User talk:Evolution and evolvability/Archive 2017

Catalytic triad of TEV protease

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THOMAS SHAFEE

Evolution and Evolvability

can you get into the genetics article assessment links?

Hi! I haven't been able to get into the ??? articles (or any others) by clicking on the entries in that table for a few days. Have you had the same trouble? Do you know what the problem is? Thanks, DennisPietras (talk) 05:45, 22 January 2017 (UTC)

@DennisPietras: Hmm, odd. I'm getting a error 504 on the site. Maybe it's just down today. I was working on Friday. I'd recommend waiting a day or two to see if the tool is fixed. T.Shafee(Evo&Evo)^talk 09:45, 22 January 2017 (UTC)

Already did the wait thing. Posted a question about it "Is there a problem with a search engine or bot, or am I experiencing a PEBCAK error?" at https://wiki.riteme.site/wiki/Wikipedia:Help_desk#Is_there_a_problem_with_a_search_engine_or_bot.2C_or_am_I_experiencing_a_PEBCAK_error.3F Nobody's given me an answer yet. Note that I got a "502" error. Maybe there has been a coronal mass ejection affecting some hard drive somewhere. At least I know it's not just my problem, but I do miss the opportunity to review all those small nucleolar RNA articles....

DennisPietras (talk) 16:07, 22 January 2017 (UTC)

@DennisPietras: That is frustrating. In the meantime, this category might be somewhat useful: Category:Unknown-importance_Genetics_articles. T.Shafee(Evo&Evo)^talk 22:36, 22 January 2017 (UTC)

That is a really cool list. It seems to update immediately after making the edit! DennisPietras (talk) 05:08, 24 January 2017 (UTC)

Everybody's a critic...

Hi Thomas! Re: File:Gene structure eukaryote 2 annotated.svg I would have broken the variable "pinkish" open reading frame region above the introns with blueish/grayish blocks. I mean, theoretically, I would have, not that I am even anywhere near being able to do it! On another topic, if you haven't yet noticed, we can search the quality and importance table again! DennisPietras (talk) 03:12, 1 February 2017 (UTC)

Nucleic acid structure

Great job with the improvements to the Template:DNA RNA structure—it looks really good! I have two minor comments. First, in the secondary structure row, "helix" should be replaced with "duplex" as the helical structure is a result of tertiary rather than secondary structure. Second, primary structure image should be a skeletal structure rather than a 3D model, since the bonding pattern of atoms is part of primary structure, while their 3D orientation is again part of tertiary structure. (This second point goes for the protein structure template as well.) Once again, thanks for making these templates, and I hope my nitpicky comments are helpful. Antony–22 (^talk⁄_contribs) 21:20, 20 February 2017 (UTC)

Heart

Thanks for your email. I'd be happy to give it a go. I am however reserved about how useful this is, the majority of advice provided by academics thus far seems to be (1) stylistic (2) substituting equivalent but less understandable terminology or (3) inclusion of miscellaneous factoids which do not always warrant inclusion on the main article page and (4) requiring much patience and time in discussions, which I do not always have. I will however give this a go. Please ping me using {{u}} in replies so I can keep track :). Yours, --Tom (LT) (talk) 01:52, 19 March 2017 (UTC)

@Tom (LT): I completely understand. It remains a challenge how to best leverage the academic community to improve Wikipedia. In addition to the raw information content, academics can struggle with the different style, tone and focus of encyclopedic writing (let alone wikipedic). As the WikiJournal of Medicine matures we are aiming to improve ways to maximise the value from contributions by academic peer reviewers. When you have a version that you are happy to submit, let me know if you have any issues with the submission process, and I can help out. T.Shafee(Evo&Evo)^talk 01:21, 20 March 2017 (UTC)

@Evolution and evolvability having thought about it, I think it would benefit the encyclopedia if some of our smaller articles, which are more likely to have occult errors, undergo review. How about Pudendal nerve?--Tom (LT) (talk) 21:07, 10 April 2017 (UTC)

Mozilla fellowships to promote open science and open data in your research organisation

I just thought these fellowships might be of interest to you or others you know, aimed at "early career researchers" Kerry (talk) 01:24, 3 May 2017 (UTC)

Editing News #1—2017

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Did you know? Did you know that you can review your changes visually? When you are finished editing the page, type your edit summary and then choose "Review your changes". In visual mode, you will see additions, removals, new links, and formatting highlighted. Other changes, such as changing the size of an image, are described in notes on the side. Click the toggle button to switch between visual and wikitext diffs. The wikitext diff is the same diff tool that is used in the wikitext editors and in the page history. You can read and help translate the user guide, which has more information about how to use the visual editor. Since the last newsletter, the VisualEditor Team has spent most of their time supporting the 2017 wikitext editor mode which is available inside the visual editor as a Beta Feature, and adding the new visual diff tool. Their workboard is available in Phabricator. You can find links to the work finished each week at mw:VisualEditor/Weekly triage meetings. Their current priorities are fixing bugs, supporting the 2017 wikitext editor as a beta feature, and improving the visual diff tool. Recent changes A new wikitext editing mode is available as a Beta Feature on desktop devices. The 2017 wikitext editor has the same toolbar as the visual editor and can use the citoid service and other modern tools. Go to Special:Preferences#mw-prefsection-betafeatures to enable the ⧼Visualeditor-preference-newwikitexteditor-label⧽. A new visual diff tool is available in VisualEditor's visual mode. You can toggle between wikitext and visual diffs. More features will be added to this later. In the future, this tool may be integrated into other MediaWiki components. [1] The team have added multi-column support for lists of footnotes. The <references /> block can automatically display long lists of references in columns on wide screens. This makes footnotes easier to read. You can request multi-column support for your wiki. [2] Other changes: You can now use your web browser's function to switch typing direction in the new wikitext mode. This is particularly helpful for RTL language users like Urdu or Hebrew who have to write JavaScript or CSS. You can use Command+Shift+X or Control+Shift+X to trigger this. [3] The way to switch between the visual editing mode and the wikitext editing mode is now consistent. There is a drop-down menu that shows the two options. This is now the same in desktop and mobile web editing, and inside things that embed editing, such as Flow. [4] The Categories item has been moved to the top of the Page options menu (from clicking on the icon) for quicker access. [5] There is also now a "Templates used on this page" feature there. [6] You can now create <chem> tags (sometimes used as <ce>) for chemical formulas inside the visual editor. [7] Tables can be set as collapsed or un-collapsed. [8] The Special character menu now includes characters for Canadian Aboriginal Syllabics and angle quotation marks (‹› and ⟨⟩) . The team thanks the volunteer developer, Tpt. [9] A bug caused some section edit conflicts to blank the rest of the page. This has been fixed. The team are sorry for the disruption. [10] There is a new keyboard shortcut for citations: Control+Shift+K on a PC, or Command+Shift+K on a Mac. It is based on the keyboard shortcut for making links, which is Control+K on a PC or Command+K on a Mac. [11] Future changes The VisualEditor team is working with the Community Tech team on a syntax highlighting tool. It will highlight matching pairs of <ref> tags and other types of wikitext syntax. You will be able to turn it on and off. It will first become available in VisualEditor's built-in wikitext mode, maybe late in 2017. [12] The kind of button used to Show preview, Show changes, and finish an edit will change in all WMF-supported wikitext editors. The new buttons will use OOjs UI. The buttons will be larger, brighter, and easier to read. The labels will remain the same. You can test the new button by editing a page and adding &ooui=1 to the end of the URL, like this: https://www.mediawiki.org/wiki/Project:Sandbox?action=edit&ooui=1 The old appearance will no longer be possible, even with local CSS changes. [13] The outdated 2006 wikitext editor will be removed later this year. It is used by approximately 0.03% of active editors. See a list of editing tools on mediawiki.org if you are uncertain which one you use. [14] If you aren't reading this in your preferred language, then please help us with translations! Subscribe to the Translators mailing list or contact us directly, so that we can notify you when the next issue is ready. Thank you! User:Whatamidoing (WMF) (talk) 19:18, 9 May 2017 (UTC)

Transcriptomics technologies Topic Page

Hi Thomas, great to see the transcriptomics technologies page published as a PLOS Topic Page - maybe you already had this planned but I wondered if you'd had any thoughts on submitting to GAN? The page looks in great shape so it shouldn't need much to get it to GA status. Thanks, Amkilpatrick (talk) 11:39, 2 June 2017 (UTC)

@Amkilpatrick: Hi, and thank you! I was considering of doing just that. The Circular_permutation_in_proteins article had a similar trajectory back in 2012. I may start the process in a few weeks, to give me some time to finish other commitments, and to give others time to edit the page before I start GAN. Any recommendations welcomed though. T.Shafee(Evo&Evo)^talk 04:13, 4 June 2017 (UTC)

Fantastic! I'm hoping to start a push to get the best CompBio articles assessed for GA and the Topic Pages should all be more or less there. Let me know when you submit it and I'll see if someone from the WikiProject would be willing to review. Thanks! Amkilpatrick (talk) 08:03, 5 June 2017 (UTC)

Help needed

Hi E&E, you helped me previously on something I was unable to edit myself. I'm wondering if you could help me now. I ran across an article that has an incorrect title, which does not match either the Wikipedia article itself, or the Google results, or the article subject's own company pages. The article is Pyotr Aven, and I posted my findings on its talk page. The title should really be "Petr Aven", but I am unable to edit the title. Could you do that for me, or explain to me how I should go about getting it fixed? Thanks very much, GreyGoose (talk) 14:12, 2 June 2017 (UTC)

Never mind, E, I was able to find out how to do this on my own, and it worked. Thanks anyway, and be well! GreyGoose (talk) 05:00, 3 June 2017 (UTC)

@GreyGoose: Sorry I didn't get back to you sooner, but well done working it out! I think the exact thing you experienced is pretty common. 'Renaming' a page is more intuitive than 'moving' a page. Great work. T.Shafee(Evo&Evo)^talk 03:04, 4 June 2017 (UTC)

RE: Wikiprojects for enzymes

Thanks. I will keep this in mind. Kind regards Jakob

Template errors

The template you posted on the talk page of Womens Health has some errors in it. Since it is a professional journal and call for papers, these may need to be corrected. {{WJM advert 2017 Jan}}

Best Regards,

Barbara (WVS) ✐ ✉ 11:16, 17 July 2017 (UTC)

@Barbara (WVS): Thank you for alerting me! I've gone through and checked links and spelling again. T.Shafee(Evo&Evo)^talk 00:21, 18 July 2017 (UTC)

Your grammar ain't so good neither and what is the tea room that you suggest that the poster be displayed? If you have a tea room, is this poster hanging on the wall? I'm just trying to humorous and probably didn't accomplish that goal. Do you mind if I take a stab at editing the announcement? If you don't like what I do please revert. Best Regards, Barbara (WVS) ✐ ✉ 23:05, 30 July 2017 (UTC)

@Barbara (WVS): Thanks, I appreciate it. Anything I write always need a million rounds of copyediting! T.Shafee(Evo&Evo)^talk 02:31, 31 July 2017 (UTC)

Signpost submission

Hi there, I was just wondering if you saw my (late) reply last month at Wikipedia:Wikipedia Signpost/Newsroom/Submissions § WikiJournal of Medicine. Thanks, - Evad37 [talk] 01:53, 19 July 2017 (UTC)

@Evad37: Thank you for reminding me. It looks like a group of coauthors and I may have an article about Wikipedia's medical content published with in the next month or so. Perhaps just after that comes out could be a good time to write something for The Signpost. Would that work for you? T.Shafee(Evo&Evo)^talk 08:05, 19 July 2017 (UTC)

Sure, that would work - Evad37 [talk] 08:46, 19 July 2017 (UTC)

Wikipedia Welcomes Medical Students

I have created Wikipedia Welcomes Medical Students as a part of the Wikipedia Welcomes X program. I invite you to develop sample guidance material as well as the prototype so that they could be made use of if and when they can be made use of at such institutes. Diptanshu 💬 10:00, 5 August 2017 (UTC)

Recent {{AI4}} template update

I'm glad it's working well with the image templates that you created. If you happen to come across any buggy alignment issues as a result of that update, please let me know! Seppi333 (Insert 2¢) 11:21, 9 August 2017 (UTC)

@Seppi333: Absolutely, will do. T.Shafee(Evo&Evo)^talk 11:23, 9 August 2017 (UTC)

I mentioned this issue at Template talk:Annotated image and subsequently noticed that someone reverted the formatting fix that I added to {{AI4}}. I've reintroduced the table formatting. I'm not really open to leaving the image rendering problem unaddressed while he/she figures out a better way to address it. In any event, I figured I'd just let you know since for the past hour and a half, the annotated image 4 template didn't incorporate the table wrapper. Seppi333 (Insert 2¢) 00:06, 11 August 2017 (UTC)

Btw, this is the issue that I'm seeing on my mobile when the page uses div formatting instead of a table: div formatting.png. The right side of the image is displayed and it doesn't scroll left, so the left portion of the image gets cut off. Seppi333 (Insert 2¢) 00:30, 11 August 2017 (UTC)

Your GA nomination of Transcriptomics technologies

Hi there, I'm pleased to inform you that I've begun reviewing the article Transcriptomics technologies you nominated for GA-status according to the criteria. This process may take up to 7 days. Feel free to contact me with any questions or comments you might have during this period. Message delivered by Legobot, on behalf of Stigmatella aurantiaca -- Stigmatella aurantiaca (talk) 11:02, 24 August 2017 (UTC)

Your draft article, Draft:Exampledraft

Hello, Evolution and evolvability. It has been over six months since you last edited the Articles for Creation submission or Draft page you started, "Exampledraft".

In accordance with our policy that Wikipedia is not for the indefinite hosting of material deemed unsuitable for the encyclopedia mainspace, the draft has been nominated for deletion. If you plan on working on it further, or editing it to address the issues raised if it was declined, simply and remove the {{db-afc}} or {{db-g13}} code.

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Thanks for your submission to Wikipedia, and happy editing. Legacypac (talk) 21:52, 25 August 2017 (UTC)

Tryptophan 7-Halogenase

Hey, thanks for looking at the article! I don't remember exactly the PDB number I used for the diagram with the ligands, but I think that 2AQJ is likely. Either that one or 2JKC, as those are the two with FAD, Cl, and W as ligands. Best, scheng23 — Preceding unsigned comment added by Scheng23 (talk • contribs) 23:08, 6 September 2017 (UTC)

@Scheng23: Thanks! T.Shafee(Evo&Evo)^talk 01:42, 7 September 2017 (UTC)

Gene Wiki Review articles

Hi there! Thanks for the suggestion/ticket you posted to Gene Wiki Central github repo. Based on the examples you provided and your description, I have created a template for use with articles updated in conjunction with the Gene Wiki Review series and could use your feedback. Is the new template too similar to the Academic peer reviewed template? Should it be used only on the talk pages? Any feedback you have on this new template and the corresponding category would be much appreciated. Gtsulab (talk) 21:10, 20 September 2017 (UTC)

@Gtsulab: I like it. My instinct is to have the template on the main page (as you've made it) for the moment. It may be moved to the talk page some day down the track if there become thousands of such articles. However, for the moment, I think it's worth using the template in the reference section to highlight both the academic version of record, and that the wiki page was reviewed by an expert on a certain date. There should also be a subcategory for Gene Wiki review articles that is some equivalent of this one for PLOS Topic pages, since the category you made will eventually have articles from a variety of different journals. The template can be made to add articles to these subcategories automatically, so it's pretty easy to make robust:

<includeonly>
{{#if:{{{nocat|}}}||
[[Category:Wikipedia articles with corresponding academic peer reviewed articles]]
[[Category:Wikipedia articles with corresponding articles published in {{trim|{{delink{{{1|{{{journal}}}}}}}}}}]]
[[Category:Externally peer reviewed articles]]
}}
</includeonly>

T.Shafee(Evo&Evo)^talk 05:01, 21 September 2017 (UTC)

Thank you so much for your input, and for the help with the categories. I'll solicit a few more opinions before deploying the template on all the Gene Wiki Review-related articles. Gtsulab (talk) 17:02, 22 September 2017 (UTC)

Help pages

I thought that you'd like to read Wikipedia:Village pump (miscellaneous)/Archive 57#Change to the edit submission button label, since I mentioned one of the pages you'd worked on as an example. Whatamidoing (WMF) (talk) 04:30, 28 November 2017 (UTC)

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About glycolysis and your suggestions

Dear Thomas Shafeer, My name is Carlos Bonafe, and e-mail is cfsbonafe@gmail.com. Thank you for your attention and suggestions. I modified the figure with the division which you suggested, with a frame (I am not sure if the frame is too much). Concerning the format ".svg", I made a conversion using a program online, but the figure become not suitable to be used. I create the files in png using the Python program, I will verify if it is possible to save in svg format without loss of quality. I am not used to use the tools of Wikipedia, so I am not sure if this is the right place to reply your comments, if not please forgive me. I have added figures in several topics in biochemistry (in Wikipedia) besides glycolysis: urea cycle, citric acid cycle, pentose phosphate pathway, glyoxylate cycle, ketogenesis and ketona bodies. if you have suggestions please let me know. Best. — Preceding unsigned comment added by Patchgood (talk • contribs) 04:25, 10 December 2017 (UTC)