Wikipedia talk:WikiProject Molecular Biology/Computational Biology/Archive 2

Archive 1 Archive 2

Tools section on main project page

Hi all, all the links to tools on the Tools subsection of the main page are broken because the site's moved.

"You may find the tool you are looking for, or another similar tool, by consulting the Tool Lab's index of tools."

"The Wikimedia Toolserver was a collaborative platform providing Unix hosting for various software tools written and used by Wikimedia editors and operated by Wikimedia Deutschland e.V. It has been replaced by the Wikimedia Labs, with the services that used to be provided by the Toolserver available through the Tool Labs project."

The links were:

all from

None of the links work, and I can't figure out where they are (if they are at all) on the Wikimedia Labs tool labs page (or on the the index of tools redirected to from the previous link, but the error message suggest they won't be there anyway).

Can anyone help? Also I'm sorry if this Talk page is supposed to be for 'meta' discussion on the project, but I couldn't see where else to write this. Thanks -- Louismaddox (talk) 23:06, 12 March 2015 (UTC)Reply[reply]

Thanks, I've updated the links - I think these should work now. Tools have been patchy for a while so not sure how long these new ones will last,though. --Amkilpatrick (talk) 01:33, 13 March 2015 (UTC)Reply[reply]
Thanks for that. Ah, yes, currently showing "Database connection is down, expect some tools to be limited or non-functioning". --Louismaddox (talk) 11:37, 13 March 2015 (UTC)Reply[reply]

Peer review for DNA Sequencing article

Hi all, I've requested a peer review for the DNA sequencing article: the review page is here. It's consistently one of the most viewed pages in WP:COMPBIO so it would be good to get this up to GA class eventually (it's currently at C class). It looks as if a request had been made for peer review in 2012 within the MCB WikiProject, but nothing happened. Any comments welcome. Thanks, Amkilpatrick (talk) 19:51, 14 April 2015 (UTC)Reply[reply]

Hackathon at EBI on September 4

See Wikipedia:WikiProject Computational Biology/EBI hackathon on September 4, 2015 for details. -- Daniel Mietchen (talk) 17:08, 8 June 2015 (UTC)Reply[reply]

Copyright Violation Detection - EranBot Project

A new copy-paste detection bot is now in general use on English Wikipedia. Come check it out at the EranBot reporting page. This bot utilizes the Turnitin software (ithenticate), unlike User:CorenSearchBot that relies on a web search API from Yahoo. It checks individual edits rather than just new articles. Please take 15 seconds to visit the EranBot reporting page and check a few of the flagged concerns. Comments welcome regarding potential improvements. These possible copyright violations can be searched by WikiProject categories. Use "control-f" to jump to your area of interest (if such a copyvio is present).--Lucas559 (talk) 16:58, 2 July 2015 (UTC)Reply[reply]

Stub contest

The Stub Contest is running again from 1-31 August 2015: the entry page is at Wikipedia:Stub Contest/Entries. WP:CompBio currently has 419 stubs, so this would be a great chance to expand some of them :) --Amkilpatrick (talk) 18:23, 6 July 2015 (UTC)Reply[reply]

New PLOS CB Topic Page Hypercycle

A rewrite for Hypercycle (chemistry) is now entering review for publication in PLOS Computational Biology as part of the Topic Pages collection. Comments and suggestions most welcome. -- Daniel Mietchen (talk) 21:18, 24 August 2015 (UTC)Reply[reply]

Ambush Gene Hypothesis

Coding sequences lack stop codons and they are often termed as "off-frame" stops. It was not clear until 2004 that the hidden stops could be used for selection hypothesis. Seligmann and Pollock devise ambush hypothesis to coherently describe how hidden stops contribute to the synonymous position state. Thus they might compensate for saving energies, reducing efficiency of the genomic and biosynthetic machinery. It is not clear whether or not experimental data is collated with this hypothesis, [1].

  1. ^

Prash (talk) 05:06, 8 January 2016 (UTC)Reply[reply]

For those interested in phylogenetics, and clade presentations

Could you have a look at this effort, here, to use clade diagrams to summarize pharma business acquisitions. My take at present is that the images created are devoid of standard quantitative meaning—nothing is captured by vertical and horizontal line lengths, as far as I can tell—and so they are a misapplication of this maths/graphic presentation method. Moreover, I argue that they are misleading (presenting a time axis, but not making spacing of events proportionate to the historical time differences), much harder to maintain (consider adding entries to a std Table versus this graphic), more likely to diminish article quality (in their ambiguity of content, again, over a std Table with clear headings), and therefore practically amenable to decay as a result. I would add to this, in this esteemed compu-bio context, that they would make those who trained us, and other purists in methodology and meaning (and Edward Tufte more generally), turn in their graves/beds. After having a look at the User page and at a couple of pages linked on that sandbox page, leave your opinion here, regarding the overall effort? Thanks for your opinion. Cheers. Le Prof Leprof 7272 (talk) 01:37, 23 March 2016 (UTC)Reply[reply]

Pinging Jytdog, who also seems to be part of the conversation. I looked at discussion on XyZAn's talk page and examples of their diagrams in use, such as at Bayer#Acquisition history. These diagrams are obviously useful visualizations of the history of corporate mergers and acquisitions. They show the essential information: which companies merged and in what order. That said, Leprof 7272 is correct: these are not cladograms and even thinking of them as metaphorical cladograms is a stretch. How to resolve this problem? I suggest retaining the diagrams, but calling them something less semantically laden. The diagrams are tree-like and hierarchical. Perhaps such a diagram could be called a merger and acquisition tree or a merger and acquisition hierarchy or more metaphorically, a corporate family tree? Something that expresses the intent of the visualization. Cheers, --Mark viking (talk) 02:53, 23 March 2016 (UTC)Reply[reply]
yes exactly. in my view the posting here is completely inappropriate and I'm sorry that le prof bugged you all. the question should be at WT:WikiProject Companies since it is about how to edit articles about companies, not how to edit articles about computational biology. But i do agree with what you say that Mark - le prof is caught up in the wrong things here. I have opened that discussion in the appropriate forum, here: Wikipedia_talk:WikiProject_Companies#Diagrams, for anyone who is interested Jytdog (talk) 02:56, 23 March 2016 (UTC)Reply[reply]
I agree that there's no particular problem with using cladograms/tree structures for representing hierarchical relationships (although note that the current templates cannot cope with companies that have merged, then subsequently split). For what it may be worth, for company mergers having time proceed left-to-right would be more intuitive for people not used to the conventions of phylogenetics. Left-to-right presentation would be appropriate for a company, where mergers are occurring (as opposed to speciation events splitting biological lineages). T.Shafee(Evo﹠Evo)talk 04:32, 23 March 2016 (UTC)Reply[reply]
Thanks for those thoughts. LeProf left this message in about five different places and it would be great if you were to comment at Wikipedia_talk:WikiProject_Companies#Diagrams. Thanks again. Jytdog (talk) 04:57, 23 March 2016 (UTC)Reply[reply]
No problem. T.Shafee(Evo﹠Evo)talk 05:26, 23 March 2016 (UTC)Reply[reply]
@Evolution and evolvability:@Mark viking:: Jytdog moved the question to a new forum, the one where it is least likely to be viewed with rigour. I reply there. I stand by the fact that these either not cladograms, or if they intend to be, they are inappropriately applied. "Which companies merged in what order," yes, but this does not encompass the square peg being forced, via this tool, into a round hole: as pointed out at the business discussion, this application of a graphic tool (they are not cladograms!) does not handle the complexity of information, failing to cover merger-split situations, and in no way accurately reflecting the chronologies—failing to cluster spates of chronologically clustered acquisitions closely, or to represent longer time intervals accurately). Bottom line, have at me all you want, but deal with the substantive matters that regard rigour, at the new venue, that Jytdog started. There—and this is said to all coming from computational biology, not just those pinged—I would appreciate if you state for the record, if you have any real knowledge on this matter (have ever actually done a molecular or other phylogenies to present a cladogram-type representation). Transparency, please. Le Prof Leprof 7272 (talk) 15:45, 23 April 2016 (UTC)Reply[reply]

Draft:Direct coupling analysis

Hi, just to make the project aware of a draft that may be of interest Draft:Direct coupling analysis. Cheers KylieTastic (talk) 17:28, 25 June 2016 (UTC)Reply[reply]

Reorganizing the pages around the ISCB competition

The pages related to the competition are currently not interlinked in a very consistent fashion, so I have set up Wikipedia:WikiProject Computational Biology/ISCB competition as a primary landing page for the contest, which should then link to the relevant subpages in an easily navigable and visually acceptable manner. Help with reorganizing this would be much appreciated. -- Daniel Mietchen (talk) 23:48, 25 June 2016 (UTC)Reply[reply]

Editathon at ISMB 2016

The International Society for Computational Biology (ISCB) is hosting a Wikipedia and Wikidata editathon at ISMB 2016, in Orlando, Florida, next Monday (11th July), 7-9pm. If you're attending ISMB, it would be great to see you there. More details on the ISMB website and at Wikipedia:WikiProject Computational Biology/ISMB 2016 Editathon. Thanks, Amkilpatrick (talk) 19:31, 5 July 2016 (UTC)Reply[reply]

Debrief is here, any comments welcome! Amkilpatrick (talk) 16:56, 16 July 2016 (UTC)Reply[reply]

Popular pages

Our list of most popular pages is down (and actually has been since the end of March!). The tool that creates this doesn't look like it'll be back, but there are some attempts to create a replacement, see   T141154 on Phabricator. Hopefully this will also track page views on mobile, which wasn't done before. --Amkilpatrick (talk) 15:45, 9 August 2016 (UTC)Reply[reply]

BioRxiv support in citations

This project's feedback would be appreciated in this discussion, as this could greatly (and positively) affect biological citations! Headbomb {talk / contribs / physics / books} 22:17, 7 September 2016 (UTC)Reply[reply]

Transcriptomics: new PLOS CB Topic Page

The draft of a new PLOS Computational Biology Topic Page on transcriptomics is now ready for review at -- Daniel Mietchen (talk) 15:38, 10 October 2016 (UTC)Reply[reply]

RFCs on citations templates and the flagging free-to-read sources


Headbomb {talk / contribs / physics / books} 16:58, 29 October 2016 (UTC)Reply[reply]

2016 Community Wishlist Survey Proposal to Revive Popular Pages

Greetings WikiProject Molecular Biology/Computational Biology/Archive 2 Members!

This is a one-time-only message to inform you about a technical proposal to revive your Popular Pages list in the 2016 Community Wishlist Survey that I think you may be interested in reviewing and perhaps even voting for:

If the above proposal gets in the Top 10 based on the votes, there is a high likelihood of this bot being restored so your project will again see monthly updates of popular pages.

Further, there are over 260 proposals in all to review and vote for, across many aspects of wikis.

Thank you for your consideration. Please note that voting for proposals continues through December 12, 2016.

Best regards, SteviethemanDelivered: 17:57, 7 December 2016 (UTC)Reply[reply]

WikiJournal of Science promotion

The WikiJournal of Science is a start-up academic journal which aims to provide a new mechanism for ensuring the accuracy of Wikipedia's scientific content. It is part of a WikiJournal User Group that includes the flagship WikiJournal of Medicine.[1][2]. Like Wiki.J.Med, it intends to bridge the academia-Wikipedia gap by encouraging contributions by non-Wikipedians, and by putting content through peer review before integrating it into Wikipedia.

Since it is just starting out, it is looking for contributors in two main areas:


  • See submissions through external academic peer review
  • Format accepted articles
  • Promote the journal


  • Original articles on topics that don't yet have a Wikipedia page, or only a stub/start
  • Wikipedia articles that you are willing to see through external peer review (either solo or as in a group, process analagous to GA / FA review)
  • Image articles, based around an important medical image or summary diagram

If you're interested, please come and discuss the project on the journal's talk page, or the general discussion page for the WikiJournal User group.

  1. ^ Shafee, T; Das, D; Masukume, G; Häggström, M. "WikiJournal of Medicine, the first Wikipedia-integrated academic journal". WikiJournal of Medicine. 4. doi:10.15347/wjm/2017.001.
  2. ^ "Wikiversity Journal: A new user group". The Signpost. 2016-06-15.

T.Shafee(Evo&Evo)talk 23:08, 13 February 2017 (UTC)Reply[reply]

Planning WP:CompBio editathon at ISMB/ECCB 2017

Hi all, Following last year's editathon at ISMB 2016, Kierano and I are organising another at this year's ISMB/ECCB conference in Prague: Wikipedia:WikiProject Computational Biology/ISMB 2017 Editathon.

Any assistance in organising, grant application writing, ideas for activities appreciated! See the talk page for more details.

Thanks, --Amkilpatrick (talk) 02:42, 9 March 2017 (UTC)Reply[reply]

I've always admired this initiative. I'd be happy to help out. I wonder whether there could be any integration with acadmic publishing for the finalists/winners. The WikiJournal of Science could be an appropriate target, or even Wiki.J.Med for medically relevant ones. Sadly, PLOS CompBiol is probably incompatible, since they require the article to be published in PLOS before publication on Wikipedia. Either way, I'd be happy to lend a hand writing the grant, publicising etc. T.Shafee(Evo&Evo)talk 06:13, 9 March 2017 (UTC)Reply[reply]
Very happy to have you on board! I've got a draft grant proposal here. I feel like the nature of the conference is such that people aren't likely to have time to make publication-sized contributions during the editathon, but it would definitely be a good thing to guide them to a path towards that as a follow-up! -Kieran (talk) 08:33, 9 March 2017 (UTC)Reply[reply]
Ah, you're right, I mixed up the editathon with the competition! Either way, I'm still happy to help out. Depending on the time that the editathon ends up being held, I may be able to help newcomers on articles remotely. T.Shafee(Evo&Evo)talk 10:28, 9 March 2017 (UTC)Reply[reply]
Excellent, thanks! We had a couple of experienced editors helping out remotely last time which worked out pretty well. Great to have you involved! :) Amkilpatrick (talk) 23:25, 9 March 2017 (UTC)Reply[reply]

Extension of 'Topic Page' review articles from PLOS Computational Biology to PLOS Genetics

The journal group PLOS is extending its 'Topic Page' review format that was spearheaded by PLOS Computational Biology to also include PLOS Genetics. In this format, accepted articles are dual-published both in the journal, and as Wikipedia pages (see Wikipedia category).

Suitable topics must either currently lack a Wikipedia page, or have only stub/start class contents. If you you would like to submit such a review article, see these guidelines. If you have any recommendations for topics to be commissioned, feel free to let any of the involved editors know: T Shafee (PLOS Gen), D Mietchen (PLOS Comp Biol).
T.Shafee(Evo&Evo)talk 12:26, 25 March 2017 (UTC)Reply[reply]

A blog post on the matter is now out. -- Daniel Mietchen (talk) 11:28, 13 April 2017 (UTC)Reply[reply]

Popular pages report

We – Community Tech – are happy to announce that the Popular pages bot is back up-and-running (after a one year hiatus)! You're receiving this message because your WikiProject or task force is signed up to receive the popular pages report. Every month, Community Tech bot will post at Wikipedia:WikiProject Molecular Biology/Computational Biology/Archive 2/Popular pages with a list of the most-viewed pages over the previous month that are within the scope of WikiProject Molecular Biology.

We've made some enhancements to the original report. Here's what's new:

  • The pageview data includes both desktop and mobile data.
  • The report will include a link to the pageviews tool for each article, to dig deeper into any surprises or anomalies.
  • The report will include the total pageviews for the entire project (including redirects).

We're grateful to Mr.Z-man for his original Mr.Z-bot, and we wish his bot a happy robot retirement. Just as before, we hope the popular pages reports will aid you in understanding the reach of WikiProject Molecular Biology, and what articles may be deserving of more attention. If you have any questions or concerns please contact us at m:User talk:Community Tech bot.

Warm regards, the Community Tech Team 17:16, 17 May 2017 (UTC)

ISMB 2017 Editathon rapid grant proposal ready for viewing -- please endorse!

Hi everyone! The rapid grant proposal to run an editathon at ISMB 2017 is drafted and open for comments and endorsements. We'd like to submit it before the end of the week, and your endorsements on the grant (signing your name near the bottom) would help!

We will also be looking for volunteers to take on (brief) shifts during the day at ISMB as mentors to new editors. I'll be putting up a sign-up sheet soon, but please also sign if you're willing to help out. -Kieran (talk) 14:22, 13 June 2017 (UTC)Reply[reply]

As of last Friday, the rapid grant proposal is now live! Any further comments or endorsements would be welcome. Thanks, Amkilpatrick (talk) 14:21, 20 June 2017 (UTC)Reply[reply]

Volunteer signup for ISMB editathon 2017

Hi folks! This is a call-out to anyone attending ISMB this year with experience editing Wikipedia to sign up to help with the editathon. The editathon will run throughout the day on a drop-in basis, and we need experienced Wikipedians to help conference attendees to share their expertise. Responsibilities will be pretty light -- just be in the room and on hand to help folks find articles in their field, and then answer questions and provide guidance as they go. The signup sheet is here, and you can sign up just by using the short form of your signature (three tildes). Thanks for your help! -Kieran (talk) 00:22, 7 July 2017 (UTC)Reply[reply]

ISMB/ECCB editathon today

Hi all, we are running the ISMB/ECCB editathon today at ISMB/ECCB in Prague! If you're attending the conference, we'd love to see you (details on the page) - remote contributions also welcome! Amkilpatrick (talk) 08:48, 23 July 2017 (UTC)Reply[reply]

Cleanup listing for WP:CompBio

A list of WP:CompBio articles by cleanup tag is now available: apparently 45% (!) of articles are tagged for cleanup. I think I'll make a start on the articles tagged with referencing issues, any other help appreciated.... Thanks, Amkilpatrick (talk) 17:39, 4 October 2017 (UTC)Reply[reply]


Hi! I found that Wikipedia has almost no articles about SNPs (Single-nucleotide polymorphism). Although there are over 140 thousands SNPs in SNPedia, I found only 22 articles in Wikipedia. I categorized them according to their positions on human chromosomes e.g. Category:SNPs on chromosome 1, Category:SNPs on chromosome 11. I think more work should be done on expanding articles about this topic. Here is a list of over 140,000 SNPs, if anyone is interested in creating new SNPs articles. I also suggest starting a special Wikiproject for SNPs expansion. --Brainist (talk) 20:41, 20 November 2017 (UTC)Reply[reply]

For anyone else interested in this, there's an active discussion over on WikiProject Genetics. Amkilpatrick (talk) 09:15, 22 November 2017 (UTC)Reply[reply]

Talk:List of protein structure prediction software

Hello folks, there's a question on talk:List of protein structure prediction software about whether the list needs a section on Model Quality Estimation/Assessment methods. Would someone here be able to help out? I am not nearly familiar enough with the subject to give a helpful answer. Richard Nevell (WMUK) (talk) 17:37, 20 December 2017 (UTC)Reply[reply]

PLINK (genetic tool set)

Hey, seems like the PLINK Wikipedia page PLINK (genetic tool-set) is not up to the standard. It is a commonly used command line tool for genetic association analysis and I wanted to make sure the article would be considered within the scope of the WikiProject Computational Biology. PalashSethi (talk) 07:29, 30 December 2017 (UTC)Reply[reply]

Hi Palash, apologies for the delay in replying. Yes - I've added the WP:CompBio banner to the article's talk page. If you want to be bold and improve that article, go for it! Thanks, Amkilpatrick (talk) 09:28, 4 January 2018 (UTC)Reply[reply]

Proposal for new Wikipedia article as entry for ISCB competition 2018

For my entry to the 2018 ISCB competition I plan to create a new Wikipedia article titled Ruzzo-Tompa algorithm. The Ruzzo-Tompa algorithm is a linear time algorithm for finding all non-overlapping, contiguous, maximal scoring subsequences in a sequence of real numbers[1]. There is an existing article on the Maximum subarray problem. The Ruzzo-Tompa algorithm is an improvement over previously known quadratic time algorithms.

The problem of find disjoint maximal subsequences is of practical importance in the analysis of DNA. Maximal subsequences algorithms have been used in the identification of transmembrane segments and the evaluation of sequence homology[2].

The description of the algorithm by Ruzzo and Tompa is somewhat hard to follow, so I think a Wikipedia page with some sort of animation as well as psuedo-code or Python code would be appropriate.

  1. ^ Ruzzo, Walter L.; Martin, Tompa (1999). "A Linear Time Algorithm for Finding All Maximal Scoring Subsequences". Proceedings. International Conference on Intelligent Systems for Molecular Biology: 234–241. PMID 10786306.
  2. ^ Karlin, S; Altschul, SF (Jun 15, 1993). "Applications and statistics for multiple high-scoring segments in molecular sequences". Proceedings of the National Academy of Sciences of the United States of America. 90 (12): 5873–5877. PMID 8390686.
Hi, it depends on what you think the general notability of the RT algorithm is to some extent, and whether or not you can get sufficient references for a new article. I have to admit this is the first time I'd heard of the algorithm! One option might be to extend the existing maximum subarray problem article to include the RT algorithm, and then branch this off if that section gets too big? On the other hand, if there you feel there's enough material related specifically to that algorithm, it might make more sense to have a new article. In that case, Smith–Waterman algorithm would be a great template to follow, that article was GA-nominated at one point. FYI, I think pseudocode is fine, but I'd avoid a python implementation (see WP:NOTCOOKBOOK). Hope that helps, Amkilpatrick (talk) 09:04, 16 April 2018 (UTC)Reply[reply]

ISCB Wikipedia competition 2018 - final stretch

Hi everyone, just a heads-up that we're coming into the final stretch of the 2018 ISCB Wikipedia competition: the period for eligible edits will end on May 25 (UTC), just over four weeks from now. If you're a student or trainee at any level, I encourage you to submit an entry; we'll be awarding prizes of up to $500 and ISCB memberships for the most improved Wiki articles in the areas of bioinformatics and computational biology! If you've any questions or comments, I'd be happy to read them on my talk page, or on the competition's talk page.

Thanks! Amkilpatrick (talk) 10:43, 26 April 2018 (UTC)Reply[reply]

New article proposal: RNA-protein Interaction Prediction


I am interested in creating a new wiki article on RNA-protein interaction prediction for the competition this year. Would this be within the scope of the project?

Thanks, Cmmann21 (talk) 17:35, 1 May 2018 (UTC)cmmann21Reply[reply]

Hi, yes I think that would be a great topic for an article. Protein–protein interaction prediction might be a good existing article to use as a template for the structure; of course RNA-binding protein will probably be of interest as well. It will likely fall under WikiProject Molecular and Cell Biology as well, if you let me know when you've created the article I'll add it to both Wikiprojects. Thanks! Amkilpatrick (talk) 17:55, 1 May 2018 (UTC)Reply[reply]
@Cmmann21: Great idea. If you want any input/help from the biochemistry community, just pop a note on the WikiProject MCB talk page. T.Shafee(Evo&Evo)talk 03:17, 20 August 2018 (UTC)Reply[reply]

Activities involving Wikidata

In the context of the ISCB contest and education more broadly, questions came up as to what kinds of activities could involve Wikidata. I have now started to compile a list of such activities here. -- Daniel Mietchen (talk) 00:43, 20 August 2018 (UTC)Reply[reply]

@Daniel Mietchen: great, thanks, I'll check it out soon! Amkilpatrick (talk) 07:30, 20 August 2018 (UTC)Reply[reply]

Invitation to WikiConference North America in Ohio October 18-21

Hello! I wanted to give a personal invitation to WikiConference North America to participants in this WikiProject. This is the 5th annual wiki-event in this series. The previous events have had 2-300 participants. In comparison to other wiki events, this one has a focus on organizing community programs and student participation.

I saw your 8th ISCB Wikipedia Competition announcement. If there is anyone in North America who would be willing to present this competition's history and announce the current round of it then I think that everyone would find this welcome and inspiration. This long-running competition has had a good output for what it is and is a model for what other fields of study could do.

If anyone would present this at the event then I think that would make an excellent candidate for getting travel sponsorship. If anyone would propose, please do so by end of day 22 Wednesday August! Sorry for the late notice. If anyone who would apply needs help with a submission then ping me.

I am asking for a presentation about the contest but anyone can join and anyone can submit. Thanks. Blue Rasberry (talk) 14:55, 20 August 2018 (UTC)Reply[reply]

Thanks for the invitation! Unfortunately it looks like it's going to be too short notice this time round. Definitely keep me updated if there would be another suitable meeting in the near future though, as we're keen to maximise the collaboration between ISCB and Wikipedia! Thanks again, Amkilpatrick (talk) 14:35, 22 August 2018 (UTC)Reply[reply]
K thanks - will post earlier next year. This event happens every year. For anyone else, submissions end tonight! Individuals can come themselves without an affiliation and anyone is welcome to apply and submit. Blue Rasberry (talk) 20:32, 22 August 2018 (UTC)Reply[reply]

Add MetaCyc database link to Chembox?

Here people maintaining MetaCyc have proposed to add to {{Chembox}} a link option to MetaCyc (external link, like KEGG and PubChem). Please discuss whether this is useful. -DePiep (talk) 08:31, 11 November 2018 (UTC)Reply[reply]

Topic Page on Selfish genetic elements

PLOS Genetics has now joined PLOS Computational Biology in its Topic Pages initiative. As part of this, an article was drafted, peer reviewed and published in PLOS Genetics and has now been copied over to the Selfish genetic element wikipedia page. Comments and suggestions welcome! T.Shafee(Evo&Evo)talk 00:41, 17 November 2018 (UTC)Reply[reply]

A new newsletter directory is out!

A new Newsletter directory has been created to replace the old, out-of-date one. If your WikiProject and its taskforces have newsletters (even inactive ones), or if you know of a missing newsletter (including from sister projects like WikiSpecies), please include it in the directory! The template can be a bit tricky, so if you need help, just post the newsletter on the template's talk page and someone will add it for you.

– Sent on behalf of Headbomb. 03:11, 11 April 2019 (UTC)Reply[reply]

Old Deprecated Banner Template?

Hi, I've been using Rater to go through unassessed articles in related projects and I came across this template as a suggestion. However, this is not the title of this Wikiproject nor have I ever actually seen this template used anywhere on Wikipedia. Worse, it doesn't even seem to have assessment arguments. It just links to your main page.

As far as I can tell it looks like all articles that might use this should be moved over, and that the template should then be deleted. Does that seem fair? Prometheus720 (talk) 01:43, 26 April 2019 (UTC)Reply[reply]

@Prometheus720: thanks for bringing this up! Our WikiProject name was changed from Mathematical and Computational Biology to Computational Biology in 2011, I think. As far as I can tell, it's only used on Talk:Mediation-driven attachment model and there's no relation to biology on that article (that article also seems to be a COI but that's a different matter!), so I'd be fine with removing that use completely and then deleting the template. If you find any other pages where it's used, let me know and I'll see if they should be migrated. FWIW, this is the first time I've seen this template too! Thanks! Amkilpatrick (talk) 10:42, 26 April 2019 (UTC)Reply[reply]

8th ISCB Wikipedia Competition: deadline extended!

The editing deadline for the 8th ISCB Wikipedia competition has been extended, to 28th June 2019. As a reminder, entry to the competition is open to students and trainees of any level, and as in previous years, we encourage contributions to Wikipedia in any language. Please drop me a message here or on my talk page if you've any questions. Thanks! Amkilpatrick (talk) 07:05, 3 May 2019 (UTC)Reply[reply]

New article: Functional annotation of genomic variants

Hi, I am interested in starting a new article and participating in the 8th ISCB Wikipedia competition.

I would like to write about predictors of genomic variants consequences. I would write basic principles of functional annotation, then I would describe chosen existing tools (VEP, ANNOVAR, SnpEff, Haplosaurus and BCFTools/csq) and write about them in detail - about the usage, data formats, algorithms...The article would include comparison based on practical examples and description of limitations of these tools.

Is it possible to participate in the competition with this article?

Best regards,

KateBrich (talk) 13:32, 16 March 2019 (UTC)Reply[reply]

@KateBrich: yes, that sounds like it should be within scope, but check out SNP annotation#Functional annotation first - that section might be a good place to start so I'd think about putting any additions there first before starting a new page (of course, if there is a decent amount of material then it can be moved to a new page as appropriate). Just be careful with "comparison based on practical examples and description of limitations of these tools" as this sounds as if it could head towards review territory, see WP:NOTREVIEW. Let me know if you've any more questions. Thanks! Amkilpatrick (talk) 14:24, 18 March 2019 (UTC)Reply[reply]
@Amkilpatrick: I think it will be better to start a new article because I have a lot of material. In fact, I am not sure about some things and I would like to ask you for help. I have written a bachelors thesis on this topic and I would like to use it for this competition. I should be the owner of this work (I need to check with the university). It was published on the university website, successfully defended and it is available online. Is it possible to do it somehow? Can I donate the rights to Wikipedia and then use it for the competition? If so, how should I do it? Also, the thesis comprises theoretical and practical part. The theoretical part is a review, which should not be a problem, but the practical part is my own research. Do I need to publish it somewhere else first, or is it enough that it has been already published on the university website? Thank you very much!
Hi Kate, I'm not sure about donating the rights, but if your thesis was published online then you'll need to be careful with copyright violations, as these can be flagged up automatically, even if it's your own work - so you may need to reword it. Re the practical part, see WP:NOR (no original research) - it would need to be published elsewhere first and even in a peer-reviewed journal may not be enough to satisfy WP policies, since it would still be a primary source: generally secondary or tertiary sources (eg published literature reviews) are more credible for WP purposes (see also WP:PSTS). Hopefully that helps a bit! All the best, Amkilpatrick (talk) 14:13, 21 May 2019 (UTC)Reply[reply]
@KateBrich: Since it is your thesis, you should be able to change what license it is published under. For example, I went back and changed my phd thesis to being under creative commons license. If you contact your library, or the thesis repository directly, you should be able to request the change. T.Shafee(Evo&Evo)talk 00:02, 22 May 2019 (UTC)Reply[reply]
@Evolution and evolvability: I hadn't considered this, this is some good info, thanks Thomas! Amkilpatrick (talk) 07:24, 22 May 2019 (UTC)Reply[reply]

A possible Science/STEM User Group

There's a discussion about a possible User Group for STEM over at Meta:Talk:STEM_Wiki_User_Group. The idea would be to help coordinate, collaborate and network cross-subject, cross-wiki and cross-language to share experience and resources that may be valuable to the relevant wikiprojects. Current discussion includes preferred scope and structure. T.Shafee(Evo&Evo)talk 03:04, 26 May 2019 (UTC)Reply[reply]

Possible project consolidation

There's a discussion going on over at Wikipedia_talk:WikiProject_Biology about whether it is worth consolidating some of the disparate biology wikiprojects. One possibility could be a merger or semi-merger of WP:GEN + WP:MCB + WP:COMBIO + WP:BIOP, since their scopes are well-aligned. Ideas and opinions welcome! T.Shafee(Evo&Evo)talk 01:14, 25 May 2019 (UTC)Reply[reply]

WP:Gene Wiki may also be included in this. We are still in the early stages of this discussion. Comments are welcome (read:needed)!!
I should also add that we are considering bringing some aspects of WP:Wikiproject X to WP:Biology and turning it into a proper meta-project. Whether COMPBIO remains independent or is merged into a larger project, there will be an opportunity to participate in that change as well. Prometheus720 (talk) 03:38, 25 May 2019 (UTC)Reply[reply]

Confirmation pre-merger

Hello, based on the consensus at the WP:Biol discussion, this is confirmation of my suggestion to merge:
WP:GEN + WP:MCB + WP:BIOP + WP:CELLSIG (possibly + WP:COMPBIO) -> into Wikipedia:WikiProject Molecular Biology (name to be confirmed)
The new main page should be able combine all of the information of each project (much of which overlaps) and the talkpage should also also centralise discussion to make it more lively and easier for newcomers! Separate tracking tables of article qualities can still be kept by making them 'taskfores' if people think that'll be useful.

If people don't object I'll go about redirecting the WP and WT pages to that centralised location next week per this process. The initial stages will also be easy to reverse, so I propose doing a couple of months trial period before the later merger steps 8-15 for WP:Compbio. T.Shafee(Evo&Evo)talk 13:14, 10 June 2019 (UTC)Reply[reply]

@Amkilpatrick:I'm tagging you because I'm not familiar with who else to tag in this project. You don't have a separate list of more active members or indexing with WikiProject Directory tools. I'd really appreciate it if you tagged a few people to kickstart this discussion. We'd like to move quickly unless there are objections. Prometheus720 (talk) 15:51, 10 June 2019 (UTC)Reply[reply]
@Prometheus720: thanks for the tag! Pinging users from the WP:COMPBIO mailing list whose names seem familiar from my watchlist, or might be interested: @Duncan.Hull, JHCaufield, Magnus Manske, Rockpocket, Daniel Mietchen, Danfdeblasio, and Kierano: (please feel free to add more!). Obviously this is just my opinion, given that I'm working on bringing more people into this WikiProject from the ISCB COSIs, I'd like to suggest that we hold off merging WP:COMPBIO in this first trial period, then reevaluate in a couple of months based on both how the merger of the other WikiProjects has gone and also any uptake over here - what do people think? Amkilpatrick (talk) 08:46, 11 June 2019 (UTC)Reply[reply]
I should let you know that there has been talk of other merges as well, within Tree of Life. Wikipedia:WikiProject Tree of Life#Scope and related projects has a cladogram of all its subprojects that I added recently. You can see many are defunct or inactive, and that's just what has been identified so far. WP:Plants may end up consuming most of its subprojects besides WP:Cannabis, for example. In addition, while we are working on this merger, I am also redesigning the WP:BIOL page. User:Evolution and evolvability went ahead and made a pretty WPX-style frontend for the final merge (which is now located at Wikipedia:WikiProject Molecular Biology), but some of the backend is missing. Meanwhile, as I work on WP:BIOL I'm doing more backend changes first and will be doing the "facelift" later. Both of us are working on different things that will prove fruitful or useful to an eventual merged project and I predict that it will be a few weeks before we have discussed everything we have learned and shared it all between the two projects. Right now, WP:Tree of Life is sort of the poster boy of the BIOL subprojects. My goal is to make this merged project, which I support including COMPBIO (though I don't much mind waiting), into something equal to the quality of (and close to the activity level of) Tree of Life. So perhaps reviewing in a month or two might be good. I would recommend that you continue to check on that page, WP:BIOL and subpages, and what User:Evolution and Evolvability and I are doing over the next few weeks. I really think that you will like the merge in time. Prometheus720 (talk) 16:00, 11 June 2019 (UTC)Reply[reply]
Yeah I'll definitely keep tabs on what's happening and thanks so much to both you and Evo&Evo for taking the initiative on this! really hopeful that this will kickstart a new phase. Re waiting a little bit for WP:COMPBIO, let's see if anyone else here wants to weigh in in the next day or two Amkilpatrick (talk) 17:44, 11 June 2019 (UTC)Reply[reply]

Given the consensus here and at the wp:biol talkpage, I've implemented the merger steps of requesting the pagemoves (can always be undone if there's a big turnaround in opinion) See the new unified talkpage. All talkpage archives should be clearly visible and searchable and the new unified WikiProject page is almost complete. I was thinking that info like the ISCB article competitions table would be good to also put on the WP:MOLBIO page? A template will need to be formatted for easier switching between the taskforces for specific items that are really better suited to them. T.Shafee(Evo&Evo)talk 12:41, 16 June 2019 (UTC)Reply[reply]

Discussion that may be of interest

Hi all, in case anyone watches this page but not the parent project page, I could use a hand with some weird-looking compbio articles. Post is here. Thanks for your help! Ajpolino (talk) 22:04, 21 August 2019 (UTC)Reply[reply]