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

This is an archive of past discussions. Do not edit the contents of this page. If you wish to start a new discussion or revive an old one, please do so on the current talk 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for various software tools written and used by Wikimedia editors and operated by Wikimedia Deutschland e.V. It has been replaced by the Wikimedia Labs, with the services that used to be provided by the Toolserver available through the Tool Labs project."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:

• Reflinks
• Checklinks
• Dab solver
• Peer reviewer

all from toolserver.org

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 toolserver.org 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)

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)

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)

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)

See

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)

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)

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)

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].

Prash (talk) 05:06, 8 January 2016 (UTC)

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)

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)

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)

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)

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)

No problem. T.Shafee(Evo﹠Evo)^talk 05:26, 23 March 2016 (UTC)

@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)

Hi, just to make the project aware of a draft that may be of interest

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

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)

This project's feedback would be appreciated in this discussion, as this could greatly (and positively) affect biological citations!

The draft of a new

• Wikipedia:Village pump (proposals)#Access locks: Visual Design RFC
• Wikipedia:Village pump (proposals)#Access Locks: Citation Template Behaviour RFC

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:

• Fix and improve Mr.Z-bot's popular pages report

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,

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: Editors See submissions through external academic peer review Format accepted articles Promote the journal Authors 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 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. doi:10.15347/wjm/2017.001 . ^ "Wikiversity Journal: A new user group". The Signpost. 2016-06-15.

T.Shafee(Evo&Evo)^talk 23:08, 13 February 2017 (UTC)

Hi all, Following

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)

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)

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)

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)

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)

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)

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

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)

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)

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)

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

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)

Hi! I found that Wikipedia has almost no articles about

For anyone else interested in this, there's an

active discussion over on WikiProject Genetics. Amkilpatrick (talk

) 09:15, 22 November 2017 (UTC)

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)

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)

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)

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.