Wikipedia talk:WikiProject Computational Biology

Things that need doing

I've been thinking of a few things that need to be one. Please add to the list and note if you are working on any of them to avoid clashes. Alexbateman (talk) 08:22, 9 June 2011 (UTC)

• Find articles that need WikiProject banner adding

To get an automated list of candidates, try this link. 1037 pages at the time of writing, but many false positives. --Magnus Manske (talk) 18:03, 12 June 2011 (UTC)

• Assess articles with existing banner
• Create table showing assesments of computational biology articles like the one at MCB: [1]

Done. The table is automatically updated every few days, or you can go here to update immediately U+003F^? 18:34, 9 June 2011 (UTC)

• Rebrand WikiProject home page. Its been suggested that WikiProject Computing is a good template for this. [2]
• Archive old discussions which are cluttering this page

Autoarchiving set up, currently at 180 days but this can be decreased if activity picks up Jebus989^✰ 18:38, 9 June 2011 (UTC)

Do you know why the earliest threads are still there? U+003F^? 18:47, 9 June 2011 (UTC)

The bot runs once a day so it took a while to kick in, there is a problem though. I've manually archived the threads the bot removed but will try to fix archiving Jebus989^✰ 09:32, 10 June 2011 (UTC) Fixed now, parameters must be on new lines Jebus989^✰ 09:41, 10 June 2011 (UTC)

• Find willing editors to help out with tasks for the WikiProject

I just saw an invitation template and copied it for our WikiProject. Please take a look and fix any bugs you notice. Please do add this to the user talk page of people who you think might be interested to join us! Alexbateman (talk) 15:35, 18 June 2011 (UTC)

Please accept this invite to join the Computational Biology WikiProject, an attempt to build a comprehensive and detailed guide to computational biology. Simply click here and add your username to the list to accept! Alexbateman (talk) 15:35, 18 June 2011 (UTC)

To add this yourself use this code {{WikiProject Computational Biology invite|Signature=~~~~}}

• Threw together a Userbox and updated the templates box. Feel free to fix or toss as you please. Code is: {{User WikiProject CompBio}} Estevezj (talk) 01:13, 13 December 2011 (UTC)

This user is a member of WikiProject Computational Biology.

PLoS Computational Biology to Contribute Wikipedia pages?

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) 19:50, 7 September 2011 (UTC)

I think it is important to find ways to give incentives for domain area experts to contribute to Wikipedia and I would welcome such an initiative. I would be happy to provide reviews of such contributions to Wikipedia if it would help. Alexbateman (talk) 15:30, 8 September 2011 (UTC)

Excellent proposal. I have long thought that very much like this is how we should get experts involved in "original research" writing that doesn't create problems with our policies. In the unlikely event that something goes terribly wrong with an article (there were some infamous problems at Citizendium), we can still treat it the same way as any other article and don't have to treat it as privileged in any way. Hans Adler 15:38, 8 September 2011 (UTC)

Excellent initiative ! and it could be an interesting example for the other journals (not necessarily about Bioinformatics)--Plindenbaum (talk) 18:51, 8 September 2011 (UTC)

I fully support this proposal, as it seems to be of benefit to all parties. However, rather than your idea of writing a page in a sandbox, why not write the page directly and utilise the existing mechanisms for peer review and good article nominations? These processes could be sped up through contacting potential referees directly or through this project, and would result in an article considered "good" in both your and Wikipedia's interpretation of the word. On a boring-but-important note, any text released to Wikipedia must have both CC-BY-SA and GDFL licensing. U+003F^? 09:00, 11 September 2011 (UTC)

Update: The project (see Signpost coverage for overview) has now progressed such that the first article to be posted has passed peer review and is in production at PLoS Comp Biol. One of the issues that remain to be addressed (apart from format conversions) is that of how to post the articles and associated image and media files. While we intend to automate the process eventually (help with that is welcome), we will initially have to start out posting manually. In order to facilitate tracking of PLoS Comp Biol contributions, it would make sense to use an account like User:PLoS Computational Biology (which we reserved) but this runs afoul of WP:ORGNAME as it stands. On the other hand, some PLoS Comp Biol authors do have an account here that they could use for this purpose (or would this fall under WP:COI?), others don't, and in any case, such an approach would make it rather cumbersome to track - other than by way of categories - contributions made through PLoS Comp Biol. As another alternative, an individual user here could post the materials on behalf of the journal. I am ready to do that but would like to invite some community feedback before getting started. -- Daniel Mietchen - WiR/OS (talk) 16:11, 17 January 2012 (UTC)

For copyright reasons, anything added to Wikipedia ought to trace back to a single person. A role account such as User:PLoS Computational Biology would not resolve to a specific person. If that account were to add material for which it was not the author, it would then need to supply confirmation via WP:OTRS that it was authorized by the copyright owner. Some of these problems might be overcome, so a discussion would be good. In principle it's a great idea for PLoS Computational Biology be helping to create useful articles for Wikipedia. In the short run, it's more persuasive if creators of such articles have their own Wikipedia accounts and prepare themselves to deal with the back-and-forth of Wikipedia feedback. Expecting the off-line review by the journal editors to cover all of the requirements is probably too optimistic. Making a category for articles that were contributed (or enhanced) by collaboration with PLoS Computational Biology should be fine, in my opinion. EdJohnston (talk) 18:20, 17 January 2012 (UTC)

I look forward to seeing the first article! I agree this should be an individual posting the article. I don't see any problem with that person being a PLOS CB employee though. I guess it would be preferable that the content was posted by one of the authors into Wikipedia. I like the idea of the content being placed into the users sandbox to undergo any reviewing and then the user can move the content across with publication. Alexbateman (talk) 15:56, 19 January 2012 (UTC)

I agree with the sandbox idea. When you do something new on this rather old and encrusted wiki you always risk furious responses by some. I would be shocked if anyone posting a high-quality peer-reviewed scientific article specifically prepared for Wikipedia in this way would not be accused by someone of spamming for the journal or some similar crime. We must plan it advance how to deal with such overreactions. It's also quite possible that the first article(s) will not quite fit into what we need here and need a bit of work. By doing this work outside article space we are probably going to avoid a lot of pressure. Hans Adler 17:53, 19 January 2012 (UTC)

On the other hand, perhaps the new material will fit perfectly. Any chance of a preview of the piece, so we can comment more concretely? U+003F^? 18:15, 19 January 2012 (UTC)

A preview woud be really useful to get an idea of the overreaction potential :) If the current article is just a stub or non-existant I think there will be fewer problems. If its got more content more diplomacy may be required. Alexbateman (talk) 21:32, 19 January 2012 (UTC)

We have been editing the article at this external mediawiki instance, so we can dual license the text. This is an extension of an article that is currently a stub and which was mainly drafted by myself. --Andreas (talk) 06:44, 20 January 2012 (UTC)

Looks great to me, I don't see any problem in its immediate uploading by you. A few minor changes are needed; the authors and acknowledgements sections should be removed, the wp: tags are not required on here, you'll have to use {{cite PMID}} rather than <pubmed>, and those refs should come after the full stops. I've knocked up a {{PLoS Computational Biology}} template; adding {{PLoS Computational Biology |source=http://pisaster.ucsd.edu/wiki/index.php/Circular_permutation_in_proteins}} to the bottom of your article will display

 This article incorporates text from PLoS Computational Biology that is licensed under the Creative Commons Attribution 2.5 License.

and also add Category:PLoS Computational Biology articles. Please edit this for the correct license. Perhaps you might consider adding the figures to Wikimedia Commons too. Cheers! U+003F^? 13:16, 20 January 2012 (UTC)

The talk page contains a list of changes which will be made for transition to wikipedia. Thanks for providing the attribution template! -Spencer Bliven (talk) 20:16, 20 January 2012 (UTC)

The template now uses doi as a parameter pointing back to the source:

{{PLoS Computational Biology|doi=10.1371/journal.pcbi.0010004}}

thus gives

 This article incorporates text from PLoS Computational Biology that is licensed under the Creative Commons Attribution 2.5 License..

-- Daniel Mietchen - WiR/OS (talk) 23:56, 29 January 2012 (UTC)

[announcement] The data for Template:Infobox_biodatabase have been released in DBPedia 3.7.

The data from Template:Infobox_biodatabase have now been integrated into DBPedia 3.7. See:

• http://en.wikipedia.org/wiki/Wikipedia:WikiProject_Molecular_and_Cellular_Biology/Announcements#Infobox_biodatabase (for reference)
• http://dbpedia.org/page/Template:Infobox_biodatabase
• http://dbpedia.org/ontology/BiologicalDatabase
• http://dbpedia.org/page/L1Base

those data can now be searched through a SPARQL query --Plindenbaum (talk) 09:55, 11 September 2011 (UTC)

Folding@home importance

Hi. I would like to know what importance Folding@home sits on the Importance Scale for this WikiProject. I believe it's either going to be high, or mid. I would argue that it is high because Folding@home is an extremely powerful distributed computing system that performs protein folding and protein structure prediction, which have obvious impacts into understanding cellular communication, disease research, and how molecules work in general. In a well-cited statement, it says that Folding@home has caused "paradigm shifts in protein folding theory". While providing thorough sampling of the aspects of protein folding, its simulations remains accurate experimentally comparable, which is considered a "holy grail" of computational biology. At the same time, it could be argued that Folding@home is of mid importance, because it only concerns itself with proteins and to a lesser degree other molecules such as the ribosome and protein aggregation, but does not simulate other aspects of computational biology. It's currently marked as mid importance, and I wanted to make sure that was correct. Thoughts? Jessemv (talk) 16:49, 4 November 2011 (UTC)

Hi, I added it as mid importance I think. That seemed about right to me. Its certainly above low importance. It has gained a lot of press and shown that the distributed model can work well. But I'm not sure that among computational biologists it is widely used in the way that BLAST or ClustalW are used. Alexbateman (talk) 14:40, 12 December 2011 (UTC)

Thanks so much. Yes, it does a very specific job, so in that sense it's limited. Glad to know the rating is correct. Jessemv (talk) 15:45, 12 December 2011 (UTC)

Difference between subdisciplines

Does anyone have any reputable sources that attempt to define the differences between the various disciplines represented here? The overlap between computational/mathematical/systems/theoretical -biology and bio- informatics/statistics is high, but their differences are not clear. Their individual articles would, I think, benefit from setting this out. The NIH defines the difference between computational biology and bioinformatics, but the other fields are not mentioned. Cheers! U+003F^? 12:51, 30 December 2011 (UTC)

I think mostly the differences are operational rather than theoretical. It just so happens that a group involved in topic x happens to describe them self as working in the domain of y... Perhaps a survey of topics / domains would help? --Dan Bolser (talk) 13:52, 12 February 2012 (UTC)

Article request: sequence feature

Perhaps I'm missing this article under a different name, but a redirect would be nice. AFAICT, there isn't any info on 'sequence features'. Its tricky, because of course its a rather abstract topic. In biology, there is no such thing as a 'sequence feature', it only exists as an abstract (and very useful) convention in computational biology. To further complicate issues, the topic is mostly practical, heavily dependent on various 'sequence feature formats', that further increases the abstract nature of the topic (you can describe anything you like within the scope of the format). Anyway, something would be nice! Cheers, --Dan Bolser (talk) 13:50, 12 February 2012 (UTC)

Some links:

• http://www.google.com/search?q=sequence+feature
• http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
• http://www.uniprot.org/manual/sequence_annotation
• ... — Preceding unsigned comment added by Dan Bolser (talk • contribs) 13:56, 12 February 2012 (UTC)

Wikipedia:WikiProject Unique Identifiers

So, there's a new project which may be of interest to some here. It arises out of Wikipedia:Village_pump_(proposals)#UID_interface_to_Wikipedia, a proposal to make wikipedia articles available by their UID - for instance by their UNIPROT number. Umm. For reasons which should be all to obvious to anyone interested in computational biology. And those two pages are all I have to show you, but I live in hope of input from you to take it all further. --Tagishsimon (talk) 20:49, 14 February 2012 (UTC)

Bit of help with diseases and Folding@home

Hey everyone, I've been heavily editing Folding@home in an effort to get it up to Good Article status. I'm feeling fairly done with the latter half of the article, but I'm having a bit of difficulty in describing the various diseases studied. This is basically the stuff under the "Biomedical research" section. Thing is, I'm learning the molecular processes essentially from scratch, which makes things time consuming since I have to read scientific publications several times before I can understand it enough to cite it. So I'm asking, can someone check my work in that section and let me know if I've incorrectly described the formation of a disease, or if I could say things better? It'll be much easier to tie in F@h's research if I know how the disease develops in the first place, but I'm not a biochem major and I know there are experts here. Any assistance would be appreciated. I'll be watching this page of course. Best, Jesse V. (talk) 06:56, 7 March 2012 (UTC)

I've taken care of several of the diseases, and I'm trying to figure out the rest. There's a checklist on the Talk page. Advice/comments on them and the rest of the article would be greatly appreciated, now more than ever. I feel that GA nominations are very close! Please let me know what you think or if there's issues that need to be addressed. Jesse V. (talk) 19:22, 17 March 2012 (UTC)

Method for assigning article class and importance

When adding the project banner to new pages, what's the procedure for choosing class and importance? Should I just use my judgment according to the quality scale and importance scale? Or should the assessment take user ratings into account? --Quantum7 01:30, 11 March 2012 (UTC)

I'd say to use your own judgement. If you have any questions or would like followup, please post here. Jesse V. (talk) 01:41, 11 March 2012 (UTC)