Wikipedia talk:WikiProject Computational Biology

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Ambush Gene Hypothesis[edit]

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. ^ www.bioinformatics.org/wiki/Ambush_Gene_hypothesis

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

For those interested in phylogenetics, and clade presentations[edit]

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)

Draft:Direct coupling analysis[edit]

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)

Reorganizing the pages around the ISCB competition[edit]

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)

Editathon at ISMB 2016[edit]

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)

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

Popular pages[edit]

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)

BioRxiv support in citations[edit]

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)