Wikipedia talk:WikiProject Computational Biology

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PLINK (genetic tool set)[edit]

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)

Proposal for new Wikipedia article as entry for ISCB competition 2018[edit]

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)

ISCB Wikipedia competition 2018 - final stretch[edit]

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)

New article proposal: RNA-protein Interaction Prediction[edit]


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)cmmann21

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)
@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)

Activities involving Wikidata[edit]

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)

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

Invitation to WikiConference North America in Ohio October 18-21[edit]

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)

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)
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)