Wikipedia:WikiProject Molecular and Cellular Biology/Announcements

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Contents

[edit] Open tasks list

Please help to keep the Biology portal's Open tasks list up to date. This is one of our main communication methods to help get newcomers more involved in editing articles. It contains a list of articles that need improving, articles that need creating, articles that need cleanup, etc. And of course, if you have the time, please help and work on some of the tasks on that list! --Cyde Weys 05:20, 24 February 2006 (UTC)

[edit] {{Wikiproject MCB}}

I found an article with this header in the article namespace: please make sure to put it on talk pages only.--Steven Fruitsmaak (Talk) 14:23, 27 August 2006 (UTC)

[edit] Molecules of the Month

Hi! I'm a contributor of Italian Wikipedia's Progetto Bio, the ortholog of your WikiProject Molecular and Cellular Biology... I have just finished uploading to Commons a great number of images from the Molecule of the Month section of www.PDB.org, since they are released in PD... This message is just to inform you that they can be used for a lot of en.wiki articles that still don't have an image... Hope this will help! Bye! --Gia.cossa 16:29, 23 September 2006 (UTC)

Thank you!!! -- Boris 17:15, 23 September 2006 (UTC)

[edit] Worklist

I just reorganized our article worklist. Feel free to move some things around if you think I've made any errors, which I probably did. Cheers! – ClockworkSoul 18:48, 15 November 2006 (UTC)

[edit] PyMol tutorial draft done

After over a month of procrastinating, I finally got around to fleshing out the PyMol tutorial we talked about oh-so-long-ago. Any comments, suggestions, or additions would be appreciated; I tried to keep it to the stuff you'd need in routine image production, but I'm sure there's something I've left out. Opabinia regalis 06:24, 24 January 2007 (UTC)

excellent !!! -- Boris 12:28, 24 January 2007 (UTC)
Great work! I've added links to the main page and our advice page (which I and everyone else seem to have forgotten existed!). I don't have spare time right now to test your tutorial out (I'm still a protein-image-creation-virgin) so can't offer much (constructive) criticism at this moment. Do we have a list of protein image requests anywhere? It might be an idea, assuming that we do have such a list, to link the tutorial to the list so people can learn and do some productive work at the same time. Do you think that screenshots might add something to the tutorial? --Seans Potato Business 20:06, 25 January 2007 (UTC)
The Requested pictures page? Added a link, though maybe someone wants to do something similar for pathway diagrams?
I thought about screenshots and a complete example or something, but I wasn't sure how useful it would really be to make it even longer. What do you think? Opabinia regalis 06:05, 26 January 2007 (UTC)
I don't think it would be very useful at all to add pictures; I just thought it would look nice and break up the text. I tried out your tutorial and created my first, very basic image, now at KRAB. I'm suprised at just how easy it was with that tutorial.
Useful additions might include: a) making the 'Display > Background' etc instructions stand out against the rest of the text (usally it's okay if they contain one word but things like 'Select all' need a re-read to understand that 'all' belongs to 'Select'. I think bold would be too severe for this purpose; maybe underlined or bold-but-grey-coloured text would be suitable. b) A cheatsheet of the most common things, or even a basic and an advanced (that's two) cheatsheet would be handy. I will go and check what resources are even available on the Pymol website.
Thanks again for all the effort, Opabinia! --Seans Potato Business 04:41, 29 January 2007 (UTC)
Glad you found it useful! (Also fixed your link to the page I bet you meant, very nice! :) How's italics for the menu options? Now that I think about it, that's what I see and use in software docs. For a cheatsheet, how much more abbreviation do you think would still be useful? It's hard to know at what point you've provided so little context that the document is no longer useful to anybody who doesn't already know how to use it. Opabinia regalis 01:23, 31 January 2007 (UTC)
Italics works great. As for the cheatsheet, I thought that it would be used by people that had already gone though the tutorial and just needed to be reminded how to execute a feature or function, so very little context would be necessary. I've gone through the tutorial and used it to produce a single protein structure but havn't used it now in three weeks. I'd probably need reminding re: what to do if I needed to do use Pymol again. --Seans Potato Business 20:37, 11 February 2007 (UTC)
OK, added to my mental to-do list ;) Opabinia regalis 06:07, 14 February 2007 (UTC)

[edit] RNA interference peer review

FYI, our December collaboration, RNA interference, is up for peer review here if you have any thoughts. Thanks! Opabinia regalis 02:20, 7 February 2007 (UTC)

[edit] Proteins wiki opened; suggestions welcome!

Hello,

Your colleague Opabinia regalis suggested that I post a message here introducing myself and a new wiki. Through my students, I've recently become aware of your efforts to produce well-referenced summaries of various topics in biochemistry and cellular biology. Based on the Featured Articles that I've seen so far, your work is impressive and your efforts to be commended. I'm intrigued by the possibilities of using wiki's for scientific collaboration and for teaching materials, although I wonder whether the vandalism might not undermine your long-term efforts. The enduring quality of your Wikipedia articles would seem to depend on the ongoing personal attention of its principal authors, is that correct? Perhaps if a large enough community of attentive editors were nucleated, the burden of upkeep might not fall on a few people's shoulders.

I now have a pressing reason for learning more about wiki's. We've recently been awarded a grant from the NSF to functionally annotate the chloroplast-targeted genes of Arabidopsis thaliana, roughly 4500 proteins in all, using a combination of experimental and computational means. We're growing up thousands of individual knockout plants and assaying them using various methods, while at the same time, trying to predict their domain structure, carry out multiple sequence alignments and structure predictions. Naturally, it's a lot of work to interpret the data and formulate functional hypotheses. So, as an experiment, I've begun setting up a Proteins wiki at this page to facilitate the distribution of our results and to foster collaboration in developing functional hypotheses. Contributors would of course be credited on any publications to result from their work. However, the aim of the Proteins wiki is to foster education and discussion on any sort of protein, not only those of A. thaliana. The initial development will be slow, however, since I and my students need to familiarize ourselves with the software and wiki's in general. I'm also teaching senior-level biochemistry this semester and working on a major grant, so my students may shoulder most of that burden; if you could help them as needed, I would very much appreciate it.

The nascent Proteins wiki is not meant to supplant Wikipedia's own coverage, but to be complementary to it, since it may accept as-yet-unpublished data. I hope that the new wiki and the MCB WikiProject will benefit from one another; for our part, we will work to earn your respect and trust. We are presently learning how to upload thousands of pages in an automated way, and will put our 200 Gflop supercomputer to work producing data that may be useful for Wikipedia as well as our own wiki. Suggestions are welcome! In earnest of a friendly working relationship, I've put your DNA clamp image as the logo for the Proteins wiki.

For my teaching, I've also developed several hundred public-domain LON-CAPA problems quizzing various features of biochemistry. I've placed a few on my user page, but I discover now that they are not easily accessed from without. Once they are made more available, you are welcome to use them, and I would appreciate any suggestions for their improvement. Thank you for your efforts in producing such excellent articles and for future help and suggestions, Proteins 22:13, 9 February 2007 (UTC)

Thanks for posting this announcement. To give an initial response to your question about article maintenance - while vandalism is an inevitable result of open editing, and is inevitably annoying, Wikipedia does a very good job dealing with 'article graffiti'. Sneaky content changes generally persist a little longer, but one of the benefits of an organized wikiproject is that articles under our purview get on the watchlists of more knowledgeable people who can tell the difference between legitimate corrections and the insertion of misinformation. It is generally true that featured articles must be maintained, if not by the original author(s), then by a similarly knowledgeable editor or group, to stave off degradation and keep the content up to date. FAs do tend to receive additional scrutiny by those who specialize in anti-vandalism activities, which helps keep their half-life above that of the average article even if unmaintained by a specific individual.
You mentioned your students' becoming familiar with wiki software and editing - are you intending to ask them to contribute to the proteins wiki (good idea) or to Wikipedia (also a good idea)? In either case, you might be interested in Wikipedia:School and university projects, which is a somewhat out-of-the-way page cataloging and organizing educational projects on Wikipedia, and might also give some useful advice for other wiki-based projects. Opabinia regalis 03:37, 10 February 2007 (UTC)

I intend for them to contribute to both, although I'm not sure what would be most useful for you all here; some guidance from you would be appreciated. For example, a bot might be able to create a page here for every presumed protein in A. thaliana (or any other genome), but my impression was that you're collectively more interested in classes of proteins, rather than instances of proteins from any one organism. Wikipedia's requirement that every article have reliable published sources would also make it more difficult to generate useful pages in a fully automated way, unless we write some literature-mining software or exploit other such compilations, such as those at TAIR. Suggestions are welcome, however! Proteins 23:07, 13 February 2007 (UTC)

Someone else might have more experience with organized student projects, but what I've usually seen people do is get their students to each choose an article on a relevant subject and substantively improve it - I assume the resulting articles are then assessed for the class. We do usually do articles on protein classes or homologs, though that doesn't mean they couldn't be seeded with Arabidopsis content and later expanded with information from other organisms. Personally, I usually stick to classes because it's not often that there's enough encyclopedia-level information on the protein from a single organism to write a real article about it. I don't currently have any good ideas on automated text import, which can be a challenge due to licensing as well as policy issues. Opabinia regalis 06:15, 14 February 2007 (UTC)

[edit] Are online biochemistry questions appropriate as "External links"?

Hello, I uploaded some biochemistry problems written for my undergraduate students here. Conceivably, such questions might be a good "External link" feature for some MCB encyclopedia articles. Some readers of Wikipedia are undoubtedly students wishing to learn a topic, and such students might appreciate having a handy test of their comprehension on the same page. The problems are graded by computer and generated on the fly; new problems on the same topic can be produced by clicking on the "New Problem Variation" button at the top. Such questions might be more suitable for the Wikiversity, but there doesn't seem to be a significant biochemistry program there as yet.

Congratulations on getting DNA on the Main Page; that seems like quite a coup and reflects well on the WikiProject. Proteins 23:07, 13 February 2007 (UTC)

I personally don't think they're quite suitable for Wikipedia (c.f. Wikiversity) but other MCB users may have another opinion. Wikiversity is probably a long way off being of much use for our purposes. Wikipedia still needs so much attention. Incidentally, it would be useful if you could have several problems on one page, and after getting all the answers right or whatever, if you could go to the next page without having to click the back button on your web-browser and choose another question. --Seans Potato Business 01:26, 14 February 2007 (UTC)
Hi Proteins, and welcome to Wikipedia! :D Thank you for the DNA congratulations, but they're somewhat misdirected; we're a friendly, sharing Wikiproject but la gloire eternelle belongs properly to its main authors and defenders. ;)
Your biochemistry problems seem neatly posed, and I'm sure that they'd be excellent for students learning biochemistry. The "New Problem Variation" button is a nifty feature, too! :) However, I agree with Seans Potato Business that they don't seem right for Wikipedia; they're more textbook than encyclopedia, don't you think so? Perhaps you'd be willing to tackle making a Wikiversity course on basic biochemistry to give them a proper home? It's a lot to ask, but maybe it might be easier for you?
The other proposal — automatically creating thousands of relevant MCB pages — is likewise sorely tempting but, forgive me, makes me even more uneasy than the analogous Pfam proposal. I'm worried that our Wikiproject would be spread too thin. We have so much left to finish on our most basic articles, such as amino acid, protein, lipid and RNA, that it seems premature to start an article on At5g43210, even if you could automatically describe it with decent prose and literature references and links to relevant databases. Your offer is very kind, and I realize that the initial pages will require no extra work from us; but perhaps we should talk it over among ourselves? Please be patient with us; thanks! :) Willow 08:25, 14 February 2007 (UTC)

[edit] RNA interference

Our December collaboration, recently GA'd and recently expanded, is up for FAC here. Comments appreciated! Opabinia regalis 06:06, 14 February 2007 (UTC)

[edit] Antioxidant

Up for FA here. Comments, edits and suggestions are welcome. TimVickers 05:20, 28 February 2007 (UTC)

[edit] TfD nomination of Template:Titin

Template:Titin has been nominated for deletion. You are invited to comment on the discussion at the template's entry on the Templates for Deletion page. Thank you. Followup to this earlier thread, after the ongoing low-level edit war broke out again. Opabinia regalis 03:13, 5 March 2007 (UTC)

[edit] Stem cell controversy

Hi there has been some animated discussion over the name of this page, particularly as the main focus of the page is embryonic stem cell controversy, rather than a general controversy over both embryonic and adult stem cells.

It has been proposed to be changed to something like stem cell ethical controversy or embryonic stem cell controversy.

I'm pretty ambivalent about a change, but I certainly think that a few more people should comment before such a bold move. I invite MCB members with stem cell interests to check out Talk:Stem cell controversy. Cheers Dr Aaron 13:37, 5 March 2007 (UTC)

[edit] Metabolism

One of our core topics, the article has been completely re-written, peer-reviewed and now nominated as a FAC here. Comments and suggestion would be very welcome. TimVickers 19:20, 25 March 2007 (UTC)

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