Wikipedia talk:WikiProject Molecular Biology/Molecular and Cell Biology

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Thanks. — Headbomb {^ταλκ_{κοντριβς} – WP Physics} 09:22, 15 March, 2009 (UTC)

Add to watch list !!

I have made a new article on genetics... could i get all to add the article to your watch list! Indigenous Amerindian genetics we need to watch for vandalism..new with no watchers .. Tks guys!!!!!

Bacteriostatic agents

Hello! We currently have two articles, Bacteriostat and Bacteriostatic agent, both apparently about the same subject, and neither of which have any supporting cites. I'd greatly appreciate it if someone knowledgeable could take a look at these, for fact-checking and possible merging. -- The Anome (talk) 16:35, 3 August 2011 (UTC)

PyMOL needs to be updated

Dear MCB Project. It looks as though the PyMOL article still reflects a pre-Schrödinger version of said software. Does anyone here have the necessary familiarity with the Schrödinger version of PyMOL to update this article? It seems like there should be a way to do this while still preserving references to its open source development and the impact Warren DeLano had on the field. I(q) = User(q)·Talk(q) 01:40, 30 August 2011 (UTC)

Is there a better place for such a request? I(q) = User(q)·Talk(q) 16:21, 4 September 2011 (UTC)

Hi. This is probably as good a place as any. I have used both pre- and post-Schrödinger versions of PyMOL and they are qualitatively the same. The program has undergone continuous improvements (see for example list of new features). In addition, there are two parallel forks. The open source version that requires compiling and the paid version for which ready to run binaries and more complete documentation are supplied. Finally not surprisingly there is tighter integration between PyMOL and Maestro, the Schrödindger GUI for MacroModel and other Schrödinger software. Looking over the current version of the PyMOL, I don't see it as seriously out-of-date, but perhaps more detail could be added about the difference between the commercial and open source versions. Boghog (talk) 16:37, 4 September 2011 (UTC)

Ah, thanks. As I said I'm simply not familiar with the newer builds, thus am not really qualified to update the article myself. It's good to hear they haven't scrapped the basic functionality, and that an open source fork still exists. I(q) = User(q)·Talk(q) 18:05, 4 September 2011 (UTC)

PLoS Comp Biol Contributions

We would like to solicit your feedback on a proposal from PLoS Computational Biology (PCB). The journal proposes to help establish new Wikipedia pages in the field of computational biology that are not currently covered, either at all, or exist only as a stub. The pages would be created in the Wikipedia sandbox. When complete they would be reviewed by a newly appointed PCB Topic (aka Wiki) Pages Editor and folks s/he solicits, and if suitable the authors would be given the opportunity to publish it as a PCB Topic Page which would appear as part of the Education section of the journal. The page would be available from PLoS under a Creative Commons Attribution License. The PCB page would be indexed in PubMed and would provide a service to journal readers. As such it provides author incentive. PCB would only publish the Topic Page when it has been released into the public Wikipedia and the PCB page would become the copy of record. The community would make further enhancements to the Wikipedia page on an on-going basis as per usual.

The upside is that authors would be inclined to provide an initial starting point of high quality material as they get a PLoS publication and are indexed in PubMed. Wikipedia gains good content.

The downside is that if this became popular (more than 2-3 per month) PLoS would need to charge to recover publishing costs, but this would not be the case initially.

Phil Bourne EIC PLoS Computational Biology — Preceding unsigned comment added by Pebourne (talk • contribs) 14:30, 7 September 2011 (UTC)

This certainly sounds like a win-win proposal benefiting both PCB and Wikipedia. We first need to make sure that the Creative Commons Attribution License used by PLoS is compatible with WP:COMPLIC. From my reading of the two licenses, it appears they are compatible, but we should get the opinion of someone who is more knowledgable. The only other potential complication I can see is that the audiences and therefore writing styles differ some what between scholarly journals and Wikipedia. Hence it may take additional work to produce an article that would be suitable for both publishing in PLoS and in Wikipedia. It would therefore be helpful to solicit input from experienced Wikipedia editors (for example by submitting a WP:PR request before the article is moved from the sandbox to Wikipedia main space) to make sure that the articles that are produced conform to generally accepted Wikipedia standards (especially with regards to WP:TECHNICAL). Boghog (talk) 16:47, 7 September 2011 (UTC)

Seems the Licenses are compatible. PCB is using CC BY 2.5 which is listed as compatible at WP:COMPLIC. --Andreas (talk) 16:55, 7 September 2011 (UTC)

Sounds like an interesting proposal. I'd be happy to help and answer questions from those contributing to this project who may be new to wikipedia. Also, you may wish to contact WikiProject Computational Biology Jebus989^✰ 17:14, 7 September 2011 (UTC)

Opps, sorry for not suggesting this earlier. Of course WP:COMPBIO sound be contacted since that is the project that most closely overlaps with this proposal. I therefore propose that we move this discussion over to the COMPBIO talk page. Thanks for the suggestion Jebus989. Boghog (talk) 18:02, 7 September 2011 (UTC)

This looks like a good opportunity, both for Wikipedia and for the potential authors. I would be happy to help review articles if this program becomes a reality. Antony–22 (^talk⁄_contribs) 06:07, 8 September 2011 (UTC)

This is an exciting idea. What sort of granularity are you thinking? Will they be strictly computational biology related or would general biology articles qualify? It might be worth looking at a few MCB featured/good articles to see if any would fit your idea of an adequate PCB article. --Paul (talk) 10:47, 8 September 2011 (UTC)

I echo every one else's enthusiasm. (Struck by how coincidentally similar the set up is to the Gene Wiki partnership I mention in the next section.) If the articles will start on Wikipedia where anyone can contribute and edit, then I imagine authorship for the PCB article may be a sticky issue to deconvolute. You could use a system like WikiTrust to assign rough authorship percentages based on text contributed, but it would be pretty approximate (and it is possible to game the system). Did you have any thoughts on how to handle that? Cheers, AndrewGNF (talk) 22:41, 9 September 2011 (UTC)

Thank you for the positive feedback on the proposal, we are planning on proceeding based on this. As a point of clarification. The original authors of the Wikipedia page, which is developed in the sandbox, would be the authors of the PLoS CB Topic Page. The living version in Wikipedia would gain authors in the usual way, but they would not be authors of the copy of record in the journal. However, given the comments feature supported by al PLoS journals, Wikipedia page authors, or others, can add commentary to the journal copy of record should they wish too. At this point we are open to suggestions for computational biology topics and possible authors to be approached to begin the work. --Pebourne (talk) 15:39, 10 September 2011 (UTC)

I echo the broad support for this proposal, though User:U+003F is right in pointing out that drafting the text here under CC-BY-SA would result in it not being publishable under CC-BY. As for assigning and crediting authorship, these issues are discussed in doi:10.3897/zookeys.90.1369. -- Daniel Mietchen - WiR/OS (talk) 23:49, 20 September 2011 (UTC)

Gene Wiki partnership with the journal Gene

Recently I've had some discussions with the editors at the journal Gene about how to encourage academics to improve Wikipedia articles on human genes. I started a discussion at the Village Pump. Please chime in there if you have any thoughts. Cheers, AndrewGNF (talk) 22:34, 9 September 2011 (UTC)

I commend your efforts here and hope that this occurs in many forums. In my view the not-so-hidden agenda of all these efforts is to further break down the barrier between the perceived value of pre vs post publication review and to highlight the value of living documents. In my area if, in the next few years, folks turn to Wikipedia for all their background reading in computational biology as opposed to expensive and inaccessible textbooks I will be very happy. --Pebourne (talk) 15:53, 10 September 2011 (UTC)

Proposed deletion of Capping enzyme complex

The article Capping enzyme complex has been proposed for deletion. The proposed-deletion notice added to the article should explain why.

While all contributions to Wikipedia are appreciated, content or articles may be deleted for any of several reasons.

You may prevent the proposed deletion by removing the {{proposed deletion/dated}} notice, but please explain why in your edit summary or on the article's talk page.

Please consider improving the article to address the issues raised. Removing {{proposed deletion/dated}} will stop the proposed deletion process, but other deletion processes exist. In particular, the speedy deletion process can result in deletion without discussion, and articles for deletion allows discussion to reach consensus for deletion. Sławomir Biały (talk) 20:20, 10 September 2011 (UTC)

Stub/article/redirect needed

Could someone please turn alanine scan into a bluelink? It seems like a pretty important technique and easily understandable (at least in understanding its results, even if not the process of doing it) to the lay public. DMacks (talk) 14:02, 20 September 2011 (UTC)

Agreed - There is an article at Alanine scanning, but it's currently a two paragraph long stub so it could stand to be expanded. (+)H₃N-Protein\Chemist-CO₂(-) 17:00, 20 September 2011 (UTC)

Thanks for finding that! DMacks (talk) 17:40, 21 September 2011 (UTC)

Metabolism

Has there been any past discussion of creating a set of pages for the biosynthesis of each amino acid and cofactor? Each amino acid has a small section, but they vary enormously in style. methionine, for example, has one of the more detailed section, but it is really hard to read and describes how E. coli does it (only enterobacteria and yeast trans-sulfurylate, use succinyl and not acetyl and few organisms need/make cobaltamine (B12 for humans)). I would be willing to spend some time on this matter, but I think a universal layout style should be present to make it navigation-friendly. Maybe it could even have a template similar to {{cladogram}} for a metabolic map. Ecocyc/metacyc has a lot of info and would make work easier, so it is not an overly hard task: the problem would be consistency. --Squidonius (talk) 07:04, 21 September 2011 (UTC)

I not aware of any previous discussion about creating amino acid biosynthesis articles. It might be better to start working on the biosynthesis sections of the existing amino acid articles and then consider splitting out if these sections become very long. A possible alternative to cladogram templates is to incorporate WikiPathways stye templates (see Citric_acid_cycle#Interactive_pathway_map as example). The WikiPathways web site already contains a pathway for methionine biosynthesis (see "Find Methionine pathways". WikiPathways. {{cite web}}: Cite has empty unknown parameter: |coauthors= (help)). However sticking to the old-fashion schematics (see File:Tryptophan biosynthesis.png for example) still might be the best solution. Boghog (talk) 20:47, 21 September 2011 (UTC)

There is also this:

The Wikibook Principles of Biochemistry has a page on the topic of: Synthesis of aminoacids

Boghog (talk) 09:48, 25 September 2011 (UTC)