on an hCG diet is completely disrespectful to Jewish people, as well as inflammatory to a ridiculous degree. It is designed to incite fear by way of bombast, not provide a comparison. An unbiased comparison would be between the normal human caloric intake required for optimal health and a low calorie hcg diet. Not comparing holocaust victims to dieters. — Preceding unsigned comment added by 108.225.56.239 (talk) 22:10, 25 January 2013 (UTC)

Thanks for bringing up your concerns. I agree that the Auschwitz comparison is both unnecessary and inflammatory therefore I have removed it. Boghog (talk) 22:28, 25 January 2013 (UTC)

Looks good for now. I wish that there was some way to include the fact that there are medically licensed clinics who have increased the caloric intake from an unsafe 500 daily all the way up to 1250 daily. This is the largest advancement in the hcg diet in over 50 years. How can we include this new information without violating Wiki policy? thanks 108.225.56.239 (talk) 00:01, 26 January 2013 (UTC)

This point is already covered in the article by the statement such diets prescribe calorie intake of between 500 and 1,000 calories. Furthermore as already stated in the article, the hcg diet is neither safe nor more effective than calorie restriction without hcg. A variant of a diet that is less unsafe, equally ineffective, and still illegal is an advance? Finally how can medically licensed clinics be supevising illegal diets? Unless of course they are not including hcg in the diet. Boghog (talk) 11:20, 26 January 2013 (UTC)

The point is that, why is it that in order to update something, I need a "peer reviewed study"? Yet the Bariatric Association who is in direct competition with any weight loss regimen, and stands to lose money, is allowed to comment on their competitors. Furthermore, the Mayo Clinic is also not a peer reviewed study, yet is cited as a resource and allowed. Im just questioning the double-standard here. To answer your questions, the "modernized" hcg diet allows for up to 1250 calories daily, is not illegal, is indeed less unsafe (hence should be distinguished from the controversial 500 calorie diet that most clinics recommend). Only a medically licensed clinic can prescribe anything, they just have to preface it with the FDA warning essentially, like a disclaimer. There is just a lot of misinformation associated with this page, and it's frustrating. And to make it worse, when you, Boghog, make a judgement, you are also solely basing it off of misinformation provided by this page! Long story short, I can find studies that confirm hCG's effectiveness in preventing muscle loss during dieting. It is true that the lowered caloric intake is ultimately responsible for weight loss, but Dr Oz actually conducted a small study on his show that compared muscle loss on hCG as opposed to simply lowered calories. The person on hCG lost only 2lbs of muscle and around 10lbs of fat, while the person not on hCG lost the same weight, around 12lbs, but 5lbs of muscle loss and 7lbs of fat. Sorry to be a pain, but I'm just sick of seeing all this misinformation posted by companies that stand to lose money, which is hypocritical. — Preceding unsigned comment added by 108.225.56.239 (talk) 18:31, 28 January 2013 (UTC)

There is one large pharmaceutical company, namely Merck & Co., the manufacturer of HCG Pregnyl, who would stand to make a lot of money if these claims were true. Merck often conducts clinical trials in order to obtain new approved indications for existing products. If there was anything behind this, why hasn't Merck tried to prove it?
Furthermore, per WP:MEDRS, medical claims in Wikipedia articles must be supported by high quality review articles. The statements concerning lack of efficacy of hCG in weight loss in the Human chorionic gonadotropin article are largely based on PMID 8527285 that meets the requirements of MEDRS. The American Society of Bariatric Physicians and Mayo Clinic are nationally recognized expert bodies and therefore also meet the requirements of MEDRS. In contrast, claims made by Dr. Oz are highly suspect.
Finally there may be some truth that including hCG in a diet treatment may bias weight loss towards fat and away from muscle since hCG may increase testerone levels. However such a claim would require a MEDRS compliant citation. Boghog (talk) 01:18, 29 January 2013 (UTC)

Can I buy you a pint?

Thanks for making my first foray into editing painless! Joehjoeh (talk) 05:03, 6 February 2013 (UTC)
Thanks for the pint to which I am quite fond. And thank you for your IP contributions (I am not sure which one since you now have a registered account, but I have recently run across a number of high quality IP edits and I just followed up with a bit of tiddying). In any case, welcome to Wikipedia and if you have any questions, please don't hesitate to ask. Cheers! Boghog (talk) 19:50, 6 February 2013 (UTC)

Updates

Thanks for the great updates to the mTORC1 and mTORC2 pages. I had it on my todo list, but the parts you factored out sound great - Davebridges (talk) 00:22, 8 February 2013 (UTC)

No problem and thanks for pointing out what needed to be done. All I did was to split out the material and add some infoboxes. There is still a bit of redundancy between the articles that will hopefully be reduced over time. Cheers. Boghog (talk) 20:05, 10 February 2013 (UTC)

MIF Wiki

Thank you for your good faith edits on the MIF page. I was preparing to revise and repair the page when you reverted me. I respectfully stand by my original statement that the page is quite messy. It is overloaded with references and underloaded with explanations. I must politely ask you--who is the audience you are writing for? An expert in the field will know how to do literature searches, and so has no need of a great pile of references. As I see it, the main audience is going to be undergrads and beginning grad students etc who would like to be taken by the hand and given a simplified Scientific American type explanation of this protein. The article does not even come close to doing that at this moment. I never questioned the notability, in my mind the mere fact that at least one paper has been published on it is sufficient to prove notability.

If this is your "pet page" or something, then I will leave it alone. But please consider my words--I would far rather see a page that says something like "MIF was found to do this" (ref) which later proved useful because of blah blah (ref) rather than a page that gives whole piles of references that no one is going to bother with anyway.

I also looked at the talk page and I gather that this is a controversial field. I understand that you have your own POV but I would prefer to see a neutral Wiki--I think it is probably better to stick to things that are NOT controversial, give the undergrads a brief intro, and (if needed) refer them to papers on the opposing sides of the controversy, where they may judge matters for themselves.Yurasis Dragon (talk) 13:41, 9 February 2013 (UTC)

There is a serious disconect between your polite explanation above and your edit to the MIF article. In particular:
  • I never questioned the notability – then why did you add a {{Notability}} tag to the article?
  • I gather that this is a controversial field – please carefully read this. Can you supply a reliable source that documents that this is a controversial field?
  • I would prefer to see a neutral Wiki – On this point, we are in complete agreement.
I also agree that the article can be written in a more accessible style, particularly the intro. But I think this article can be useful to both a general readers and specialists. I also think you completely misunderstand the point of the references. The references are primarily to support statements in the article and seconardily provide more details for those that are interested. No one is forcing you to read the references. If you don't want to read them, ignore them. But it is essential that they be included in the article. Boghog (talk) 15:22, 9 February 2013 (UTC)
I have a few additional questions:
  • Why was the {{PBB/4282}} infobox removed from the article? This infobox provides a wealth of valuable information about the MIF gene and the protein encoded by that gene. These infoboxes are included in approximately 10,000 Wikipedia articles as part of the Gene Wiki project.
  • Why was the interwiki link to the French article removed?
  • What is so controversial about the following statement:
"Macrophage migration inhibitory factor assembles into a trimer composed of three identical subunits". This statement was supported by the citations at the end of the paragraph. Also the graphic of the crystallographic structure in the infobox provides rock solid evidence that this protein forms a trimer.
Boghog (talk) 15:45, 9 February 2013 (UTC)

Sorry I did not insert any templates. What I did was remove a lot of spurious biased editing before you reverted my work. Whether you believe it or not, or choose not to acknowledge it, your editing appears to be extremely biased towards a POV. Mind you, I am not saying you are wrong, but you must not try to hijack a page to present a non-neutral POV. I am sure that I could find many published and widely cited references to support any POV you like (check out flying saucers, alien abductions, or for that matter, religious texts like the Bible). Controversy is evident from the talk page. All that I ever said was that if you want to include a pile of references to papers by your best friend, boss, or whatever, you should take the time to weave them into the text. Simply picking references because you happen to know or like someone is not acceptable behavior. Wikipedia is not a billboard to advertise your POV. Instead, try to answer questions--like, why is it macrophage migration etc? Does it inhibit macrophage migration? Reference? Your behavior has turned a competent article into a swamp. Please consider your actions, as they are contrary to Wiki principles. Yurasis Dragon (talk) 21:21, 9 February 2013 (UTC)

OK, let's cut to the case. Why do you dislike Richard Bucala? Has he wronged you in some way? Just to be clear, I did not insert these citations. Furthermore I have no connection whatsoever to Richard Bucala. However I do question why you insist on deleting relevant high quality citations that are co-authored by Richard Bucala. He has published a large number of papers on this topic and it would be difficult to write an authorative article on this protein without citing some of his papers. Purging the article of papers from Richard Bucala would also be introducing a strong POV.
Finally I agree that the much of the article is pretty dense so I have started to edit it to make it more accessible. Boghog (talk) 21:42, 9 February 2013 (UTC)
In direct response to your assertions:
  • "if you want to include a pile of references to papers ... you should take the time to weave them into the text" – The references directly support the text in the article. Can you find a single example in the article where an in-line citation is not relevant to the text? Boghog (talk) 22:42, 9 February 2013 (UTC)
  • "Controversy is evident from the talk page" – I repeat the question I raised above but received no answer: Can you supply a reliable source that documents that this is a controversial field? Boghog (talk) 22:42, 9 February 2013 (UTC)

Obviously I have not spoken clearly enough. I do not question the references, I am merely suggesting that you take the time to integrate them into the text. Imagine if you wanted a history of Big Name City and someone handed you a phone book. What does it teach you? Yes, you can find lots of references to MIF, many highly cited. What purpose does it serve to list them? How does that teach anyone anything? Again, I think that you are writing for an audience of zero. Experts know the literature, and can find search engines, etc. Novices will be bewildered by references that are not explained in a neutral fashion.

I have nothing against anyone you have cited. I merely find it strange that you insist on including references to someone and fight so hard to do it. If the discussion in the text warrants it, then fine. I do not see the point of selecting references and forcibly adding them. That and the evident controversy from the talk page makes me suspicious of your motives.

As far as "reliable" sources exhibiting the existence of controversy, I do not consider Wikipedia itself to be a reliable source. No one is going to stick their neck out saying a paper is wrong. Just because a paper is published does not mean it is correct (look at a "retracted" papers list).

My position remains the same--the right thing to do is to present a simplified, dumbing down if you will, view of the situation. I seriously doubt an expert in MIF whatever is going to go to Wikipedia for answers. They know them, they will read the original papers and do whatever. The folks who read Wiki on this are likely beginners who want a sound bite or two for their term paper. An avalanche of references that are not directly referenced in the text serves no one. If you cannot spend the time to do the right thing, perhaps you should leave it for editors who have the time.

Yurasis Dragon (talk) 00:13, 10 February 2013 (UTC)

In response to your statements:
  • "I am merely suggesting that you take the time to integrate them into the text." – As I already stated above, these references are already integrated into the text. And as I already requested above, show me a specific example where a reference is not integrated.
  • "What purpose does it serve to list [highly cited references]?" – As required by the Wikipdia's core verifiability policy, all wikipedia articles must be based on reliable sources. And as explained in WP:CITE, these citations should ideally be in-line so that is clear what citation supports which statement. Finally per WP:SCIRS:
"In general, scientific information in Wikipedia articles should be based on published, reliable secondary sources, or on widely cited tertiary and primary sources. Sources that are robust in methodology, published in high quality venues, and authored by widely cited researchers are preferred."
  • "Just because a paper is published does not mean it is correct" – A paper is more likely to be correct if it is highly cited (because it has been checked and reviewed by other scientists). Furthermore a secondary source that reviews primary sources are also more likely to be correct. Hence the former are preferred over the later. However please keep in mind that secondary sources are not automatically better than primary sources. A high quality primary source may be superior a superficial review article published in an obscure journal.
  • "I do not consider Wikipedia itself to be a reliable source" – Of course it isn't. That is why we must cite reliable sources to support statements made in Wikipedia articles. There are already a number of high quality sources in the article that directly support statements made in the article. If you think that a particular statement in the article that is already supported by a reliable source is controversial, then the burden of proof is on you to supply a second reliable source to document that controversy. So far you have supplied none.
  • "No one is going to stick their neck out saying a paper is wrong." – It happens all the time. This is how science works.
  • "you are writing for an audience of zero" – Wikipedia conforms to the long tail. There are basic articles like gene and protein where it is especially important to write in a way that is understandable by a wide auidence. Then there are more specialized articles like MIF who are much less likely to be read by the general public and more likely to be read by a technical auidence that includes undergraduate science majors, graduate students, and even professionals who just want a quick introduction to the subject. Of course a professional that is very interested in a subject will thoroughly read the relevant scientific literature, but a well written Wikipedia article can nevertheless provide a valuable introduction.
  • "An avalanche of references that are not directly referenced in the text serves no one" – Again, show me a specific example where a reference is not integrated and relevant to the text.
  • "If you cannot spend the time to do the right thing" – removing high quality relevant references from an article is not the right thing to do. Defending these references is the right thing to do.
Finally I have been working to make the introduction of the article more accessible. For example, I have recently added the following to the article:
Bacterial antigens stimulate white blood cells to release MIF into the blood stream. The circulating MIF binds to CD74 on other immune cells to trigger an acute immune response. Hence MIF is classified as an inflammatory cytokine. Furthermore glucocorticoids also stimulate white blood cells to release MIF and hence MIF partially counter acts the inhibitory effects that glucocorticoids have on the immune system. Finally trauma activates the anterior pituitary gland to release MIF.PMID 16677407
Is this clear enough? Boghog (talk) 06:38, 10 February 2013 (UTC)

Glad to see that you took my advice and started cleanup on this messy article. Saves me the trouble of doing it myself. Thank you very much!

Incidentally, you may choose to look at the Wiki page on myoglobin. Even though myoglobin is undeniably a far more important protein than MIF, there are far fewer references than there are in the MIF page, and none to the author you mentioned. I wonder why that is.

Happy editing, and thanks again! Yurasis Dragon (talk) 21:50, 10 February 2013 (UTC)

C-reactive protein reference

You may want to have a look here at the page I'm going to link. The citation journal template examples shown have the full name of the journal written out. I don't think it matters if the other references in the article are written that way, that would just mean they all need to be changed and are currently formatted incorrectly. Please look here at the examples. It is true that some of the examples here write the pages in a 91-8 format but other show a 91-98 format so there's no reason to undo my addition on that either. Where you moved the URL in the reference is fine. Please make the appropriate changes to the reference or I will since most of my reference method was correct per the template:cite journal page seen here: http://wiki.riteme.site/wiki/Template:Cite_journal TylerDurden8823 (talk) 00:12, 11 February 2013 (UTC)

It is not incorrect to use abbreviations for journal names. Abbreviated journal name are frequentely used in journals themselves and also in the widely used Vancouver system. The examples in the {{cite journal}} template documentation are just that, examples. There is no Wikipedia requirement that full journal names must be written out in citations. Most of the citation in the C-reactive protein article were created using User:Diberri's Wikipedia template filling tool (instructions). This tool in turn obtains citation data from PubMed that abbreviates journal names. I used this tool to reformat the citation that you added to the article so that it was formatted consistly with the rest of the citations in this article.
I don't have any strong preference for abbreviated or full journal names but ideally citations within one article should be formatted consistently. Furthermore per WP:CITEVAR, one should normally follow a pre-estabished citation style if one already exists. Concerning the page number format, per MOS:ENDASH please note that an en dash instead of a simple dash should seperate the beginning and ending page numbers. Again, I don't have any strong feeling if the full or abbreviated page number is used to designate the end of the page range, but one style should be used consistently through the article. Boghog (talk) 07:04, 11 February 2013 (UTC)
Well, it doesn't look like the preferred method is to abbreviate the journal name. It also does not look like it was incorrect to use the full name of the journal and therefore should not have been changed. While true that if an established citation style exists on a page, as a guideline, you should follow it. However, if the article is consistently using an incorrect method of citation, this does not mean it should still be followed. It simply means the other citations should be corrected. I never said that abbreviating the journal is wrong, but that it was unnecessary to change the way I put it since it was not wrong either and certainly did not appear to be the standard from the cite:journal template page that I showed you. The way you formatted the page numbers seems to be common but it was far more common on that cite journal template page to use the full name of the journal. So, my method was not wrong either. I wasn't referring to the dash for page numbers but the 11-9 vs. 11-19 formatting difference. Anyway, what's done is done but I think next time you should think a bit more about changing it regarding the journal name. The citation journal template examples should not be ignored. TylerDurden8823 (talk) 07:19, 11 February 2013 (UTC)
Just to be clear, per WP:CITEVAR, one should follow a pre-existing citation style (in this case the use of journal abbreviations in citations) if one already exists. Your introduction a full journal name to this article is contrary to CITEVAR, while my abbreviating this journal is consistent with CITEVAR. Boghog (talk) 07:33, 11 February 2013 (UTC)
This FAQ is also relevant. Editors of any particular article may use any style they want, just as long as it is internally consistent and respects CITEVAR. The style in the C-reactive protein article follows the Vancouver system which normally uses abbreviated journal names. Boghog (talk) 04:53, 12 February 2013 (UTC)

Infobox nonhuman protein

let me know if there is something I can do to help, or if you think the link format is acceptable, then never mind :) thank you. Frietjes (talk) 16:44, 12 February 2013 (UTC)

Hi. Thanks for your offer of help with the {{Infobox nonhuman protein}} template. I am having a relatively minor formatting problem as you can see in with the infobox PDB parameter in the article dnaG. The external hyperlink works, but if the list of available PDB accession codes is long, the infobox becomes very wide. I am trying to figure out a way produce a link that is both functional and would automatically wrap over more than one line so the width of the infobox would remain constant (e.g., based on the PDB parameter, produce a displayed string that contains spaces; would need a {{Str repc}} function that can do search and replace multiple times). Is there any way to do this? This is not a big deal and I can easily wait for the release of Lua template scripting where problems like this should be easy to fix. Cheers. Boghog (talk) 05:57, 13 February 2013 (UTC)

wikidata getting started

Boghog, the wikidata project seems to be moving forward and we are about to enter a big development phase. Would love to have your input over there. In particular have a look Wikidata:Property_proposal#Biochemistry_and_molecular_biologyGenewiki123 (talk) 22:58, 19 February 2013 (UTC)

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TAS-108

Thanks for your help! I looked at the documentation for Drugbox and realized I didn't really know how to find that information. Disavian (talk) 20:38, 24 February 2013 (UTC)

No problem. The Drugbox syntax is a bit complicated and takes some getting use to. It is also a challenge to track down the data. Cheers. Boghog (talk) 20:44, 24 February 2013 (UTC)

Ephrin

In this revision last month to Ephrin, you changed a sentence in the lead from: "...Eph receptor, which compose the largest known subfamily of receptor protein-tyrosine kinases (RTKs)" to: "Ephrins compose the largest known subfamily of receptor protein-tyrosine kinases (RTKs)." This seems to me to change the meaning of the sentence from saying that the receptors that ephrins are ligands for are the biggest subfamily of RTKs to that ephrins themselves are the largest subfamily of RTKs without a citation verifying this change. I've started a discussion on Talk:Ephrin, and would appreciate your input there. Regards, 137.43.188.147 (talk) 17:43, 25 February 2013 (UTC)

Thanks for the heads up. I have replied on the articles talk page and fixed the typo in the article. Cheers. Boghog (talk) 21:38, 27 February 2013 (UTC)

gp41

Thanks, looks a lot better now! Xtothel (talk) 10:20, 11 March 2013 (UTC)

Likewise, thank you for your edits. A real team effort! Cheers. Boghog (talk) 20:55, 11 March 2013 (UTC)

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from Arnowt-RoidCalc

>>If you feel the link should be added to the page, please discuss it on the associated talk page rather than re-adding it.
Where can I discuss it? please link...thanks

---------------------------------------------------------
I think that this link should be on every page with a description of any medical esters.
It helps to understand the saturation in the body by these substances.
RoidCalc help many novice athletes not to make mistakes.
See for yourself and make sure it is working http://roidcalc.powerbody.ru/?langid=8
I have written this calculator for the Russian part of the Internet.
Now translated into English for the world.
He is often referred to the Russian Wikipedia page
http://ru.wikipedia.org/wiki/%D0%9D%D0%B0%D0%BD%D0%B4%D1%80%D0%BE%D0%BB%D0%BE%D0%BD%D0%B0_%D0%B4%D0%B5%D0%BA%D0%B0%D0%BD%D0%BE%D0%B0%D1%82
---------------------------------------------------------

Arnowt(talk) —Preceding undated comment added 07:26, 21 March 2013 (UTC)

Please read about edit

Thank You
We have to relate zinc fingers and schizophrenia for a school project, so thats why we have the schizophrenia section in this article. PLEASE DO NOT REMOVE IT RIGHT NOW, you can take it down after a couple of weeks after it gets marked

Thank you! Hulksad (talk) 03:11, 22 March 2013 (UTC)

Thank You!

Thank you for helping clean up Diphenhydramine article. I think we can get this to GA article with a little bit of work if we work together. I dont know if you would be interested in that? (Lowkeyvision (talk) 16:59, 17 March 2013 (UTC))

Likewise, thank you for your recent edits. I am far from an expert on diphenhydramine but I will see what I can do to help out. There are two immediate things that I think need to be done. First of all, we need to make sure that the sources of the medical/clinical parts of the article conform to WP:MEDRS. Second, we should make sure that the entire article conforms to WP:PHARMMOS. Cheers. Boghog (talk) 18:31, 17 March 2013 (UTC)
First, I am very glad I found someone else who is interested in this article!!! This article has a lot of potential to fix up and two heads are better than one. I think we have good synergy. Second, I saw that you added a section on pharmacokinetics. On the right side there is a panel which shows pharmacokinetics already. Is there a reason why you wanted to restate the pharmacokinetics in the article in addition to the side profile? (Lowkeyvision (talk) 07:31, 20 March 2013 (UTC))
Hi. Thank you for all your hard work as well. While the pharmacokinetics section does repeat some of the information in the drugbox, it also contains information not found in the infobox. I intend to expand this section further. In addition, including a separate pharmacokinetics is recommended in the WP:PHARMMOS style guide (see sections). Also per WP:PHARMMOS, I think it is better to keep "medical uses", "available forms", and "brand names" in separate sections. We must avoid the appearance of recommending a particular brand for a particular indication. Boghog (talk) 07:50, 20 March 2013 (UTC)
Sound good :) (Lowkeyvision (talk) 11:46, 20 March 2013 (UTC))
Do you think the article is almost complete? (Lowkeyvision (talk) 04:46, 22 March 2013 (UTC))
The Guidance Barnstar
For your guidance to a rookie Wikipedia editor and for your help in fixing the table, adding the pharmacokinetics section, adding/fixing citations and helping the overall clean up of the Diphenhydramine page!
Was looking at the table: I switched it so central and peripheral come afterwards. I dont know what you think. Revert it to the other way if you like. Just wanted you opinion. (Lowkeyvision (talk) 13:19, 23 March 2013 (UTC))
I don't have a strong feeling either way, but I thought placing the main therapeutic use for this drug which occurs in the periphery should be at the top of the table whereas the central activity is generally regarded as a side effect. BTW, thanks for the barnstar, but it may be slightly premature since are not quite done with the GA editing. :-). Anyway, I think we are now very close. I will expand the pharmacokinetics section soon. Cheers. Boghog (talk) 13:51, 23 March 2013 (UTC)
I am okay with that change. :) The sedative property is also used as a therapeutic effect, but nowhere near the anti-allergic use and so your change is definitely appropriate. Whether this reaches GA or not, you deserve the Barnstar for the guidance you provided. That being said, I hope you will continue to work with me to improve this article and we can collaborate on more in the future. :) (Lowkeyvision (talk) 14:40, 24 March 2013 (UTC))

A cheeseburger for you!

It was nice to see the huge amount of work you have done in your field on Wikipedia. It is really inspiring. Thanks. Abhijeet Safai (talk) 12:19, 30 March 2013 (UTC)

by way of the GW-whatever article

I have posted at WT:MED regarding what I see as a possible need for a WP:NTHERAPEUTIC. The GW research chem case we're both involved in might be germane. I think I explain my thinking more extensively, and hopefully more clearly, over there. -- [ UseTheCommandLine ~/talk ] # _ 08:20, 31 March 2013 (UTC)

Yes, I definitely also see a connection. I will follow the discussion and may join if I have something useful to contribute. Thanks for the heads up. Boghog (talk) 09:20, 31 March 2013 (UTC)

Thanks for your help with Cycle (gene)

My group and I are working on a class project where we edit Wikipedia articles pertaining to our fields of study. We are all Wikipedia novices, so your help with formatting and protein boxes has been greatly appreciated. Thank you! — Preceding unsigned comment added by Dudas 91 (talk • contribs) 19:44, 13 April 2013 (UTC)

And thank you and your classmates for your valuable contributions to this interesting set of circadian rhythm gene articles. If you have any questions about the infoboxes or any other questions, don't hesitate to ask. Cheers. Boghog (talk) 07:24, 14 April 2013 (UTC)

Blue about Genes

Thank you for the advice. It was very constructive and very much appreciated. I'm hesitant to rename articles if they're outside my areas of knowledge (unless they're quite obviously incorrect). I suspected that changes since the articles were written were partly to blame. My primary focus is really on the "underlinked" tags and trying to reduce that backlog (13,000+ articles!), but the English Teacher in my brain wouldn't let me pass up those opening sentences. I'll confine myself to linking from now on. I hope I haven't caused too much damage. (I'm only up to "C").WQUlrich (talk) 22:16, 27 April 2013 (UTC)

Thanks for your reply and no worries. The links that you added were useful and appreciated. Logically you are correct about the article name/lead sentence agreement. We probably should have named these after the protein name from the beginning, but it was easier for the bot that created these articles to use the gene names. Perhaps we should have another bot run to rename the articles. Cheers. Boghog (talk) 22:21, 27 April 2013 (UTC)

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XRCC4

Hey, I do appreciate the suggestions you've left on the talk page and I think the students have done their best in the time that they've been given. Since their assignment ends tomorrow, I'm thinking about diving in to this one myself - I know you do a lot of molecular bio stuff already, would you be interested in working together? :) If not, I'll be taking the rest of your suggestions into account when I dive in. Thanks again. Keilana|Parlez ici 21:33, 9 May 2013 (UTC)

Thanks for your interest in this subject. I agree the students have done a great job in expanding the article. After their assignment ends, I would be delighted in working with you on improving on the article further. Cheers. Boghog (talk) 21:46, 9 May 2013 (UTC)
Awesome! I'll message you in a couple days and we can get started. Best, Keilana|Parlez ici 22:05, 9 May 2013 (UTC)

Please mind the Wikipedia Education projects

Hi, Boghog, I am an OA for this education program course, and I have noticed that in at least one page (XRCC4), you've been making some pretty substantial edits (here and here). The students are in the middle of a semester-long project to improve this article, and notwithstanding the merits of any of your edits, it was a bit disruptive. Please, could you check for a Wikipedia education program template first, and if you see one, then at least discuss any major edits on the talk page first? Klortho (talk) 19:18, 21 April 2013 (UTC)

I had responded in detail on the article's talk page. Boghog (talk) 04:54, 14 May 2013 (UTC)
What does this mean? Doc James (talk · contribs · email) (if I write on your page reply on mine) 01:14, 14 May 2013 (UTC)
I short, I didn't realize that the article was the subject of an educational assignment. I had (and still have) concerns that too much background material on the NHEJ pathway was added to the article hence the article and especially the lead was no longer focused on the XCCR4 protein. My edits were an attempt to refocus the lead on the XCCR4 protein and this had caused some disagreements with the student editors. Subsequently I tried communicating with them on the article's talk page but these attempts were only partially successful. To their credit, the students did condense some of the background material that was not in the lead. The whole experience was rather frustrating for me and also probably for the students. Boghog (talk) 04:54, 14 May 2013 (UTC)
Yes it is important to make clear to students that they need to work with others on Wikipedia and that they should usually follow the advice of long term editors. Seems like everything under control though. Doc James (talk · contribs · email) (if I write on your page reply on mine) 09:28, 14 May 2013 (UTC)

Drugs/compounds and diseases?

I just posted discussions on expanding our bot-driven maintenance and expansion efforts to both drugs/compounds [1] and diseases [2]. I've definitely seen your fingerprints on compound pages that I've looked at, and it wouldn't be surprising at all to see them on many disease pages as well. Anyway, your feedback on either/both of these ideas is particularly welcome. And if you might be open to directly working together on these ideas, we'd definitely be open to that as well... Hope all is going well! Cheers, Andrew Su (talk) 22:12, 13 May 2013 (UTC)

RNA-dependent RNA polymerase

Ha, I was about to do that, too. Nice work! --bender235 (talk) 17:26, 18 May 2013 (UTC)

Oh, sorry to beat you to the punch. And likewise, thank you for initiating the cleanup. Cheers. Boghog (talk) 19:03, 18 May 2013 (UTC)

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FAM149A (check to confirm | fix with Dab solver)
added links pointing to Transcription, Expression, NCBI and Promoter

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Ja, Beierhund

Wenn ist das Nunstuck grit und Shlotermeyer? Ja Beierhund das oder die Flipperwaldt gersput. 70.137.136.125 (talk) 15:45, 12 May 2013 (UTC)

Der tödlichste Witz der Welt. "Zat's not funny!" 😵 Boghog (talk) 17:32, 12 May 2013 (UTC)

Meanwhile in Germany in Peenemunde they are working on an own version: Spectacled scientist, clearing his throat, reading: "Die ist ein Kinnerhunder und zwei Mackel über und der bitte schön ist den Wunderhaus sprechensie. 'Nein' sprecht der Herren 'Ist aufem borger mit zveitingen.'" Gestapo-man: "We'll let you know." (shoots him) 70.137.136.125 (talk) 19:37, 12 May 2013 (UTC)

→ RIP Boghog (talk) 20:52, 12 May 2013 (UTC)

Q: Will the Monty Python comedy troupe ever get back together again? A: No. Q: What would it take to get them back together? A: Since Graham Chapman has already died, I'd imagine a couple of bullets each would do the trick. 70.137.136.30 (talk) 03:07, 15 May 2013 (UTC) Q: Why is it the world never remembers the name of Johann Gambolputty de von Ausfern-schplenden-schlitter-crasscrenbon-fried-digger-dingle-dangle-dongle- dungle-burstein-von-knacker-thrasher-apple-banger-horowitzticolensic-grander- knotty-spelltinkle-grandlich-grumblemeyerspelterwasser-kurstlich-himbleeisen- bahnwagen-gutenabend-bitte-einnürnburger-bratwustle-gerspurten-mitz-weimache- luber-hundsfutgumberaber-shönendanker-kalbsfleisch-mittler-aucher von Hautkopft of Ulm? A: Good question. 70.137.136.30 (talk) 01:57, 16 May 2013 (UTC)

With above samples of British humor, it is not surprising that as a German expat to the US I have been continuously bee teased by the British colleagues with the war (don't mention the war! One pickled Goering, two prawns Goebbels and a Kolditz salad...) and with all kind of shooting phantasies as well as references to Nazis and antisemitism. Only the American hosts didn't recognize the British humor and took everything at face value! I wonder how public education is in the US. The teachers I have met were largely "PC nazis". The picture of Germany is largely Hollywood e.g. Stalag 17, Hogans heroes etc. Hard times for foreigners, particularly after 9/11. I should start with letting a monocle fall from one eye, to satisfy the expectations, also exhibit arrogance and SS-like mannerisms. 70.137.130.14 (talk) 22:21, 21 May 2013 (UTC)

Oh, sorry. I just saw your message. As with all good comedy, no one is safe from Monty Python's barbs. I am an expat in the other direction and sometimes I am embarrassed by the parochialism of my fellow countrymen. How could Switzerland be playing Sweden in the hockey finals? Aren't they the same country? ;-) Boghog (talk) 23:03, 21 May 2013 (UTC)

Omg, essentially I learned in the US not only that Germans are all Nazis and Commies, which is the same! I also learned that French is the lingua franca all over Europe, that Berlin is a suburb of London, that also Berlin is the red light district of K-town, where the Americans are stationed, that Amsterdam is a complete whore house and hell hole, located in Germany, that I believe to be an "Aryan" and that we want Hitler back. Shudder. So I had to tell them that "yodeling" was indeed invented when a Swiss guy got his family jewels caught in the cog railroad mechanism somewhere in Switzerland, which is located in central Germany. 70.137.142.31 (talk) 18:23, 22 May 2013 (UTC)

Invitation for taking a short survey about communication and efficiency of WikiProjects for my research

Hi Boghog, I'm working on a project to study the running of WikiProject and possible performance measures for it. I learn from WikiProject Molecular and Cellular Biology talk page that you are an active member of the project. I would like to invite you to take a short survey for my study. If you are available to take our survey, could you please reply an email to me? I'm new to Wikipedia, I can't send too many emails to other editors due to anti-spam measure. Thank you very much for your time. Xiangju (talk) 15:04, 22 May 2013 (UTC)

Right direction for merger, wrong bit of content.

A chembox from s-methylmethionine iz off to the wrong inclusion criteria. Right direction, though. 75.152.123.238 (talk) 17:02, 23 May 2013 (UTC)

Please note that I made the appropriate modifications to the MF, MW, CAS number etc. so that correspond to the chloride salt. The only thing that needs updating is the graphic of the chemical structure. Boghog (talk) 17:07, 23 May 2013 (UTC)
75.152.123.238 (talk) 18:32, 23 May 2013 (UTC)
The way I figure it, you hav about five other chemboxes to add, unless you delete one. How can you read Vitamin_U without concluding that anti-Ulcerogenic factors are in cabbage juice other than MMSC?
Yoh mommuh soh stinky she mayd an unyun kry.

Education project re: your post on Ronburgandee's talkpage

Hey Boghog, I forwarded your message to my instructor, and he told me that he'd get in touch with you about his class. If you don't hear from him, you can leave me another note on my talkpage if you'd like. Thanks for taking the time to comment on our pages. Ronburgandee (talk) 15:37, 26 May 2013 (UTC)

Thanks Ronburgandee! If your instructor prefers, a private e-mail (see Toolbox/Email this user to the left) can be sent to me. Posting directly on my talk page will also work. Cheers. Boghog (talk) 16:31, 26 May 2013 (UTC)

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Condensing pmids

entire discussion transferred to User talk:75.152.116.193 so that it is easier to follow

75.152.116.193 (talk) 07:36, 2 June 2013 (UTC)
I want to put the whole article in bot format, because it's easier to read, and it's easier to be sure that pmid citations are complete. The only thing the bot won't do iz pull a useful verbatim quotation from the abstract or article. I can put those in with an edit to the citation. It's up to you. If the article iz in Vancouver-style, then I guess it stays that way.
There are no facts; only interpretations.
-- Friedrich Nietzsche

75.152.116.193 (talk) 08:10, 2 June 2013 (UTC)
You offer three choices: inline, segregated, and transcluded. I still prefer transcluded. Never consider the machine and load times, because they are difficult to measure, and price/performance divides in half about every eighteen months according to Moore's Law. What's important iz people time. Inline citations are made by humans (using different versions of the same software, or manually), and probably are more inconsistent than the bot, which can do its work over again very quickly if it malfunctions. I know, because I advised the operator regarding the bot providing two kinds of name. Segregated iz a kind of citation that most people do not know about. While it duz make source more readable, this iz the first I've seen of it. While I understand the syntax, I am not sure that everybody else would.
My thoughts are legal in thirty-seven states.
75.152.116.193 (talk) 08:27, 2 June 2013 (UTC)
Even when the bot iz blocked, it iz not really a problem with transcluded pmids, because someone should be double-checking that the abstracts say what someone thinks they say. The citation points to the pmid instantly.
Jugglers do it with their balls in the air.

Identifying Reviews on pubmed

Reality is a crutch for people who cannot face up to quantum physics.
Statistics. It looks like about ten times az meny people know about Brassicaceae than know about Vitamin_U.

This iz a review. I see no easy way of figuring that out, though. Actually, I do, now. Just click on an article in the side-bar and hope that the article on the side-bar lists that review az such.75.152.116.193 (talk) 11:51, 2 June 2013 (UTC)

It looks like a very relevant review. You can click on the "Publication Types, MeSH Terms, Substance, Grant Support" plus symbol which is found below the article abstract to find out if the article is a review or not. Boghog (talk) 12:05, 2 June 2013 (UTC)

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Wikipedia:Section blanking

Hello Boghog, you blanked a section I added on Water fluoridation, that has citations and is on topic. You stated that I needed to seek consensus first on the talk page. I already have posted to the talk page Talk:Water fluoridation prior to your Wikipedia:Section blanking on the page, and you didn't bother to respond (or maybe check it) before blanking. Please revert my edits unless you have something to add to the conversation. Thanks Jtbobwaysf (talk) 12:04, 7 June 2013 (UTC)

I missed your comment since it was placed at the top of the talk page. Per WP:TALK, comments should be ordered chronologically. In any case, the discussion had not yet finished. You need to allow others time to respond. Boghog (talk) 13:16, 7 June 2013 (UTC)

I rarely do reversions.

Where in the war does Micro$oft want to take me today?
What is wrong with active voice?

  • "The horse was kicked by the dog". or "The dog kicked the horse".

Why should I use specific chemicals, when my research iz on many different ones that fall into two categories, and I do not need to explain that if I put this fact in the intro?
I've kicked research for being on the fence.
What iz wrong with being more definite?
75.152.116.193 (talk) 19:53, 2 June 2013 (UTC)

Nothing is wrong with active voice. However indole ≠ diindolylmethane. That is definitely making things less definite. Boghog (talk) 19:45, 2 June 2013 (UTC)
Some things are more important than money, but they won't go out with you if you hav no money.
It's two indole nuclei connected by a methyl group, so yes, DIM iz an indole. I would be surprized if it iz not already in the category. If that's the only mistake I made, then a reversion wuz still inappropriate.75.152.116.193 (talk) 19:54, 2 June 2013 (UTC)
There are many more things wrong with your edit. I just don't have time right now to explain. Your contributions are creating a lot more disruptions than they are worth. This needs to stop. Boghog (talk) 20:00, 2 June 2013 (UTC)
Sounds more like you need some sleep. You hav all the time in the world. There iz no deadline. Other people can deal with my fuck-ups. My plan iz to put translation tags in.75.152.116.193 (talk) 20:38, 2 June 2013 (UTC)
I apologize for my temper. Your are right and I need some sleep. [(－－)] zzz Boghog (talk) 20:42, 2 June 2013 (UTC)
"Can YOU think?", I asked, putting Descartes before the horse.
Weasel words are a problem. The article should be more definite. I will point them out. I would rather clear them away, like I did in my edit.75.152.124.222 (talk) 23:22, 9 June 2013 (UTC)

Being definite iz wize.

If I write that little green men are probably dumb, then somebody else will write that little green men can be smart. The orijinal research probably says that little green men are IP numbers that edit wikipedia with an intellijese quotient of about 120. 75.152.124.222 (talk) 23:56, 9 June 2013 (UTC)

List with genes with a wikipedia page

Hi Boghog, we work at the UCSC genome browser and are trying to contact you to get a list of all genes with a page. We found the existing tab-sep and rdf files but have the impression that many genes are missing. Could you get back to me? thanks. Maximilianh (talk) 18:43, 12 June 2013 (UTC) — Preceding unsigned comment added by Maximilianh (talk • contribs) 18:24, 12 June 2013 (UTC)

 Done Hi Maximilianh. I just sent you the list that you requested via e-mail. Let me know if you haven't received it. Cheers. Boghog (talk) 20:53, 12 June 2013 (UTC)

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The Wikipedia Library now offering accounts from Cochrane Collaboration (sign up!)

Cochrane Collaboration is an independent medical nonprofit organization consisting of over 28,000 volunteers in more than 100 countries. The collaboration was formed to organize medical scholarship in a systematic way in the interests of evidence-based research: the group conducts systematic reviews of randomized controlled trials of health-care interventions, which it then publishes in the Cochrane Library.

Cochrane has generously agreed to give free, full-access accounts to 100 medical editors. Individual access would otherwise cost between $300 and $800 per account. Thank you Cochrane!

If you are stil active as a medical editor, come and sign up :)

Cheers, Ocaasi t | c 19:56, 16 June 2013 (UTC)

June 2013

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Wikipedia talk:Articles for creation/Skin immunity

Are you still working on Wikipedia talk:Articles for creation/Skin immunity or can I accept it? If so, what is your suggested page title? Pol430 talk to me 18:50, 19 June 2013 (UTC)

Sorry for not following up on this sooner. The article itself needs a lot more work, but in its present form, it meets the basic requirements for notability and is adequately sourced. Hence I have no objections if you accept it. I will continue working on it as I find time. Cheers. Boghog (talk) 19:42, 19 June 2013 (UTC)
Thank you for your expertise in this subject area and for taking to the time to clean it up. I have accepted it as a start class article. Pol430 talk to me 19:05, 20 June 2013 (UTC)

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A bowl of strawberries for you!

Thanks for reverting those edits I made with AWB. (t) Josve05a (c) 18:16, 23 June 2013 (UTC)
Sorry for not leaving an explanation earlier. In many cases adding {{Underlinked}} tags to Gene Wiki articles is not appropriate. For example, the ADC (gene) article contains exactly one line of prose and that line contains two wiki links, one to protein, and the second to gene. Adding more wiki links to this line would normally be considered overlinking. The problem is not that the article contains too few wiki links, but rather the article needs to be expanded. In any case, the vast majority of your edits are constructive and I apologize for any confusion. Carry on. Cheers. Boghog (talk) 18:22, 23 June 2013 (UTC)
It's okey! Thanks for the explanation. Cheers! -(t) Josve05a (c) 18:28, 23 June 2013 (UTC)

Thingz that may be false are not facts.

I found JESUS! He was in my trunk when I got back from Tijuana.
I noticed that you are defending evasive terms on Cruciferous vegetable. I want you to back them up and make them definite, to avoid people reading these long sentences with disbelief. Why investigate sources where wikipedia says nothing clear? You claim barnstars for your activity in biochemistry. Here iz your chance to understand how difficult the field iz. Wikipedia iz a reviewer, and preferably a reviewer of reviews. You can find reviews that are more definite. I find that reviews tend to do exactly the same thing you did: Water down research and demand more research, when it iz not needed. I think you will find reperfusion studies to be among the most interesting and convincing. You hav a chance to earn stripes az a researcher. 75.152.124.222 (talk) 11:55, 13 June 2013 (UTC)

The most recent review articles in this area summarize the current state of knowledge. If the authors of these review articles are cautious in their conclusions, this means the available clinical evidence does not allow a more definitive conclusion. Furthermore if the review articles are cautious, what we write must also be cautious. The only other option is to delete the material entirely. Boghog (talk) 05:14, 14 June 2013 (UTC)
Since you hav had a week or two to find clear reviews, I am recommending deletion of the material. It iz speculation. I will copy the citations to the talk page in hopes that it may lead me to more definite summaries.75.152.127.203 (talk) 12:38, 25 June 2013 (UTC)

A cardboard belt would be a waist of paper
Talk:Cruciferous_vegetables 75.152.127.203 (talk) 23:44, 26 June 2013 (UTC)

PTPRN2

Thanks for cleaning up PTPRN2 for "me." I'm new to editing Wikipedia, and although I have researched PTPRN2 extensively of late, I am definitely a layman when it comes to genetics. — Preceding unsigned comment added by Mossytangle (talk • contribs) 15:23, 28 June 2013 (UTC)

No problem. Thanks for expanding the PTPRN2 article. Cheers. Boghog (talk) 07:03, 29 June 2013 (UTC)

VisualEditor

Hey Boghog

I'm sending you this because you've made quite a few edits to the template namespace in the past couple of months. If I've got this wrong, or if I haven't but you're not interested in my request, don't worry; this is the only notice I'm sending out on the subject :).

So, as you know (or should know - we sent out a centralnotice and several watchlist notices) we're planning to deploy the VisualEditor on Monday, 1 July, as the default editor. For those of us who prefer markup editing, fear not; we'll still be able to use the markup editor, which isn't going anywhere.

What's important here, though, is that the VisualEditor features an interactive template inspector; you click an icon on a template and it shows you the parameters, the contents of those fields, and human-readable parameter names, along with descriptions of what each parameter does. Personally, I find this pretty awesome, and from Monday it's going to be heavily used, since, as said, the VisualEditor will become the default.

The thing that generates the human-readable names and descriptions is a small JSON data structure, loaded through an extension called TemplateData. I'm reaching out to you in the hopes that you'd be willing and able to put some time into adding TemplateData to high-profile templates. It's pretty easy to understand (heck, if I can write it, anyone can) and you can find a guide here, along with a list of prominent templates, although I suspect we can all hazard a guess as to high-profile templates that would benefit from this. Hopefully you're willing to give it a try; the more TemplateData sections get added, the better the interface can be. If you run into any problems, drop a note on the Feedback page.

Thanks, Okeyes (WMF) (talk) 21:46, 28 June 2013 (UTC)

GABRD. - reverted your citation edits

When you revised the citation I added to GABRD, you destroyed content instead of improving or adding ... Which is why I reverted your changes. --User:Ceyockey (talk to me) 21:32, 2 July 2013 (UTC)

You are absolutely wrong in your reversion .. But I am not going to do anything further on the matter. --User:Ceyockey (talk to me) 21:35, 2 July 2013 (UTC)

There is a previously established citation style in this article. You have introduced a new one. Per WP:CITEVAR, if you want to introduce a new citation style, you should first seek consensus on the article's talk page. Boghog (talk) 21:40, 2 July 2013 (UTC)
If you insist on introducing "first1, last1, first2, last2, ..." parameters in a citation in an article that otherwise uses the Vancouver system author format, please also include:
" | authorformat = vanc | author-separator=, | author-name-separator =   "
in the citation template. In this way, the citations will at least be rendered in a consistent format. Boghog (talk) 22:05, 2 July 2013 (UTC)

Discussion started as a byproduct of our edit "skirmish"

Nothing confrontational ... an inquiry about trying to avoid confrontation. → Wikipedia talk:Citing sources#Indicators of predominant citation style - are they available for addition to article or talk page?. --User:Ceyockey (talk to me) 00:50, 3 July 2013 (UTC)

Thanks for the heads up. As a compromise, I have re-added the "first1, last1, first2, last2, ..." parameters and in addition added " | authorformat = vanc | author-separator=, | author-name-separator =   " and in addition moved this citation using list defined references. The first modification ensures that the rendered citations are consistently formatted. The second modification moves this long citation template out of the text and to the reflist template for easier viewing. Boghog (talk) 17:48, 3 July 2013 (UTC)

PCSK9

What change? Nothing has changed as far as the citations look. They just come from a standardized place. Moreover, because I made all the references alphabetical, you were easily ably to decide which were necessary and remove them. What consensus do you need to make things easier & smarter.

I think inline citations are a real pain, trying to spot where one ends and the next one starts. WP:LDR is much easier. PMIDs represent the true citation, without the spelling mistakes of transcription.

John of Cromer (talk) mytime= Sat 21:21, wikitime= 20:21, 13 July 2013 (UTC)

Please take a more careful look at the changes that I made in this edit. I have kept the WP:LDR citations but have only restored {{cite journal}} in place of the {{cite pmid}} templates. And the two citation templates do differ in the way the authors are formatted. Boghog (talk) 20:59, 13 July 2013 (UTC)
User:Citation bot that fills in the {{cite pmid}} templates is not the only automated way to create citations that are free of transcription errors. In case you haven't seen this yet, please check out User:Diberri's Wikipedia template filling tool (instructions). Given a PubMed ID, one can quickly produce a full citation that can be copied and pasted into a Wikipedia article. This is the tool that I used to convert back to {{cite journal}} template. I also inserted a few PMIDs in my edits that were previously missing that you had undone with your edits (5 to be exact, compare 19 PMIDs after my edits vs. 14 PMIDs after your edits). In addition, I ran citation bot after my changes (see here and here). Citation bot respects WP:CITEVAR. The changes that you made do not. Boghog (talk) 21:24, 13 July 2013 (UTC)

Time perception

Stop icon

Your recent editing history at [[:also read WP:OWNER]] shows that you are currently engaged in an edit war. Being involved in an edit war can result in your being blocked from editing—especially if you violate the three-revert rule, which states that an editor must not perform more than three reverts on a single page within a 24-hour period. Undoing another editor's work—whether in whole or in part, whether involving the same or different material each time—counts as a revert. Also keep in mind that while violating the three-revert rule often leads to a block, you can still be blocked for edit warring—even if you don't violate the three-revert rule—should your behavior indicate that you intend to continue reverting repeatedly.

To avoid being blocked, instead of reverting please consider using the article's talk page to work toward making a version that represents consensus among editors. See BRD for how this is done. You can post a request for help at a relevant noticeboard or seek dispute resolution. In some cases, you may wish to request temporary page protection. John of Cromer (talk) mytime= Sat 21:54, wikitime= 20:54, 13 July 2013 (UTC)

In contravention to WP:CITEVAR, you have made a major change in the citation format of an article without first gaining consensus on the article's talk page. I have merely restored the previous citation style. If you disagree, please take this up on the article's talk page. See also User_talk:Johnmperry#Cite_journal_to_cite_PMID. Boghog (talk) 21:08, 13 July 2013 (UTC)

Updated PBB stub creation code

Hi Boghog, FYI, I finally dug into our stub creation code to fix some of the changes that you were continually making by hand. For example, here is an example of what will be automatically created by http://biogps.org/GeneWikiGenerator/. Any other changes you'd like me to make? Hmm, just realized I should add a check not to create the Further Reading section if there are no references available... So aside from that, any other changes? Cheers, Andrew Su (talk) 21:30, 12 July 2013 (UTC)

Hi Andrew. Your fixes to the stub creation code look great and will save me a lot of work. While you are at it, it would be nice if the stub creation code would also add the following to the article's talk page:
{{WikiProjectBannerShell|
{{WikiProject Gene Wiki|class=stub|importance=low}}
{{Wikiproject MCB|class=stub|importance=low}}
}}
Other than that, I don't see anything else that needs changing. Thanks for taking care of this. Boghog (talk) 22:12, 12 July 2013 (UTC)
Embarrassingly, I think I've just about exhausted my patience with my rapidly degrading programming skills... ;) However, if you (or anyone else interested) wanted to make the change yourself, the code repository for the CGI is here (and the change I'm pretty sure would need to be made in gwgenerator.cgi). (Note also that the plugin depends on the genewiki module in this second repo.) Sorry to give up on this one! Cheers, Andrew Su (talk) 00:27, 13 July 2013 (UTC)
Thanks for the pointers. In the gwgenerator.cgi script, the code:
retcode = genewiki.upload(title, content)
print retcode
appears to create the wikipedia article. I am not certain where the print output is going, but it appears to be directed to Wikipedia itself (i.e., article creation). Hence if the above were modified to:
# create Gene Wiki article
retcode = genewiki.upload(title, content)
print retcode
# create corresponding talk page with appropriate project banners
talk_title = "Talk:" + title
talk_content = """{{WikiProjectBannerShell|
{{WikiProject Gene Wiki|class=stub|importance=low}}
{{Wikiproject MCB|class=stub|importance=low}}
}}"""
talk_retcode = genewiki.upload(talk_title, talk_content)
print talk_retcode
in principle it should also create the talk page. Thoughts? Boghog (talk) 15:08, 13 July 2013 (UTC)
Working through some technical difficulties on our end. For some reason your code works from the interactive python shell, but not the online CGI. More debugging required, more soon... Cheers, Andrew Su (talk) 00:47, 16 July 2013 (UTC)
Got it! Example: LY6G6E. As usual, a dumb oversight on my end... Cheers, Andrew Su (talk) 01:16, 16 July 2013 (UTC)
Great! I do appreciate that you got this working. It will save me some additional work. The print statement was certainly non-obvious way to create a Wikipedia page. Cheers. Boghog (talk) 07:38, 16 July 2013 (UTC)

Never use a big word when a small word will do.

Never do today what you can con someone else into doing.
My revision of hepatology included coinage that iz very descriptive and yet easy to understand, "hepatic drug decay". Wikipedia wuz hit number two on that search, until you changed it. The source included wuz only chosen to illustrate a last sentence. I had intend to support every sentence. My version went bang. Your version lacks lustre, although it iz better than what wuz there, mostly because it iz practical to understand and support it. Please understand that it iz not customary to revert all words (with longer sentences, and bigger words, I might add) tersen them, and then support it. The usual challenge to a fact iz {{fact}}, and you can put anything about weak sources in between ref tags. A common one in medicine iz {{medrs}}. A very good list of rules for effective style iz at the end of politics and the english language (by George Orwell).75.152.119.213 (talk) 15:34, 30 June 2013 (UTC)

Drug metabolism is a widely accepted term that is supported by reliable sources. "Hepatic drug decay" until you introduced the term into this Wikipedia article did not previously exist. This amount to WP:OR and is completely unacceptable and will be reverted. Boghog (talk) 23:36, 30 June 2013 (UTC)
It iz a strong, clear, concise, easily understood term. Anybody can understand that metabolism and decay are related terms if not synonymous. Never use a big word when a small word will do. There are thousands of three word inventions on wikipedia.75.152.127.191 (talk) 21:59, 16 July 2013 (UTC)
Never invent a new term when a clear, precise, and widely accepted term already exists. Metabolism is commonly associated with what humans do to food. Decay is more commonly associated with what bacteria do to food (e.g., tooth decay and decomposition). Furthermore the term metabolism is much more widely used and understood term than hepatic. So when a layman reads the phrase "hepatic drug decay", it may be parsed as "hepatic – don't known what that means, skip", and then "drug decay – break down of the drug by bacteria?". So now you have completely mislead the general reader. Compare with "drug metabolism" which will be parsed as "metabolism – the body is breaking down something" and then "drug – the body breaking down a drug, got it". By using the phrase "hepatic drug decay" will confuse the lay reader and will annoy the specialist. This phrase does not clarify. Quite to the contrary it may lead to confusion. Boghog (talk) 05:29, 17 July 2013 (UTC)
He who go to bed with itchy butt, wake up with stinky finger.
I think you are getting my point, and wasting time by guessing that other people won't get it. In jeneral, if you do not know what a word like hepatic means, then you should be following a link. The advantage in using "decay" in this context iz that it also means "drop in volume" to a musician, or just "drop" to a statistician. Livers make drug concentrations decay. The other advantage in using "decay" iz a closer alliance with catabolism. Catabolism iz the usual effect of a liver on a drug. Metabolism consists of anabolism and catabolism. Even when livers conjugate a drug with something else, it iz a step towards excretion, which leads to decay in the bacterial sense.75.152.127.191 (talk) 23:12, 18 July 2013 (UTC)
To repeat, metabolism is much more widely used and understood term than hepatic. In addition, we can just as easily provide a link to drug metabolism as to hepatic. Furthermore, drug metabolism also includes anabolism-like effects (e.g., phase II metabolism and prodrug → drug). Finally if a reader is interested in learning more about drug metabolism and goes to Google, the reader will find lot of good leads using drug metabolism – 1,760,000 results vs hepatic drug decay – 3 results (hmm the only place where this is being discussed is on my talk page ;-). Using obscure made up terms like "hepatic drug decay" is not at all helpful for the general reader. We are writing for a general audience, not the whims of individual Wikipedia editors. Boghog (talk) 09:10, 19 July 2013 (UTC)

Never consider the machine's work.

Segregated and inline citations are both more work for people. I used transcluded pmid citations, because those citations are the easiest to use, ignore, and copy. I want more editors to see them, because they save people a lot of work, and that iz what counts.

When wikipedia servers fetch a page three hundred (or maybe only fifty) times a day, that page is cached in RAM, az HTML, so the page load time iz damn near zero, even with fifty transcluded citations, until the page iz modified, when it might take fifty milliseconds to fetch transclusions. Network transmission time iz more significant than page loading time, and I rather like all those citations which can be individually edited, especially since citation-bot iz not quite perfect.

Never consider the machine's work. Please change the citation format of Cruciferous_vegetable to entirely transcluded format if your widjet will do that. 75.152.119.213 (talk) 15:46, 30 June 2013 (UTC)

There was a pre-existing citation style in this article that did not include {{cite pmid}} templates. Per WP:CITEVAR, if you wish to change that citation style, you first need to gain consensus on the talk page. So far, you have not done so. Boghog (talk) 23:44, 30 June 2013 (UTC)

Ditto RGS4. Using standardised citations via {{cite pmid}} is a vastly superior approach. Your reference to WP:CITEVAR is a complete red herring: the citation style has not changed one iota. Compare outputs. I am uninterested in machine considerations, I am looking to improve the standardisation of citations across Wikipedia. John of Cromer (talk) mytime= Tue 00:44, wikitime= 23:44, 1 July 2013 (UTC)

Ditto above. You changed the citation format without first gaining consensus on the talk page in clear violation of WP:CITEVAR. The {{cite pmid}} template comes with the following warning:
Boghog (talk) 23:51, 1 July 2013 (UTC)
And also yes, please compare outputs, especially how authors are formatted. Just to be clear, the original citation format used a Vancouver system author system. The {{cite pmid}} template uses first1, last1, first2, last2 author parameters which renders the authors to include periods after author first initials, first and last names separated by a comma and authors separated by semicolons. The Vancouver system omits the periods and the comma between the last and first names. And while you may not care about page load times, others do. Boghog (talk) 23:59, 1 July 2013 (UTC)
Polaroids are what Eskimos get from straining too much.
Citation formats do not affect page load times any more than the extra network traffic caused by slightly longer citations. Because RAM speeds and disk speeds are orders of magnitude higher than network transmission rates, Wikipedia servers spend well over 99% of their time waiting for the network. There iz a request kyuu, for both reading and writing. It iz long and almost instantly filled. Filled requests wait for the network. People time iz far more important than page load time. The network will get faster. At that point, the demand for terse citations, and citations that can be amended on their own page, will get louder. At that point, all of the time you spent putting pages into the segmented style will be wasted. 75.152.127.191 (talk) 23:50, 18 July 2013 (UTC)
Finally, as describe here and here, there are legitimate reservations about using cite pmid templates. Boghog (talk) 21:53, 2 July 2013 (UTC)

Never There is a 100% Guarantee

Hi(gh). Regards. http://wiki.riteme.site/wiki/User_talk:Gary_Dee#Malicious_links --Gary Dee 20:33, 21 July 2013 (UTC)

BogBot editing error

Bogbot made this edit that rearranged the chembox on the nystatin page. This edit also removed about half of the IUPAC name.

Cheers Bboppy (talk) 17:13, 23 July 2013 (UTC)

Thanks for fixing that. The changes that BogBot made to the {{Drugbox}} templates was a one time run. Parsing these templates, especially the IUPAC name was especially difficult and I was not able to eliminate all the bugs. A few like nystatin slipped through. Hopefully there are not too many more. Cheers. Boghog (talk) 17:26, 23 July 2013 (UTC)

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Thank you

Hi Boghog, about a month ago Wikimedia UK was running a workshop helping people learnt to edit. You came across a couple of these new users, Tatman37 and Davidebertoldo, and I wanted to say thanks for reaching out to them and mentioning Diberri's template filling tool. Richard Nevell (WMUK) (talk) 15:01, 6 August 2013 (UTC)

Hi Richard. Thanks for the background information. We need more editors like Tatman37 and Davidebertoldo. I hope they stick around. Cheers. Boghog (talk) 19:43, 6 August 2013 (UTC)

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Interleukin 19 (check to confirm | fix with Dab solver)
added links pointing to IL-10 and IL6
Interleukin 24 (check to confirm | fix with Dab solver)
added a link pointing to IL-10

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Typo in image

commons:File:Caffeine synthesis.tif has theophylline spelled "theopylline" (missing "h"). DMacks (talk) 16:51, 11 September 2013 (UTC)

 Fixed Thanks for catching the spelling error which I have now corrected. Cheers. Boghog (talk) 11:52, 22 September 2013 (UTC)

adenyl cyclase reference

Did you mean to change the reference I added on sAC on the adenyl cyclase page? your reference does not mention mitochondria. — Preceding unsigned comment added by Lrunge (talk • contribs) 09:22, 22 September 2013 (UTC)

Thanks for the heads up. I generated the citation from the incorrect PMID that was in the article and I should have checked to the rest of the citation to make sure that it matched. The error is now corrected. Cheers. Boghog (talk) 10:06, 22 September 2013 (UTC)

Hi, I notice that you recently made some changes to the polyneuridine-aldehyde esterase page. I appreciate your help with this, but if possible - would you be able to hold off on editing this page for the next two months or so. My undergraduate student in Biochemistry is putting together this page as part of an honors project, and she'd really appreciate being able to work on this gradually. She can also work on it in her sandbox, but it's great for her to be able to see her edits live. While they're not perfect (she's still learning), they're an important opportunity for her to learn. Please feel free to email or reply. Best wishes, Vweake (talk) 16:29, 22 September 2013 (UTC)Vikki Weake Biochemistry Professor Purdue University

Nomination for deletion of Template:Infobox drug mechanism

Template:Infobox drug mechanism has been nominated for deletion. You are invited to comment on the discussion at the template's entry on the Templates for discussion page. eh bien mon prince (talk) 22:28, 22 September 2013 (UTC)

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Nomination for deletion of Template:Infobox metabolic pathway

Template:Infobox metabolic pathway has been nominated for deletion. You are invited to comment on the discussion at the template's entry on the Templates for discussion page. eh bien mon prince (talk) 17:45, 27 September 2013 (UTC)

Nomination for deletion of Template:Infobox protein family clan

Template:Infobox protein family clan has been nominated for deletion. You are invited to comment on the discussion at the template's entry on the Templates for discussion page. eh bien mon prince (talk) 06:56, 28 September 2013 (UTC)

Regarding removed link.

Hi Boghog, I think you were ok to remove to the link. I suppose it is an interesting link and would be a great addition to the whole article. I suppose I could put it in the external links rather than as a reference. Am I correct? — Preceding unsigned comment added by 2601:8:200:360:41BC:A6DC:434D:CECB (talk) 11:57, 7 October 2013 (UTC)

PERK

Hi Boghog. I made a page for this interesting compound that has recently been reported, GSK2606414 which is a selective inhibitor of the enzyme known as PERK. However after reading a few sources I have become a bit confused as to whether "Protein Kinase R (PKR)-like Endoplasmic Reticulum Kinase" is in fact the same enzyme as "Eukaryotic translation initiation factor 2-alpha kinase 3", or whether they are related enzymes from the same family but not actually identical. I don't suppose you could shed any light on this at all? Meodipt (talk) 20:43, 10 October 2013 (UTC)

Hi Meodipt. I think you got it right. An alternate UniProt name (Q9NZJ5) for the kinase encoded by the EIF2AK3 gene is "PRKR-like endoplasmic reticulum kinase" which is very close to the name of the enzyme in the GSK2606414 papers you cite. Cheers. Boghog (talk) 06:15, 11 October 2013 (UTC)

Collagen, Type XXIII, Alpha 1

Hi Boghog, I'm user BQUB13-Mperalta. I've seen your improvements in the Collagen, Type XXIII, Alpha 1 page. I'm a college student, and some classmates and I created the page for a biochemistry project. We are aware that the page needs to be improved, but we are still working on it. While we appreciate your help, we wanted to ask you if you could stop editing the page during a week or so in order to let us finish it. By the way, it wasn't me nor my classmates who deleted one of your last edits, a friend of ours did thinking that she was helping us, so we're sorry about that.

Thank you in advance,

--BQUB13-Mperalta (talk) 21:38, 23 October 2013 (UTC)

Books and Bytes: The Wikipedia Library Newsletter

Books and Bytes

Volume 1, Issue 1, October 2013

by The Interior (talk · contribs), Ocaasi (talk · contribs)

Greetings Wikipedia Library members! Welcome to the inaugural edition of Books and Bytes, TWL’s monthly newsletter. We're sending you the first edition of this opt-in newsletter, because you signed up, or applied for a free research account: HighBeam, Credo, Questia, JSTOR, or Cochrane. To receive future updates of Books and Bytes, please add your name to the subscriber's list. There's lots of news this month for the Wikipedia Library, including new accounts, upcoming events, and new ways to get involved...

New positions: Sign up to be a Wikipedia Visiting Scholar, or a Volunteer Wikipedia Librarian

Wikipedia Loves Libraries: Off to a roaring start this fall in the United States: 29 events are planned or have been hosted.

New subscription donations: Cochrane round 2; HighBeam round 8; Questia round 4... Can we partner with NY Times and Lexis-Nexis??

New ideas: OCLC innovations in the works; VisualEditor Reference Dialog Workshop; a photo contest idea emerges

News from the library world: Wikipedian joins the National Archives full time; the Getty Museum releases 4,500 images; CERN goes CC-BY

Announcing WikiProject Open: WikiProject Open kicked off in October, with several brainstorming and co-working sessions

New ways to get involved: Visiting scholar requirements; subject guides; room for library expansion and exploration

Read the full newsletter


Thanks for reading! All future newsletters will be opt-in only. Have an item for the next issue? Leave a note for the editor on the Suggestions page. --The Interior 21:23, 27 October 2013 (UTC)

Template filler on Wikilabs?

Getting anywhere? I think Debian-Apt-PM may be useful for locating the appropriate Ubuntu perl packages to satisfy dependencies. I think this provides an online interface. I need to check my older machine for the filler CPAN package. I'll add a list of it's dependencies if useful. RDBrown (talk) 01:35, 23 October 2013 (UTC)

Thanks for the tip. I have set up a Tool Labs account and have been been approved for shell access. I have been very busy in real life, but I should have some time this weekend to see if I can get this to work. Cheers. Boghog (talk) 05:18, 23 October 2013 (UTC)
I think you need the following
# (On my ubuntu 13.10 box these are all available)
apt-get install perl-base libhtml-parser-perl libtie-ixhash-perl liburi-perl \
	libwww-mechanize-perl libxml-libxml-perl 
# Need to use apt-add-repository to a debian repository - think they're pure perl.
apt-get install libcache-cache-perl libdate-calc-perl  libwww-search-perl \
	libxml-writer-perl 
# Then need to install these packages with CPAN
echo  WWW-Search-PubChem  WWW-Search-DrugBank  WWW-Search-PubMedLite \
        WWW-Search-HGNC      WWW-Wikipedia-TemplateFiller
I'm confused as to whether the CPAN source has been updated, but if not you may need to make the fix mentioned in this section, pity no code is given.
The Meta::CPAN page seems a much better way of getting dependencies than my grepping around. Hope this is useful RDBrown (talk) 00:06, 25 October 2013 (UTC)
Again, thanks for the tips! I will see if I can get it running this weekend. Cheers. Boghog (talk) 04:35, 25 October 2013 (UTC)
Hi RDBrown. I can't seem to get the method you described above to work because it appears that root privileges that I do not have are required. The method described here and here seems to work and I was able to install WWW-Wikipedia-TemplateFiller (except for problems with WWW-Search-DrugBank and WWW-Search-HGNC dependancies which are optional). As far as I can tell without a web browser on the local account, the tool server is functional (invoking ./index.cgi from the command line from my Tools Lab account returns an html page as raw text). However when I try to access this cgi script:
from an external web browser, it generates an internal error and I am not sure what the problem is. I added a .htaccess file to the cgi-bin directory that includes the lines "Options +ExecCGI" and "AddHandler cgi-script cgi pl". This made no difference. I am not sure how to proceed. Any suggestions? Boghog (talk) 17:17, 27 October 2013 (UTC)
I have verified that a non-web browser version of the program works on the server (given a pubmed_id, it returns the correct cite journal template). I have also verified that simple test perl scripts are accessible from an external web browser.
#!/usr/bin/perl
print "Content-type: text/html\n\n";
print "Hello, world!\n";

test.cgi

However as soon as I add
#!/usr/bin/perl
use lib "/data/project/citation-template-filling/perl5";
use WWW::Wikipedia::TemplateFiller::WebApp;
print "Content-type: text/html\n\n";
print "Hello, world!\n";
to the test script, test2.cgi, as you can see, it generates an internal error. This same script returns "Hello, world!" when run from the command line within the server.
The /data/project/citation-template-filling/perl5 directory seems to have the appropriate protections (world read access for files and world read and execute privileges for directories). Boghog (talk) 19:48, 27 October 2013 (UTC)
On root access, sorry I should have said that Ubuntu provides that by *sudo*. Had I been thinking I would put in the leading /usr/bin/sudo in the apt-get examples.
/usr/bin/sudo apt-get install w3m lynx
should install those text mode browsers. I am a novice at setting up web servers. RDBrown (talk) 20:50, 27 October 2013 (UTC)

Unfortunately sudo doesn't help either. For example: 

boghog@tools-login:/home/boghog$ sudo ls
[sudo] password for boghog: 
Sorry, user boghog is not allowed to execute '/bin/ls' as root on tools-login.pmtpa.wmflabs.

Sigh. Boghog (talk) 21:24, 27 October 2013 (UTC)

I had assumed it was Ubuntu with your own virtual machine, with root access via sudo.
Tools/Help#Web Services says

Running scripts

All scripts are run with the permissions of the account that owns the script, which should be the tool account in almost all cases. Scripts may be placed in one of two directories:

~/public_html/ (which maps to http://tools.wmflabs.org/toolname) ~/cgi-bin/ (which maps to http://tools.wmflabs.org/toolname/cgi-bin)

Maybe try putting/installing the perl modules under or in ~/public_html and adjusting the use lib statement. (guessing). If that fails I'd be tempted to see if cpan would install the perl modules into /usr/local..., but access to that is unlikely. The documentation says to ask for additional packages with a bugzilla request, which may have been what was required to use the Ubuntu & debian packages. If you think it could be useful, I can ask for access to the account. Good luck RDBrown (talk) 04:57, 28 October 2013 (UTC)

Thanks for the additional suggestions. I tried moving the perl5 library into the cgi-bin library and that didn't help either. After googling, I found this this discussion. Per the suggestions there, I have set "chmod -R a+rx" to the local library folder. In addition, I have verified that every directory from /perl5 up has o+rx permission. Unfortunately it still does not work. Boghog (talk) 07:17, 28 October 2013 (UTC)
A perl mentor for tools.wmflabs would help. A debugging suggestion
use lib 'Junk';
print join "\n", @INC;
print "\n";
foreach $dir (@INC) {
    -d "$dir" || print "not dir:\t", $dir, "\n";
    -d "$dir/XML" && print "XML in\t", $dir, "\n";
    -d "$dir/WWW/Wikipedia" && print "WWW/Wikipedia in\t", $dir, "\n";
}

That is comment out the failing use WWW::Wikipedia:... and dump the search path (after the content-type stuff). 

$ perl -w useerr.pl 
Junk
/etc/perl
/usr/local/lib/perl/5.14.2
/usr/local/share/perl/5.14.2
/usr/lib/perl5
/usr/share/perl5
/usr/lib/perl/5.14
/usr/share/perl/5.14
/usr/local/lib/site_perl
.
not dir:	Junk
XML in	/etc/perl
XML in	/usr/lib/perl5
XML in	/usr/share/perl5
not dir:	/usr/local/lib/site_perl

Tried eval, but it doesn't seem to trap failing use commands. 12. Debugging and Testing CGI Applications might give a useful hint. Hope this helps RDBrown (talk) 09:44, 28 October 2013 (UTC)

Again, thanks for the tips. It turns out that including the line "print join "\n", @INC;" without any "use lib" command at all results in an "Internal error" when the cgi script is run from an external browser. Revealing any details about the internal environment to an external web browser is a apparently prohibited. Internally the script works fine. Debugging from an external web browser appears to be out of the question. I think this is some sort of Apache web server security issue. I have posted a question on the Wikitech site hoping someone over there can help. Boghog (talk) 20:23, 28 October 2013 (UTC)
As usual, I haven't been clear. You need the print "Content-type: text/html\n\n"; prior to the rest. The example was a quick standard alone script. The O'Reilly book chapter mentions this

The headers must be output before any other data, or the server will generate a server error with a status of 500.

Hope that gets us further. RDBrown (talk) 20:51, 28 October 2013 (UTC)

OK and thanks for your patience. Your debugging script (with minor modifications to make the output easier to read) now works: 

#!/usr/bin/perl
# 
# test2.cgi -- debugging perl script!

print "Content-type: text/html\n\n";
print "Hello, world!<br>\n";

use lib '/data/project/citation-template-filling/perl5/';
use lib '/data/project/citation-template-filling/perl5/lib/perl5/';
use lib 'Junk';

print join "<br>\n", @INC;
print "<br>\n";

print "\n";
foreach $dir (@INC) {
    -d "$dir" || print "not dir:\t", $dir, "<br>\n";
    -d "$dir/XML" && print "XML in\t", $dir, "<br>\n";
    -d "$dir/WWW/Wikipedia" && print "WWW/Wikipedia in\t", $dir, "<br>\n";
    -d "$dir/WWW/Wikipedia/TemplateFiller" && print "WWW/Wikipedia/TemplateFiller in\t", $dir, "<br>\n";
}

#use WWW::Wikipedia::TemplateFiller::WebApp;

And the link to run and view the output of the above script is here: test2.cgi. However when I uncomment the last line, I get the usual "Internal error". When I run the script directly on the server using command line, the script does not generate any errors. I am not sure what to do next. Suggestions? Boghog (talk) 23:06, 28 October 2013 (UTC)

While we could change the test script to check that WWW/Wikipedia/TemplateFiller/WebApp.pm is readable (-r is readable, -x executable), I'd try the following.
  • check that the Template filler cgi/index.cgi has been updated to change __PATH_TO_TEMPLATES__ as mentioned in the the INSTALL file.
  • Try adding the use lines in WebApp.pm (with TemplateFiller last) to check for unmet dependancies. (though CPAN should have done that).

Hope this helps RDBrown (talk) 01:31, 29 October 2013 (UTC)

Hi. Sorry for not responding sooner. Thanks again for your suggestions. In response, the WebApp.pm and all directories above it have world read and execute privileges. The "__PATH_TO_TEMPLATES__" was already changed to "/data/project/citation-template-filling/cgi-bin/templates". Adding "use WWW::Wikipedia::TemplateFiller::WebApp" also generates an internal error. Accessing only the local perl library without using it generates the internal error. Furthermore the entire cgi script works when accessing internally. An equivalent installation on my PowerBook works fine. At this point, I am fairly certain that this is a Apache security issue. As you suggested above, I think I need advise from a Wikitech perl guru. Hence I have requested help here. Cheers. Boghog (talk) 21:14, 31 October 2013 (UTC)

It now works!!! At least "PubMed ID" and "PubMed Central ID" work. The link for running the tool is here: citation-template-filling.

The key to getting this to work was to add the following line to the cgi script: 

use CGI::Carp 'fatalsToBrowser';

Adding this single line gave some very useful feedback that indicated despite using cpanm for the installs, there were a still a few unfulfilled dependencies. After installing these missing modules, the script finally worked. I still need to get url and isbn options to work, but at least the most commonly used options now work. Again, thanks for your suggestions. Cheers. Boghog (talk) 15:26, 1 November 2013 (UTC)

A barnstar for you!

The Technical Barnstar
For getting the Diberri citation program up and running at http://tools.wmflabs.org/citation-template-filling/cgi-bin/index.cgi Thanks! WhatamIdoing (talk) 16:10, 1 November 2013 (UTC)
Thanks. It is not fully operationally yet, but at least the parts that editors are likely to use most (pmid and pmc searches) now work. Boghog (talk) 12:52, 2 November 2013 (UTC)

A kitten for you!

Applause, I've used the template filler in anger, fixed my scripts to call it. Thanks for your work.

RDBrown (talk) 12:38, 2 November 2013 (UTC)

Used it in anger? :-O I guess that's why diberri called it Wikipedia Template Filling or wtf for short ;-) Again, thanks for your pointers and encouragement. Cheers. Boghog (talk) 12:52, 2 November 2013 (UTC)

Thank you and...

Thank you for getting my favourite template filler up and running again. Do you have any idea how we can get Rich's Special:RecentChangesLinked/Wikipedia:WikiProject Medicine/Recent changes working again? (Discussion at Wikipedia:Village pump (technical)/Archive 119#Help needed tracking recent changes to medical content). --Anthonyhcole (talk · contribs · email) 06:21, 5 November 2013 (UTC)

And thank you for your support. While I have used BogBot for one-time special purpose tasks, I do not have any experience in running bots continually on a server. It does look like you have attracted the attention of bot owners who are far more experienced with this type of task than I am. I will keep an eye on how things develop but I hope one of more experienced bot owners can get the recent changes bot working again before I jump in. Cheers. Boghog (talk) 22:21, 5 November 2013 (UTC)
Yep. There are a few people working on it now. They're using it as the prototype for a generic wikiprojects watchlist. Looking good. --Anthonyhcole (talk · contribs · email) 06:45, 6 November 2013 (UTC)

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HRG triplets codon populations

dear sir Borhog,

on your deletion for "too esoteric" of

It has been shown that there is a certain overall unity of the HRG triplets codon populations across the whole genome J.C. Perez, The “3 Genomic Numbers” Discovery: How Our Genome Single-Stranded DNA Sequence Is “Self-Designed” as a Numerical Whole, Applied Mathematics (Biomathematics issue October 2013)

you could verify by yourself that this article is not a bit ESOTERIC. Both reasons: 1/ it is a peer reviewed article 2/ a pre review and strong discussions were run with a master leader of genetics: professor george <church

please see acknowledgements:

.../..."Strong thanks to individual genomics pioneer Professor George Church (http://arep.med.harvard.edu/gmc, MIT, Boston University, Cambridge University, UK) for his highly critical analysis reviewing of this paper, particularly on the human genome 13 and 2 numerical ratios possible understanding and explanations..../..."

Particularly we discussed on the evidence that the whole human reference genome triplets codon populations is constraint by integer numerical proportions, demonstrationg that our human reference genome (HRG) constitutes a WHOLE.

Manay thanks

Nota: all results are reproductible

Best regards

dr jean-claude perez

Hi. Thanks for taking the time to discuss this. I am not disputing that the publication doi:10.4236/am.2013.410A2004 is notable. The concern that I have is that I do not think it should be included in a general article about the human genome. It is way too specialized for a general article that is widely read by a non-technical audience. A highly technical subject such as this must be put in context so that it can be understood by a wide audience. A general audience will have no idea of what a "triplet codon" is. These concepts must explained. Furthermore this subject matter is very specialized and therefore does not meet WP:BALASPS, especially in a article about a general concept like the human genome. In addition, secondary sources are strongly preferred. Your publication is a primary source. Without mention in independent review articles, it is not at all clear how significant your publication is. Finally as the author of this paper, you have a major conflict of interest. Wikipedia does not exist as a vehicle to promote the personal work of individual editors. Self-promotion is strongly discouraged. You should not be inserting your publications into Wikipedia articles. If you think your publication is relevant and significant, you should mention it on the talk page and ask someone else to insert it. Boghog (talk) 17:30, 9 November 2013 (UTC)

Jean-claude perez (talk) 16:47, 12 November 2013 (UTC)

Dear Boghog,
Many thanks for all this

Here also others secondary sources: http://scholar.google.fr/scholar?bav=on.2,or.r_cp.r_qf.&bvm=bv.56146854,d.d2k,pv.xjs.s.en_US.zw3S-PWncBk.O&biw=1366&bih=630&um=1&ie=UTF-8&lr=&cites=9886294698991636441 — Preceding unsigned comment added by 82.229.26.74 (talk) 08:18, 11 November 2013 (UTC)

Jean-claude perez (talk) 16:47, 12 November 2013 (UTC)

Unless I am missing something, the above does not qualify as a reliable secondary source. Reliable secondary sources in the sciences typically are review articles published in peer reviewed journals by authors other than the primary source authors. Boghog (talk) 21:13, 13 November 2013 (UTC)

Belated but heartfelt Barnstar

The Medicine Barnstar
For Boghog, with deep gratitude and heartfelt thanks for getting the (formerly Diberri) citation filling template working again! I know it was probably a lot of work, and keeping it in shape may entail work for years, but it makes everything easier for so many others !! Best regards, SandyGeorgia (Talk) 19:45, 13 November 2013 (UTC)
Thanks for the Barnstar! It was more work than it needed to be, mainly because of my inexperience with installing scripts on web servers. Once I figured out what was causing the problem, it was easy to fix. I will do my best to keep it running. Cheers. Boghog (talk) 21:19, 13 November 2013 (UTC)

Citation error reintroduced by unexplained revert

You appear to have reverted edits to Template:PBB/3630 and Template:PBB/10203, without explanation. For each page, the version to which you reverted contains a citation error. The edits that you reverted had fixed those citation errors (and made no other changes). You have posted in multiple places to state that you do not like these particular citation errors, so it is clear that you are aware of the existence of these errors and the reason behind the edits that you reverted.

Do you have a plan to fix these citation errors in a different way? I encourage you to seek community consensus before reverting any more of the fixes that have been made to articles with these citation errors. – Jonesey95 (talk) 21:00, 14 November 2013 (UTC)

Please provide me a link where it was decide to deprecate the month parameter. At best, you are making a lot of unnecessary edits. At worst, you are introducing the possibility of inconsistently rendered citations. Why fix something that isn't broken? Boghog (talk) 21:07, 14 November 2013 (UTC)

Hi. Thank you for your recent edits. Wikipedia appreciates your help. We noticed though that when you edited FBXL4, you added a link pointing to the disambiguation page SCF (check to confirm | fix with Dab solver). Such links are almost always unintended, since a disambiguation page is merely a list of "Did you mean..." article titles. Read the FAQ • Join us at the DPL WikiProject.

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November 2013

Hello, I'm BracketBot. I have automatically detected that your edit to Steroid may have broken the syntax by modifying 1 "()"s. If you have, don't worry: just edit the page again to fix it. If I misunderstood what happened, or if you have any questions, you can leave a message on my operator's talk page.

List of unpaired brackets remaining on the page:
  • * 1950 (Physiology) or Medicine) [[Edward Kendall]], [[Tadeus Reichstein]], [[Philip Hench]] – on the structure and biological

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Template editor

Hi, I thought it would probably be easier if you make these edits yourself because you are more familiar with the template. So I've added the template editor right to your account; I hope this is okay. (Although I just noticed that Template:Cite doi is cascade-protected, so it won't help in this case.) Regards — Martin (MSGJ · talk) 11:23, 28 November 2013 (UTC)

Hi. Thanks for your quick response and for granting me template editor rights. No rush on modifying {{cite doi}}. As this is a highly used template, I think it is prudent to wait a few days and get input from other editors before implementing the change. Cheers. Boghog (talk) 17:25, 28 November 2013 (UTC)

Thank you, but excuse m for a minute! :)

Hey, I'm working on the aldosterone synthase page as a pretty important project and you've altered it before I got a chance to save my own copy... anyway we could pause this so I could get my own work back...? — Preceding unsigned comment added by Gjpallen46 (talk • contribs) 07:49, 30 November 2013 (UTC)

Thanks - sorry for any trouble

Thank you, I may have just redid some of your work - so I would suggest perhaps undoing what I just redid! I'm pretty new to wiki and stressing out over the potential that my project could get shifted about (nobody wants to jump into a presentation with new info point blank!). Much appreciated - and thanks from the new guy. — Preceding unsigned comment added by Gjpallen46 (talk • contribs) 08:09, 30 November 2013 (UTC)

Deletion of Titin full name

Dear Boghog,

why did you delete my collapsible box on the Titin article that I've done with so much devotion? Have you ever seen the full name on the internet with line breaks every 100 characters and superscript grey little numbers attached to it? It's not that I wrote like 5 times, please please please do not delete this for like a few days - just to see how it turns out? It's not like this box is ruining the article whatsoever. I'm offended. Please don't do this.

Wuschelkopf (talk) 22:40, 19 November 2013 (UTC)

As explained in more detail here, the reason I deleted the full name from titin is that the current consensus is not to include the full name. Before attempting to re-insert the full name, please do so if and only if a new consensus is established on the talk page. However I do believe that you will have a difficult time changing the current consensus. Boghog (talk) 20:52, 20 November 2013 (UTC)
I add my name to the reported consensus that exists on this matter, to not begin including IUPAC names for biological polymers (the discovery of larger examples of which will continue, and whose accepted practical scientific nomenclature is not the IUPAC name). Bohog took the time to summarize the reasons leading several editors, including content matter experts, to this consensus (see http://wiki.riteme.site/wiki/Talk:Titin#.22Longest_word.22_in_collapsible_box). Opponent argument seems largely to be: including it would be educational [sic.] and "why not?". I concur with with the points of the Bohog summary, and suggest nothing substantive would be gained by adding blogger-suggested, transient Guinness-Book-of-World-Records content to Wikipedia science articles. Moreover, much would be lost by any such systematic change to Wikipedia protein and gene articles—imagine generating a IUPAC name for the the largest isolated and sequenced polynucleotide fragment, just so a new longest name might appear. Wuschelkopf, et al, please go to the archive and aquaint yourself with both sides of the issue. If you wish to come back with the same persuasive effort on your side of the matter (akin to Bohog's), we will certainly read. Until then, I argue, the status quo (no IUPAC name) is acceptable, that a sentence in the article summarizing the name controversy might remain (so the sought-after education does take place), and then, that other Wikipedia articles referencing a Tintin longest name should be edited to reflect the scientific substance that's been captured here (but not in the blogosphere). LeProf — Preceding unsigned comment added by 50.179.92.36 (talk) 19:05, 1 December 2013 (UTC)

Need your assistance

I'm not familiar with your journal abbreviation scheme, so I was wondering if you help me with making these journal titles consistent:

[1] [2] [3] [4] [5] [6] [7] [8] [9] [10] [11]

Journal names in order:

  1. Drug Metabolism Reviews
  2. Journal of Occupational and Environmental Medicine / American College of Occupational and Environmental Medicine
  3. Tetrahedron Letters
  4. The Journal of interdisciplinary histor
  5. Clinical Toxicology
  6. Internet Journal of Criminology
  7. Neuropsychopharmacology
  8. Neuropsychopharmacology
  9. Pharmacotherapy
  10. JAMA
  11. Nihon Shinkei Seishin Yakurigaku Zasshi

I abbreviated #3 as Tetra. Lett. (Tetrahedron Letters) yesterday - not sure if that's right. Wasn't sure if #10 should be JAMA or J. Am. - something, so I added it. For #11, should I just cite a different source? hehe.
Several of these are just 1 word titles, so I also just listed them in the event you happened to miss them in abbreviating - wasn't sure if they'd needed an abbreviation.

Thanks in advance! Seppi333 (talk) 03:04, 15 November 2013 (UTC)

References

  1. ^ Musshoff F (2000). "Illegal or legitimate use? Precursor compounds to amphetamine and methamphetamine". Drug Metabolism Reviews. 32 (1): 15–44. doi:10.1081/DMR-100100562. PMID 10711406. {{cite journal}}: Unknown parameter |month= ignored (help)
  2. ^ Cody JT (2002). "Precursor medications as a source of methamphetamine and/or amphetamine positive drug testing results". Journal of Occupational and Environmental Medicine / American College of Occupational and Environmental Medicine. 44 (5): 435–450. doi:10.1097/00043764-200205000-00012. PMID 12024689. {{cite journal}}: Unknown parameter |month= ignored (help)
  3. ^ Brussee J, Jansen ACA (1983). "A highly stereoselective synthesis of s(-)-[1,1′-binaphthalene]-2,2′-diol". Tetrahedron Letters. 24 (31): 3261–3262. doi:10.1016/S0040-4039(00)88151-4.
  4. ^ Rasmussen N (2011). "Medical science and the military: the Allies' use of amphetamine during World War II". The Journal of interdisciplinary history. 42 (2): 205–233. doi:10.1162/JINH_a_00212. PMID 22073434.
  5. ^ Schep LJ, Slaughter RJ, Beasley DM (2010). "The clinical toxicology of metamfetamine". Clinical Toxicology (Philadelphia, Pa.). 48 (7): 675–694. doi:10.3109/15563650.2010.516752. ISSN 1556-3650. PMID 20849327. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  6. ^ Wilson A (2008). "Mixing the Medicine: The unintended consequence of amphetamine control on the Northern Soul Scene" (PDF). Internet Journal of Criminology. Retrieved 25 May 2013.
  7. ^ Volkow ND (2012). "Long-term safety of stimulant use for ADHD: findings from nonhuman primates". Neuropsychopharmacology. 37 (12): 2551–2552. doi:10.1038/npp.2012.127. PMC 3473329. PMID 23070200. {{cite journal}}: Unknown parameter |month= ignored (help)
  8. ^ Soto PL, Wilcox KM, Zhou Y, Kumar A, Ator NA, Riddle MA, Wong DF, Weed MR (2012). "Long-term exposure to oral methylphenidate or dl-amphetamine mixture in peri-adolescent rhesus monkeys: effects on physiology, behavior, and dopamine system development". Neuropsychopharmacology. 37 (12): 2566–2579. doi:10.1038/npp.2012.119. PMC 3473325. PMID 22805599. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  9. ^ Teter CJ, McCabe SE, LaGrange K, Cranford JA, Boyd CJ (2006). "Illicit use of specific prescription stimulants among college students: prevalence, motives, and routes of administration". Pharmacotherapy. 26 (10): 1501–1510. doi:10.1592/phco.26.10.1501. PMC 1794223. PMID 16999660. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  10. ^ Habel LA, Cooper WO, Sox CM, Chan KA, Fireman BH, Arbogast PG, Cheetham TC, Quinn VP, Dublin S, Boudreau DM, Andrade SE, Pawloski PA, Raebel MA, Smith DH, Achacoso N, Uratsu C, Go AS, Sidney S, Nguyen-Huynh MN, Ray WA, Selby JV. "ADHD medications and risk of serious cardiovascular events in young and middle-aged adults". JAMA. 306 (24): 2673–2683. doi:10.1001/jama.2011.1830. PMC 3350308. PMID 22161946. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)
  11. ^ Inazu M, Takeda H, Matsumiya T (2003). "[The role of glial monoamine transporters in the central nervous system]". Nihon Shinkei Seishin Yakurigaku Zasshi (in Japanese). 23 (4): 171–178. PMID 13677912. {{cite journal}}: Unknown parameter |month= ignored (help)CS1 maint: multiple names: authors list (link)

For reasons that are not completely clear to me, some of the journal title abbreviations in citations in the amphetamine article contained periods after words that were abbreviated. For the sake of consistency, I manually went through all the citations and added a period after every abbreviated journal title word. I may have forgot to do this for the most recently added citations. JAMA is an unusual case since this abbreviations is included in the official full journal name ("JAMA: the journal of the American Medical Association") by the journal itself (see here and here). So in this case, JAMA is really a full word that does not require periods after it.

So in answer to your question, the journal names in order:

  1. Drug Metabolism Reviews – PMID 10711406 → Drug Metab Rev → Drug Metab. Rev.
  2. Journal of Occupational and Environmental Medicine / American College of Occupational and Environmental Medicine → PMID 12024689 → J Occup Environ Med → J. Occup. Environ. Med.
  3. Tetrahedron Letters → not indexed in PubMed, use American Chemical Society CAS Source Index instead → Tetrahedron Lett.
  4. The Journal of interdisciplinary history → PMID 22073434 → J Interdiscip Hist → J. Interdiscip. Hist.
  5. Clinical Toxicology → PMID 20849327 → Clin Toxicol (Phila) → Clin. Toxicol. (Phila.)
  6. Internet Journal of Criminology → not indexed in PubMed → not sure, IJC is used by the journal itself, may be too short, "Int." may be confused with International, perhaps best to use full journal name
  7. Neuropsychopharmacology → PMID 23070200 → Neuropsychopharmacology (not abbreviated)
  8. Neuropsychopharmacology → PMID 22805599 → Neuropsychopharmacology (not abbreviated)
  9. Pharmacotherapy → PMID 16999660 → Pharmacotherapy (not abbreviated)
  10. JAMA → PMID 22161946 → JAMA
  11. Nihon Shinkei Seishin Yakurigaku Zasshi → PMID 13677912 → Nihon Shinkei Seishin Yakurigaku Zasshi (not abbreviated)

Cheers. Boghog (talk) 07:21, 15 November 2013 (UTC)

Thanks! I'll update the relevant journal titles. Regards, Seppi333 (talk) 20:36, 15 November 2013 (UTC)

Metabolites

I went back to the metabolites since I have nothing else to do at the moment - I found this ref (see bottom left and top right columns of page H-20) that indicates alpha-hydroxy-amphetamine enantiomers are the norephedrine enantiomers; I updated the metabolite pathway based upon that. I also found another amphetamine pathway on page 55 of this pdf, but I have no clue what half of these are: http://miki.pharm.uic.edu/MDCH561/4.11.Drug%20Metabolism%20Cytochrome%20P450.pdf (I'm painfully ignorant of chem, as you've probably noticed ) Would you be able to identify those? I figure I should probably try to cross reference them with other sources. Best, Seppi333 (talk) 16:45, 16 November 2013 (UTC)
Unfortunately Google Books is not letting me look at page H-20 (no preview available for this page). However there appears to be some confusion about nomenclature in this source. Beta-hydroxy-amphetamine is synonymous with norephedrine. Alpha-hydroxy-amphetamine is rather unstable and undergoes deamination to form phenylacetone. The Kozikowski slide #55 which depicts the FMO oxidation of amphetamine looks plausible but is perhaps not the best source. These reactions are consistent with that reported in PMID 10027866 and PMID 19580. The N-hydroxylamine, dihydroxylamine, nitroso, and oxime metabolic intermediates are somewhat unstable and toxic (see for example PMID 11080052). These intermediates appear to be rapidly detoxified by conversion into phenylacetone and hence are not normally detectable as metabolites. I think level of detail is excessive for the amphetamine article, especially considering that the details of these reactions have not been completely worked out. Boghog (talk) 22:18, 16 November 2013 (UTC)
Ah, ok. In light of that, I'll just revert back to the image from two days ago. I'd rather be conservative with information than wrong. Seppi333 (talk) 00:39, 18 November 2013 (UTC)
Re your abbreviations, a few years ago, Pubmed used a slightly different approach to punctuating journal name abbreviation than did the ISO. It seems they've now come to use a common standard. Template talk:Infobox journal#ISO or NLM abbreviation of journal title? refers. LeadSongDog come howl! 18:14, 4 December 2013 (UTC)

Full text of final reply to your D...B...T... accusation, tendencies comment, and in general to our brief collaboration

Sorry mate. I read what I could find on this insult-intending WP reference you like to use, and it seems to me you are redefining a WP to address your pet peeve (rather than following the text of the WP, prima facie for what it says). Sminthopsis84 was doing D...B... work in his recent edit at Steroids; I do write in Talk why I make the edits I do, and so simply have not been violating this, were you fair. But you take ages to yield on your smallest errors, so let's drop it. Otherwise, mate, note, you wield WPs far too frequently and far too self-servingly. Physician, heal thyself.

As for your reference to my "tendencies", Doc, thanks, but no thanks for the arm chair analysis: you have no real clue. For every tag you see, there are many hours of work in wikipedia venues where I can be productive. Tags are almost always placed when there is a rampant, externally un-solvable citation issue, or perhaps just a really bad article (as in the case of an RNAi guy writing about hit selection as if only RNAi existed, citing his work, and providing no small molecule content whatsoever).

Otherwise, I yield to the inevitable here.

First, I am One of Many and Sminthopsis84 have sapped the last of my strength, and steroids will be of no use to bring it back. Repeated reversions in the last 24 hrs of the Partial and total synthesis subsection, with me explaining in Talk what I did, but no explanations going the other direction—this is the last straw. This stray nonsense, adding to other rounds and rows, makes it clear this venue is a waste of time.

Second, we have two different of "approaches", Bohog, you and I. Producing citation-free prose is relatively easy for an expert, as you know. You will do this; I will not. (Such is essentially what you did in response to my comment in Talk at Hit-to-Lead.) Producing fully cited, correctly illustrated, finished, reader-worthy prose takes much more time. I coach students to budget about half the time to get things 90% done, the other half to finish it as a reader- and print-ready job. This is one of several reasons why we cannot work together: Differences in what constitutes a contribution, and what constitutes a reader-ready job. I outline and work on much more draft prose, and leave much more of it in Sandbox, than it appears you ever will. You appear to think it proper to use the article itself as the holding-bin for draft work; I simply do not. I think if a text-in-place is short of accurate and authoritative, readers should be alerted through tags; you do not. Irreconcilable differences.

Otherwise, regarding suggesting versus generating, see the above on your having "no clue". But also be aware, in venues where my initial efforts are received without immediate, real-time reversions (this article team sets a record), I do write immediately, I do not just suggest. The suggestions you see show you how much I care about generating accurate text with appropriate scope. Here, however, it is clear, effort will be wasted. If not for battles with you (which are drawn out, but seem in the end to be productive), then for the real D...B...'s of Sminthopsis84 and the fundamentally content-disinterested intrusions of the likes of I am One of Many. In light of all this, various other unencumbered articles are far grater priority, for the hour a day I can squeeze in on this.

"It is now time for you to act on those suggestions." You really are something, lol. Your age/ego show in your patronising manner sometimes. I am sorry I cannot continue here as a mirror for you. You desperately need an iron-sharpens-iron sparring partner, just as I do. With you alone to contend with, maybe. But with the general out-of-control nonsense, here, I'll have to leave that fun job to someone else. Cheers/bye. LeProf — Preceding unsigned comment added by 50.179.92.36 (talk) 21:12, 6 December 2013 (UTC)

In re: your additions to my associated talk page

You can do as you please, of course, but I would ask removal of the insulting questions you placed on my talk page. The issue at hand is one of overgeneralization, and where the line is drawn between being fully accurate to a complex reality, and being simple enough to be widely understood. If it is not clear that I understand the concepts, thoroughly and deeply, then you are not reading me anywhere nearly as closely as I am reading you. On these matters I have a scholar's understanding. Read the last couple pages of the cited Prelog paper to appreciate what I mean. — Preceding unsigned comment added by 50.179.92.36 (talk) 12:46, 30 November 2013 (UTC)

OK, I will remove the comments, but you really need to understand why I put them there in the first place. I was trying to have a conversation with you on the steroid talk page and instead you were insulting me by trying to school me in things that I learned over 25 years ago in graduate school and have not forgotten. My first comments were very polite and there was no direct response to my question. Only more condescending comments. My comments became more pointed as my frustration grew. I finally got your attention. Some friendly advice. Your condescending attitude is not going to fly in Wikipedia. You need to treat fellow editors not as you students, but as equals with respect. Otherwise you will continue to receive strong pushback from me and other editors.
I understand the concepts, thoroughly and deeply" – You are dead wrong about the Evans student problem. It is a trick question. A right answer would include an explanation of why both are inflexible. Your arrogance is blinding you from the right answer. Boghog (talk) 23:09, 30 November 2013 (UTC)
Your representation of me on the Evans matter is disingenuous: I have repeatedly acknowledged that despite underlying differences in cis- vs. trans- AB (decalin) systems, the CD addition has the impact you describe. But as one with a comparable period of experience split between pharma and academia, I'd say I'd give half credit for that simple "both are inflexible" answer. As I said above, in my experienced opinion, the "what" of any factual presentation is important, but so is the "why", and so glossing can lead to unacceptable inaccuracy. Moreover, a student that memorizes an answer can give that answer; a student that understands the "why" can do much more—here, hypothesize conformational flexibility of a system under non-physiologic conditions relevant to reactivity (such as in a refluxing solvent) or develop hypotheses regarding the differential reactivity of dfferent sites on the steroid framework, or the flexibility and changes of conformation in derivatives/relatives. For these and the foregoing reasons, I'd say I may often be near dead, but rarely dead wrong.
And context is also important; realize that the discussion of the matter of conformational isomerism began after I read a clear, bold statement that all steroids are tetracyclic and rigid, when we both know that as long as secosteroids (etc.) are steroids, "all" are not t. and r. How am I to respond when I know this unequivocal generalization is untrue? Second, after NIH fellowship funding placed an expert on cholesterol transport, dynamics, and function on my committee 20 years ago (with whom I have subsequently published), setting it deeply in my psyche that CHOL side chain conformational flexibility, alongside sterol hydroxyl group position, relative lipophilicity, and relative ABCD ring- vs. side chain cross-sectional areas define interaction of CHOL with PLs (and therefore near to all of its biological functions), how am I to respond to your stridency marginalizing this aspect of this most abundant steroid's real conformational isomerism? Granted, there were misunderstandings about where the conformational isomerism link was removed (and if these things should appear in lead vs. body), but being accurate when making bold, unequivocal assertions is important in my book. Readers of introductory articles in encyclopedias are going to lose nuance, not add it themselves.
Regarding who was frustrated first, and why one or other of us played the competency card or name-called first, I will just say (since you insist on us acting as moral mirrors to one another): I'm guilty, both of declaring my competency first, and of calling arrogant repeated reversion of tag content. Guilty. I have never had a fellow editor revert tag content, at all, and certainly not while I was yet creating. Or carte blanche remove tags within hours of my placing them (an observation of the rapidity of your protective response that I believe others have made on the Steroid talk page). I propose that the same knee-jerk confidence in your being completely right (e.g., about the Evans student problem) and unwillingness to consider subtlety of opponent argument (same example, but also in general) leads to you miss things. (That the [Boger] "Lecture Notes themselves do not mention steroids" being the obvious, if understandable case, but ignoring all the clear evidence in the citation list I offered that was in favour of my perspective, and reporting back only that which supported your rigidity claim is the real point.) Can you not understand how these contribute to a perception of you?
This is truly what began the conflict—go back and review, and see if my "condescension" was not in response to an apparent tight control. And you still insist on using I'm-right-you're-arrogant-and-dead-wrong prose, despite olive branch overtures. It's this inflexibility and narrowness of perspective that led me to use language suggesting you have a personal stake. And as long as you believe it is your right to rapidly revert anything but vandalism or other nonsense, thus preventing others from viewing another editor's perspective... I will continue to call it your article, and limit my participation to suggestion-making.
This is the first time I have disagreed with a scientific peer, here at wikipedia, and so I expected a good, fair, clean fight over real issues. But the rapidity and adamancy of your responses, and the continuing personalization of the matter—e.g., the nonsense that with all I've written and referenced, that I might not understand what is meant by the fundamental term, conformational isomerism, or that I am arrogant for not agreeing on your approach to answering the Evans question—these are firsts for me, from a fellow scientific editor. These have led to an unwise stridency and length of my responses. So with this User Talk response, apart from content suggestions, I am done. It is too bad I cannot write, but there is much that can be done elsewhere without disrespectful conflict; your unwillingness to acknowledge any truth in my argument and approaches, or to cede anything but the obvious small mistake like the Boger (nothing more subtle or nuanced acknowledged) makes our working together on this impossible.
Finally, the closest I've had to our row is an "edit war" that I found myself in with the self-appointed chief editor of the Marco Rubio article—for my adding detail like a second vocational interest for his wife (in addition to the solitary reference to her having been a cheerleader), and for adding a couple sentences and references to a similarly selective presentation regarding the Senator's parents' immigration. In that case as well, I lost—everything I added was removed, and the article remained fully as the chief editor wanted. That interaction, and further outrageous editor behaviour (his presenting in Talk personal information of mine after google searches based on the limited disclosures on my User page) that went undisciplined here—these led to my first departure from Wikipedia, which continues indirectly in my logging <10% of my work.
Such interactions and system failures will, I imagine, ultimately lead me elsewhere. As much as I enjoy the iron-sharpens-iron substantive scientific aspect of this, the general disrespect for real expertise, the many unbending natures involved (many unqualified), the lack of any truly functional and timely arbitration mechanism, the power the system consequently places in the first to revert and in cliques, and the complete lackadaisical attitude toward citation-free text (i.e., plagiarism)—taken together, these leave me close to a final departure. LeProf — Preceding unsigned comment added by 50.179.92.36 (talk) 18:12, 1 December 2013 (UTC)
I think our disagreements over the steroid conformation issue is more one of semantics. Please keep in mind that the question in the original discussion was Do steroids have any Conformational isomers as implied by Conformational isomerism. In other words, are steroids as a class, good examples of molecules that possess conformational isomerism? Since a large majority of steroids possess a rigid tetracyclic core and what defines steroids as a class is this core, a reasonable answer is no. In contrast conformational isomers in carbohydrates are common and hence would be a much more appropriate example.
To state the obvious, at physiological temperatures, only a very small fraction of the conformational ensemble of fully saturated trans-trans-trans or cis-trans-trans steroids (Umesh Desai nomenclature) adopt conformations where one or more of the rings is in boat or other strained ring conformation. The vast majority of the conformational ensemble is devoted to a single conformation where each of the A-, B-, and C-rings adopt a chair conformation. Hence for all practical purposes, trans-trans-trans or cis-trans-trans steroid cores are rigid. This only breaks down at much higher temperatures. This is not an over simplification, this is reality. Furthermore this is not just memorization, it can easily be explained. In order for the A- and B-rings of cis-trans-trans steroids to inverconvert, the B-ring has to flip from one chair conformation to the other. However this flip is made impossible by the trans B/C-ring fusion. There are exceptions of course (e.g., introducing unsaturation into the A-ring makes the A-ring more flexible), but the fully saturated cores are very rigid.
To reiterate, I have not reverted a single piece of content that you have added to this article. All I did was to focus what you were requesting in the attention banner to make it more likely attract help from other editors. And you reverted my edit. Boghog (talk) 22:40, 1 December 2013 (UTC)
WP:Outing is very serious and is grounds for a permanently ban. There are ways of handling this (see suppress).
Verifiability is a core Wikipedia policy. Content that is not supported by reliable sources is not acceptable. If sources cannot be found to support the content, then the content will be removed. In practice, it may take a while before this happens. Wikipedia is not perfect, but then nothing is.
Finally nice work in creating the Biomimetic synthesis article. It would be a shame if did leave. You clearly have much to contribute. Boghog (talk) 22:31, 1 December 2013 (UTC)
Thank you for the kudos on the Biomimetic stub. Was redirected to Bionic when I first looked for Biomim Synth, and this clearly would not do. With Wikipedia's success in being hit by Google, etc., there is clear need to have the new stub fleshed out. I am gathering possible contributors, as we speak.
On the rest, I am exhausted with it, and would just make these four closing points, as we agree to disagree, and then leave the work with you:
First, I am past taking any time to rely on, or even look at, any WP policies or rules, or to try to seek recourse through them. They simply are not, in my experience, enforced uniformly, consistently, or even-handedly. Even if they were, the fundamental principles guiding them and operational practices executing them are (in my opinion) deeply flawed. Hence, Outing may technically be forbidden, but it is hopeless to act in any fashion against any well-connected editor, and certainly not toward a severe end such as banning, however much it might be deserved. Regarding Verifiability: Recently, after several visits over the past couple of years to a biological article, Species, I felt compelled to remove from the article a lengthy (1600 word) block of text that was essentially devoid of real referencing (1 actual citation, and a couple of allusions via author's names in more than a dozen full paragraphs). The first tag indicating it lacked all referencing was placed in 2009 (!), so in 4 years, 1 citation had been added. Moreover, on surveying the article, it was clear that a culture of using text without citation had developed. I added further citation-needed tags, and explained the section removal in Talk:Species. Momentarily, non-expert User:Obsidian Soul reverted, eliminated my citation-needed tags as "bombing", and proceeded to deny in Talk any argument allowing any other course than forensic referencing (authors other than the original trying to piece together sourcing for the article text). So, based on my earlier experience with the Rubio article overlords, though I argued a bit, I placed two "tags" in Talk, and then punted. I know I could not muster a consensus against a well-entrenched editor. Though I am correct, I see no hope of a positive outcome with regard to that article's content. However, the first-to-revert editor sits pretty, because he knows that in an edit war, he has the advantage. The system is not biased in favour of what is correct, or accurate, or true, but in the the direction of consensus (editor networks), and so the new guy coming in, expert or not, correct or not, stands no chance. (How can a subject matter expert be expected to have the time for the fight?) So, the earth, in some places, will have to remain flat. As Galilei found, there are, in places and at points of time, practically un-winnable battles.
''Second, and returning to our agree-to-disagree disagreement: Note, within a sentence of your opening, you redirect from the question that I addressed to a perhaps subtle but nevertheless different question, which therefore necessitates divergence of opinion. ("Do steroids have any Conformational isomers as implied by Conformational isomerism" cannot be rephrased ("[i]n other words") as you did, to ask "are steroids as a class, good examples of molecules that possess conformational isomerism?") My view is that the relevant question of steroid chemistry, history, and inherent chemical nature (and so this article) is the first. The second is a pedagogic question related to content of the conformational isomerism article, where I would agree that the answer might be to exclude steroids except for a passing mention of decalin, history, and Barton. In re: the first, unaltered question: As long as temperature-dependent NMR reveals changes (even small), as long as various conformers of specific steroids are found bound to receptors, as long as some specific steroids interconvert (even if the largest part of most do not at ambient temperature), as long as long as A-ring dehydro, brominated, and seco- subclasses of the overarching steroid class vary markedly from the rest in this property, and as long as the greatest single class representative, CHOL, shows dynamic behaviour that underlies its broad biological functions, I will not support the simple, absolute answer of "No" to the unaltered question—not here, not in something that I am peer-reviewing, not in EB, or anywhere.
Third, and relatedly, the existence of the acknowledged ensemble is key, the devil is in the details, and one must steer clear of absolutes out of respect for ones own ignorance. A principle sterol, CHOL, has seen selection to accomplish its broad functions, and so it is a unique molecule with a rigid, slab-like portion with a projecting hydrogen bonding element, and a side chain that can adopt a number of different comformations. Why both of these "regions" are so crucial to its function, we do not know. [While many things can replace cholesterol in in vitro assay (http://www.ncbi.nlm.nih.gov/pubmed/19655814), essentially nothing really can in vivo, especially not variants restricting or otherwise markedly altering its "side chain". We do not know, we cannot see, what conformations this side chain adopts in different contexts, but our ignorance does not suggest (and no one in this field believes) them to be non-existant or unimportant for our inability to see them). The devil remains in details we have not yet gleaned. To put this more broadly, I would say that to argue that steroids are all about the ring system is a chemocentric, and then a simplistic chemocentric view that fails to acknowledge how (as the EB article points out boldly in its lead) even the slightest change in functionalization can lead to enormous change in biological activity. You perhaps perceive that all of this SAR arises from changes that exclude any impact on conformational equilibria/small molecule dynamics; I do not. Hence, it's a healthy respect for our (the whole of science and medicine's) ignorance that keeps me from saying that steroids—not a specific one, not a portion of one, but steroids, comprehensively as a class of all its subclasses, across all of chemical and pharmacologic space—display no conformational isomerism (thus sidelining as necessarily unimportant extent dehydro-, seco-, bromo- and other outlier examples, ambiently low-proportion higher energy conformations possibly increasingly present during chemical reactions and binding interactions, etc.). I can't confidently extrapolate in this fashion, at all. To paraphrase Jack Halpern, on the mechanism of Wilkinson's catalyst in hydrogenation, just because its hard for us to "see" at any point in time, by any single given experimental means of "seeing", does not imply that what may be there in limited proportion, or transiently, is not critically important.
Fourth, and finally, regarding "no reversions" ... this issue distils to my perception, and no post hoc statement can change another's original perception. Your decisions to change tag message content and, in the end, to remove them completely, sent a clear message to me of the way that the article was being viewed/controlled. The only bits I placed into the text (tag explanations), issue was taken, and they were "overruled". And rather than say I reverted you (!), one might just as accurately say, "Based on Bohog input [which might have been made as a suggestion in Talk, rather than as a overruling tag edit], LeProf returned to his original tag content, trying to edit it both in line with his aims, and with the suggestions made by Bohog." (The result of which, you reverted!) Now, tags are very often less controversial (e.g., than changing another's invested prose). It's in vain that you argue you should be perceived as one who would not exert the same persona when issues of content arise. You were quick to act, remain very confident in your conclusions—how many times did I have to insist about steroids appearing in Boger before you could see?—and remain fixed to a simple explication of steroid dynamics (no story). Who has time for these mutually exhaustive attempts to persuade the other? If we were long friends and co-authors, e.g., of a hardcover so what we created could in some fashion last, maybe. Bottom line, having dipped my toe, and seen churning of the water, I don't feel an invite for a further swim (in waters likely more dangerous). I think we must agree to disagree, and let you go on. Suggestions in Talk will appear. What you do with them will be yours to decide.
[Realize, too we have not yet ventured into more philosophical waters. I believe un-infomed users should not be subjected to text about which experts disagree (our case), and certainly should be shielded from text where an expert is being reverted by a hobbyist who is simply better established, has more non-expert friends, or who simply who has more time to pursue a WP end (not our case). This sets me up to fail at contributing, and so if there is even a whiff of fundamental difference in the way a subject is viewed (again, our case), I plead no contest and walk. And with apologies to you (for you did not impose this structure), the ability to immediately revert, to do so without discussion, to tally reversions such that the person offering edits to a status quo necessarily "loses" in the case of a strong difference of opinion about content—my view is that these WP's keep plagiarism in place, bad articles from being improved quickly, etc. I have had it with this aspect of wikipedia.]
Bottom line, for you to consider, as a final statement of my position... Earlier, I called attention to several of your interspersed comments that I thought formed the beginning of a reasonable statement regarding conformational isomerism in steroids (with explanation of nomenclature, illustrated image, and a bit more on history needing to be added). As well, above, you wrote (and you were not stating the obvious, at Wikipedia):

at physiological temperatures, only a very small fraction of the conformational ensemble of fully saturated trans-trans-trans or cis-trans-trans steroids... adopt conformations where one or more... rings... [are in a] boat or other strained ring conformation. The vast majority of the... ensemble is... a single conformation where... the A-, B-, and C-rings [all] adopt a chair conformation. Hence for...[most] practical purposes, ... [t-t-t or c-t-t] steroid cores are rigid... [, a generalization that ] only breaks down at ... [high] temperature... [This is]... easily... explained... [For instance, i]n order for the A- and B-rings of [c-t-t] steroids to inverconvert, the B-ring has to flip from one chair conformation to the other... [a flip] made impossible by the trans B/C-ring fusion. There are exceptions of course (e.g., introducing unsaturation into the A-ring makes the A-ring more flexible), but... fully saturated [ABCD-steroid ring systems] are [generally] very rigid...

— Bohog, Talk, this section above
and I think the above from you is, with clear sourcing, a good start on a section on steroid conformational isomerism.
My contribution of a summary might run something like: "Steroid subclasses with intact ABCD rings with common ... ring junctures, e.g. ... , present relatively rigid, planar core frameworks—though at elevated temperatures relevant to chemical synthesis, and in constrained environments such as protein binding sites and nanotechnology materials, higher energy conformers may still be accessed and be important. As well, the class displays conformational isomerism through their pendant chains and groups, and further mobility in specific steroids and steroid derivatives arising from alterations to a simple, unaltered, contiguous hydrocarbon ABCD-ring (gonane) core, e.g., through ring scission (to provide secosteroids such as vitamin D3), or through particular changes to bond order or functional groups (e.g., to provide A-ring dehydro- or bromo-steroids)."
"Do dogs wag..."? The answer is yes, though of course we must amplify, and specify ... "mostly, their tails, but in particular dogs..." (http://www.youtube.com/watch?v=b9yT2l_udl4) LeProf
If you have an answer to this, let it appear as text in a "Steroid conformations and conformational analysis" section in the article. As I indicate below, I am off. Cheers. LePRof — Preceding unsigned comment added by 50.179.92.36 (talk) 21:18, 6 December 2013 (UTC)

Please reply at Natural product talk...

...to let me know you have read my last, longer Talk entry. Thank you. LeProf — Preceding unsigned comment added by 50.179.92.36 (talk) 18:08, 7 December 2013 (UTC)

Can you please...

...use edit in talk, and copy my new lead text, and flag the "peacock" parts of text you take issue with? That accusation, without any references, floored me. Thank you. LeProf — Preceding unsigned comment added by 50.179.92.36 (talk) 19:47, 7 December 2013 (UTC)

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I am One of Many interjection, and course of our conversation

I was preparing to respond to you at NP, when I am One of Many interjected. I responded to him. Whether I need to respond further to you, and how, depends on his response to me there. Please hold, and see what he says. LeProf

I had, during the course of the conformational analysis arguments, hopes to meet you professionally. Now I only hope you can find someone to help you take a good look at yourself. Enjoy NP, it seems this will also be your article. We are done (but I will likely elevate your stalking). Cheers. Bye. LeProf, or as you like to say, 50.179.92.36, since you cast yourself as Javert to my number-only Jean Valjean. Lol. You are something. — Preceding unsigned comment added by 50.179.92.36 (talk) 22:19, 7 December 2013 (UTC)
LeProf. I am convinced by working together, we can make the natural product article better. Perhaps it would be good if we both took a short break and resume working on this tomorrow. Cheers. Boghog (talk) 22:25, 7 December 2013 (UTC)
We are done. There was little enough trust after Steroids, there is none with you following me to Natural Product. Enjoy the world you are creating for yourself. 50.179.92.36Leprof 7272 (talk) 06:21, 8 December 2013 (UTC)
I am sorry that you feel that way. You need to understand however that the lead that you wrote is appropriate for a new natural product chemistry article, but is simply not appropriate for the current natural product article. It is important to keep both the target audience and the scope of the article in mind (see WP:MOSINTRO). The lead that you wrote unfortunately fails both criteria. The lead should be written in a way that can be understood by a wide audience, the vast majority of whom are not organic chemists. Furthermore the scope of natural products is far wider than organic chemistry. Please note that I have reintroduced most of your previous lead as a new Natural_product#Impact_on_chemistry subsection of this article. My suggestion is that you expand that section and eventually split it out as a new natural product chemistry article. Boghog (talk) 11:39, 8 December 2013 (UTC)

A barnstar for you!

The Technical Barnstar
I wanted to say Thank you for all your help with the journal citation formatting on amphetamine, as well as for providing your chem expertise and helping me expand the pharmacology section. Seppi333 (talk) 22:31, 6 December 2013 (UTC)
And thank you for the barnstar and for the incredible job you have done in driving the amphetamine article toward FA status. Cheers. Boghog (talk) 12:28, 8 December 2013 (UTC)

ARG1

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The Wikipedia Library Survey

As a subscriber to one of The Wikipedia Library's programs, we'd like to hear your thoughts about future donations and project activities in this brief survey. Thanks and cheers, Ocaasi t | c 15:36, 9 December 2013 (UTC)

Weird one

When boghog citation filling for 20565525, I got an error message:

Error: http://www.ncbi.nlm.nih.gov/gquery/:1: parser error : Content error in the external subset ^

SandyGeorgia (Talk) 17:32, 10 December 2013 (UTC)

{{cite journal |author=Calabria B, Degenhardt L, Hall W, Lynskey M |title=Does cannabis use increase the risk of death? Systematic review of epidemiological evidence on adverse effects of cannabis use |journal=Drug Alcohol Rev |volume=29 |issue=3 |pages=318–30 |year=2010 |month=May |pmid=20565525 |doi=10.1111/j.1465-3362.2009.00149.x |url=http://dx.doi.org/10.1111/j.1465-3362.2009.00149.x}}
It works now. There sometimes used to be glitches with the template filler not populating fields, that David guessed may be a PubMed load issue. RDBrown (talk) 22:07, 10 December 2013 (UTC)
Thanks SandyGeorgia for alerting me to the problem and RDBrown for the diagnosis. I agree that this seems to be a transient problem which suggests it is not problem with the template filler itself, but rather a temporary problem either with the Wikimedia Tool Labs or PubMed server or the communication between the two. If the later times out, the former will generate either a error message or some other strange result. Boghog (talk) 22:18, 10 December 2013 (UTC)

Technical feedback

Hey Boghog, someone from the Amph FAC-nom wants to hear the thoughts of another editor on the pharmacodynamics section. Seeing as how you're probably the only other editor of the article that understands the material, I was wondering if you could put provide some feedback at WP:Featured_article_candidates/Amphetamine/archive1, provided you have the time.

Don't worry about it if you're busy though.

Seppi333 (talk) 23:37, 10 December 2013 (UTC)

Also, what do you think about this image? I was planning on giving it a caption with an explanation in plain English for people without the relevant background knowledge.
Large image

Insert witty caption here

A wall of text goes here.

I based it upon the left one: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3005101/figure/F1/

I should probably crop out the sides to reduce the width if I put it in though.

Seppi333 (talk) 02:08, 11 December 2013 (UTC)
Hi. I am busy in real life, but I should have time this weekend to take a closer look. Cheers. Boghog (talk) 08:37, 11 December 2013 (UTC)

Your reverts

You seem to be edit warring. The deprecation of |month= is a longstanding fact. It is worked into all major and almost all minor citation templates. When you get consensus to overturn that, then undo my edit. Debresser (talk) 00:29, 15 December 2013 (UTC)

I see you are almost the sole contributor to Template:PBB/7442. Please note though that per WP:OWN you do not own this template. Please do not behave as its owner. Debresser (talk) 00:31, 15 December 2013 (UTC)

Where was the consensus to deprecate the month parameter? I have asked and have not received an answer. Why fix something that isn't broken? Boghog (talk) 00:34, 15 December 2013 (UTC)
Also this is a WP:CITEVAR issue that trumps WP:OWN. Concerning citation styles, one should "defer to the style used by the first major contributor". Boghog (talk) 00:39, 15 December 2013 (UTC)
I understand what you are saying regarding WP:CITEVAR. But that is not really the same issue. The deprecation of |month= is Wikipedia wide, and that trumps even WP:CITEVAR.
Regarding the decision to deprecate |month=. It was made practically, but not officially. I know, because I was one of the editors who were involved. This was a few years ago already, so this is a longstanding status quo. I would have no problem with overturning that, as I said above, but at the moment it is a fact, and the associated error category is very real. Debresser (talk) 00:47, 15 December 2013 (UTC)
An unofficial deprecation that was made without consensus trumps a Wikipedia guideline that is based on consensus? Boghog (talk) 00:53, 15 December 2013 (UTC)
Someone may have had the intention to deprecate this parameter a few years ago, but it was only very recently that month was added to the error category. The fact that the error category is real is irrelevant. It was still made without consensus. Boghog (talk) 00:58, 15 December 2013 (UTC)
It was not "someone". It was a group of editors who were very active in the field of maintenance categories. And there was discussion. But I don't think that discussion was Wikipedia wide, rather local on some citation templates talkpages.
The deprecation took place on 20+ citation templates, including all the major ones, and they were all added to an error category. That category was changed a few months ago, because of the changes in citation templates. So the deprecation was very real, and the error causing parameters were replaced on many articles, and after that the month and day parameters were removed from most citation templates. Do not make it look as though this is something new.
In any case, it is a status quo of quite some years now, and as such you will need broad consensus to overturn it. Debresser (talk) 01:22, 15 December 2013 (UTC)
Debresser, I have to agree with Boghog on this - unless there's an actual pressing reason to deprecate the month parameter, this just results in the need to do the pointless, tedious, and time-consuming chore of manually converting "...| month=ABC| year=YYYY..." to "| date=ABC YYYY" for dozens of citation templates in just 1 large article. Seppi333 (Insert 2¢) 02:17, 15 December 2013 (UTC)
Seppi333, why would you need to do that? The fix in the template is stand-alone. The article will be fixed by bots in due time. Apart from that, I am more than willing to help. Debresser (talk) 02:44, 15 December 2013 (UTC)
Update: TRPV1 is no longer in that error category. Debresser (talk) 02:55, 15 December 2013 (UTC)
One one here requested your help on TRPV1. Why was month added to the error category in the first place? Status quo ≠ consensus. Furthermore IMHO, if the month parameter must go, it would be cleaner to leave the year parameter alone and just delete the month parameter than concatenate month and year into date. Boghog (talk) 09:55, 15 December 2013 (UTC)
As Trappist the monk has stated, "deprecation does not mean disallowed". I have also asked for and still not received a clear explanation for why this deprecation was necessary in the first place. The only reason why the "deprecation was very real" is because month was added to the error list on 30 October 2013. This edit does not answer the question why. It would be far simpler to remove month from the error list than to change the citation templates in countless articles for reasons that no one has been able to explain to me. Boghog (talk) 11:01, 15 December 2013 (UTC)
You said above that it is better to remove the month altogether, and right away started doing that([3]). Why you say it is better to remove the months, is an utter riddle to me! The fact that you don't understand something, or think you do understand something, is not reason to right away jump and start editing. Discuss, think it over, then edit. Really. Debresser (talk) 11:48, 15 December 2013 (UTC)
As to the fact that month and year were merged into date. That is what has been done with all such cases for the last few years, on literally thousands of pages. Would you care to explain why all of a sudden you have to reinvent the wheel and say it is not good? Debresser (talk) 11:50, 15 December 2013 (UTC)
I have thought this through. As I have previously stated, concatenating the month and year into a single parameter makes it more likely that dates will be inconsistently formatted. Furthermore with journal citations it normally is not necessary to include the month. There are rare situations when month might be useful to establish priority between citations, but normally it is not needed. Boghog (talk) 11:55, 15 December 2013 (UTC)
Large numbers of changes to the date format to cite journal articles has only occurred after the month parameter was added to error category. Furthermore you still have not explained why this change is necessary in the first place. Boghog (talk) 12:00, 15 December 2013 (UTC)

"concatenating the month and year into a single parameter makes it more likely that dates will be inconsistently formatted" That is actually not true. Is remains just as likely. Just that now the two parameters are one.

"with journal citations it normally is not necessary to include the month" What do you base that one? Journals are rarely published only one a year, so the month parameter is needed to distinguish the multiple editions of each year.

By the way, the edit where |month= was deprecated was this one, or more precisely this one.

I suppose the main reason is that people prefer to type one time a date parameter, rather than 2 or three parameters (like day, month, year). Debresser (talk) 12:06, 15 December 2013 (UTC)

With separate month and year parameter, consistent rendering independent of the order of the parameters:
  • Rubinstein MH (1976). "A new granulation method for compressed tablets [proceedings]". J. Pharm. Pharmacol. 28 Suppl: 67P. PMID 12345. {{cite journal}}: Unknown parameter |month= ignored (help) ({{cite journal | author = Rubinstein MH | title = A new granulation method for compressed tablets [proceedings] | journal = J. Pharm. Pharmacol. | volume = 28 Suppl | issue = | pages = 67P | year = 1976 | month = December | pmid =12345 }})
  • Rubinstein MH (1976). "A new granulation method for compressed tablets [proceedings]". J. Pharm. Pharmacol. 28 Suppl: 67P. PMID 12345. {{cite journal}}: Unknown parameter |month= ignored (help) ({{cite journal | author = Rubinstein MH | title = A new granulation method for compressed tablets [proceedings] | journal = J. Pharm. Pharmacol. | volume = 28 Suppl | issue = | pages = 67P | month = December| year = 1976 | pmid =12345 }})
With a single date parameters, rendering can differ:
  • Rubinstein MH (1976 December). "A new granulation method for compressed tablets [proceedings]". J. Pharm. Pharmacol. 28 Suppl: 67P. PMID 12345. {{cite journal}}: Check date values in: |date= (help) ({{cite journal | author = Rubinstein MH | title = A new granulation method for compressed tablets [proceedings] | journal = J. Pharm. Pharmacol. | volume = 28 Suppl | issue = | pages = 67P | date = 1976 December | pmid =12345 }})
  • Rubinstein MH (December 1976). "A new granulation method for compressed tablets [proceedings]". J. Pharm. Pharmacol. 28 Suppl: 67P. PMID 12345. ({{cite journal | author = Rubinstein MH | title = A new granulation method for compressed tablets [proceedings] | journal = J. Pharm. Pharmacol. | volume = 28 Suppl | issue = | pages = 67P | date = December 1976 | pmid =12345 }})
Boghog (talk) 12:19, 15 December 2013 (UTC)
You are right. As though anybody would write "1976 December". And if they did, they shouldn't. It's that simple. Debresser (talk) 12:20, 15 December 2013 (UTC)
Because they shouldn't doesn't mean they won't. Also months are normally not needed in a journal citations. The issue parameter when present makes the month parameter redundant. The vast majority of scientific journals themselves do not include month in citations either. Boghog (talk) 12:28, 15 December 2013 (UTC)
The issue may be "Spring 2011", while the date would be "April 2011", so that the month is yes needed often, even when issue is specified. Debresser (talk) 12:44, 15 December 2013 (UTC)
If they will, then somebody else will need to fix it for them. That is what error categories are about. :) Debresser (talk) 12:50, 15 December 2013 (UTC)
If the vast majority of scientific journal articles don't include month or seasons in their reference lists, why do Wikipedia articles need them? The issue parameter is sufficient to unambiguously track down the original print publication. Why fix something that isn't broken, especially if it introduces the possibility of introducing new inconsistencies and errors? Boghog (talk) 13:08, 15 December 2013 (UTC)
For starters, not all journals are scientific. Even if many journals don't add a date, some do, and we should allow for that possibility. In addition, additional information is always useful. Debresser (talk) 14:13, 16 December 2013 (UTC)
In the article in question, all the cited journals were scientific. Furthermore I agree that we should allow the possibility of cleanly specifying the month by not deprecating the month parameter. Boghog (talk) 19:35, 16 December 2013 (UTC)

December 2013

You currently appear to be engaged in an edit war. Users are expected to collaborate with others, to avoid editing disruptively, and to try to reach a consensus rather than repeatedly undoing other users' edits once it is known that there is a disagreement.

Please be particularly aware, Wikipedia's policy on edit warring states:

  1. Edit warring is disruptive regardless of how many reverts you have made; that is to say, editors are not automatically "entitled" to three reverts.
  2. Do not edit war even if you believe you are right.

If you find yourself in an editing dispute, use the article's talk page to discuss controversial changes; work towards a version that represents consensus among editors. You can post a request for help at an appropriate noticeboard or seek dispute resolution. In some cases it may be appropriate to request temporary page protection. If you engage in an edit war, you may be blocked from editing.

I have come here to discuss with you. I have pointed out to you that you should take it easy with your reverts. Will you stop reverting now? Or you will be blocked for edit warring! Your behavior is annoying and, frankly, a little disrespectful. I am trying to have some dialog with you here, and all you do is click that revert button of yours. Debresser (talk) 12:16, 15 December 2013 (UTC)

Likewise, I also am trying to have a discussion. And no, I am not just clicking the revert button. I have explained my reasons above. Boghog (talk) 12:21, 15 December 2013 (UTC)
Where is the consensus that if a month parameter is present, it should be merged into a single date parameter along with the year? To reiterate (1) month is redundant with issue, (2) concatenating month with year introduces the possibility of inconsistent rendering of dates. Better to delete the month parameter entirely and leave the year parameter alone. Boghog (talk) 12:41, 15 December 2013 (UTC)
Your reiterating your position or hammering on the same question will not make you right. The more so that it does not give you the right to continue to revert. Your question has been answered many times, your concerns addresses. And, just to make it abundantly clear what I mean, a question is not in itself an argument. And an argument does not make you right. And being right does not give you the right to revert. If you don't get the point, then there is not much anybody can do. Debresser (talk) 12:48, 15 December 2013 (UTC)
Asking for a clear and concise explanation is a reasonable request. The previous discussion never really answered my question. The explanation that you offered above:
  • I suppose the main reason is that people prefer to type one time a date parameter, rather than 2 or three parameters (like day, month, year).
is insufficient to justify deprecation and active removal of a parameter that has been widely used for a long time and has not caused any major problems. Furthermore the year parameter has not been deprecated and when used in combination with the issue parameter, should be sufficient for most purposes. Boghog (talk) 13:25, 15 December 2013 (UTC)
Concerning TRPV1, every single citation contains an issue parameter hence there is no meaningful information loss by removing the month parameter. Furthermore by concatenating the month and year parameter introduces the possibility of inconsistent formatting in the future. Hence I would appreciate if you would restore this edit. Boghog (talk) 14:04, 15 December 2013 (UTC)
This, and your last edit in the section above, is precisely what I mean. I already explained there that I do not agree with you. That the issue number does not tell me automatically the month and year. And again you want to remove that information. You simply to get a point when it is explained to you. Sorry to say. Debresser (talk) 14:39, 15 December 2013 (UTC)
WP:LISTEN arguments are only valid when a consensus has actually been established. Everyone is in agreement that the deprecation of the month parameter was not widely discussed outside of template talk. So it is debatable if a consensus has actually been reached to deprecate this parameter. Furthermore the question of what to replace the month parameter with is a related yet distinct question and no evidence has been provided that a consensus has been reached concerning this issue. For scientific publications with year, month, and issue parameters, removing the month parameter and leaving the year parameter untouched is an arguably better solution. I get that the point that information is being removed. My counter point is that the amount of informational loss is insignificant and in the vast majority of cases this information is not needed. I am listening to what you have to say and I would appreciate if you would return the favor. Boghog (talk) 17:27, 15 December 2013 (UTC)
This issue is very relevant. It demonstrates that problems can arise if wide consensus is not first obtained. It also demonstrates that consensus can change. Boghog (talk) 19:01, 15 December 2013 (UTC)
There was consensus. This is relevant to citation templates, and that is where it was discussed, by editors active on citation templates. How much of a consensus do you need? And is several (3 or 4) years not enough to turn something into consensus? And that argument holds even if it wouldn't have been discussed at all. What do you mean "consensus can change"? You are referring to yourself only! Debresser (talk) 14:19, 16 December 2013 (UTC)

I do not see a link to the discussion of this alleged decision to deprecate the month parameter in the discussion above; where is it? SandyGeorgia (Talk) 14:20, 16 December 2013 (UTC)

I never gave it. Nor do I have it. I would have to look at the talkpages of a few citation templates over a 2-3 year range. Probably this was on Cite web. What I wrote above is what I remember after all that time, and is not necessarily accurate in all details. Frankly speaking, I don't think it matters much at this point in time. The deprecation is a fact and has been actively taking place for the last few year. Debresser (talk) 17:00, 16 December 2013 (UTC)
It matters a great deal. Perhaps the previous discussions would provide a clear explanation why this deprecation was necessary. Neither the above nor this discussion provides such an explanation. Boghog (talk) 19:10, 16 December 2013 (UTC)
Again, does it matter. You obviously are of a different opinion, so if you want, you are free to open the discussion anew. I would do so on the talkpage of the citation module and post a link to it on the Technical Village Pump. Debresser (talk) 22:36, 16 December 2013 (UTC)
Here is one link to a discussion of deprecation of |month= during April and May of 2013. I do not know of others. – Jonesey95 (talk) 04:46, 17 December 2013 (UTC)
This is the most recent discussion of |month=.
Here is a discussion of the month parameter in relation to RefToolbar.js, from May 2013.
Here is a link to a discussion of |day= and |month= from March 2013.
A discussion of removing a number of parameters from {{Cite AV media}}, circa December 2009.
A discussion of cite journal from April 2008, in which |month= apparently did not exist in {{cite journal}}.
And a link to the Wikipedia page on deprecation. That's all I've been able to find. I hope it helps shed some light on this discussion. – Jonesey95 (talk) 05:55, 17 December 2013 (UTC)
The one from Cite AV media I remember, and it is one of the discussions I had foremost in mind. Debresser (talk) 07:44, 17 December 2013 (UTC)
Thanks Jonesey95 and Debresser for the links. I will read them carefully and try to look at this issue from both sides. Boghog (talk) 21:43, 17 December 2013 (UTC)

Technical advice sought on citations

Hi there, thanks for edits at Myoglobin where I have been working lately. I am a content guy and confess to paying little attention to the gizmo's that underpin Wikipedia. So could you explain the merits of {{cite journal | author = Drago RS | title = Free radical .. vs the simpler <ref>Author, "title" Journal, date etc </ref> format? Do they appear better in browsers - is that the reason? Thanks, --Smokefoot (talk) 19:38, 24 December 2013 (UTC)

Hi and thank you for improving the myoglobin article. The main reason for using the {{cite journal}} template is to (1) insure citations are consistenly formatted, (2) provide appropriate external links (urls, dois, pmid, pmc, etc.), and (3) allow bots to maintain the templates (see for example this edit). Also there are various tools for creating these templates that can save you a lot of work. The one I prefer is User:Diberri's Wikipedia template filling tool (instructions). Given a PubMed ID, one can quickly produce a full citation that can be copied and pasted into a Wikipedia article. Unfortunately the tool seems to be down at the moment. I will see if I can get it running again. Boghog (talk) 20:19, 24 December 2013 (UTC)
The template filler tools works intermittently. It appears to be a problem with the tool server and not the template filler script. Boghog (talk) 22:10, 24 December 2013 (UTC)

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Granularity of author names in citations

I'm curious - why do you favour combining authors into a single string for the authors param in citations, rather than using the finer-grained params (first1, last1, etc.) ? Alexbrn talk|contribs|COI 11:26, 29 December 2013 (UTC)

Because the firt, last business creates a huge mess to work around in edit mode, and yields punctuation inconsistent with the Diberri/Boghog format favored in medical articles. SandyGeorgia (Talk) 14:42, 29 December 2013 (UTC)
I agree with SandyGeorgia. If "first1, last1, first2, last2, ..." parameters are used with a long author list, the filled out {{cite journal}} template becomes very verbose. In addition, using these finely grained author parameters renders the citation in a style that differs with the pre-existing citation in the vitamin D article (see WP:CITEVAR). This could be fixed by adding the following to the citation template:
  • | authorformat = vanc | author-separator = , | author-name-separator = &#32;
but this solution make make an already long template even longer.
One reason offered for using "first1, last1, first2, last2, ..." parameters is that it can generate COinS meta data. But does anyone actually use this? Most of the journal citations in the vit D article contain pmid and if some one where interested in loading this citations in a reference management database, using pmid would be easier and less error prone. Boghog (talk) 15:20, 29 December 2013 (UTC)
Thanks for the responses. I wasn't objecting, but was genuinely curious. I am lazy so generally just put {{cite journal|pmid=xxxxxxxxx}} and then get a citation bot to populate the fields via the widget available from preferences (and it uses first1, first2, etc.) - and I suppose in general I don't mind heavy markup, and tend to use fields if they're there - certainly in STM publishing it's common practice to split names into their constituent parts, though I agree in practice the small loss of information in not doing so doesn't really matter. Alexbrn talk|contribs|COI 15:27, 29 December 2013 (UTC)
And then I have to fix all your citations, so the time you save is time I spend :)) On medical articles that already use the Diberri/Boghog format, you can generate a citation template by putting the PMID into this citation template filler. (Because I usually works on FAs, I'm accustomed to the need for citation consistency, and inconsistent citations are best fixed as soon as one sees them. SandyGeorgia (Talk) 15:45, 29 December 2013 (UTC)
A solution that is particularly relevant for the vitamin D article is User:Diberri's Wikipedia template filling tool (instructions). Given a PubMed ID, one can quickly produce a full citation that can be copied and pasted into a Wikipedia article. (Unfortunately this does not work with PMID 24308073 because it is part of the NCBI bookshelf). Finally it should be noted that RefToolbar (first, last, coauthors) and Citation bot (first1, last1, first2, last2, ..) are somewhat inconsistent. Boghog (talk) 15:50, 29 December 2013 (UTC)

Finally, after 7 months ...

Amphetamine mixed salts (medication) was moved back to Adderall. Seppi333 (Insert 2¢) 01:00, 30 December 2013 (UTC)

Thanks! Finally common sense prevails. Cheers. Boghog (talk) 02:14, 30 December 2013 (UTC)

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More Protein boxes needed

Hi Boghog, I noticed you added the very useful protein box (PBB info box) for IFT140. Can you also add it for a few more genes I added recently? Thanks, Avilella.

https://wiki.riteme.site/wiki/FBXL4 https://wiki.riteme.site/wiki/FBXL4 https://wiki.riteme.site/wiki/DCSH1 https://wiki.riteme.site/wiki/SZT2

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