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. |
Archive 1 | Archive 2 |
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for various software tools written and used by Wikimedia editors and operated by Wikimedia Deutschland e.V. It has been replaced by the Wikimedia Labs, with the services that used to be provided by the Toolserver available through the Tool Labs project."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 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)
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 Wikipedia:WikiProject Computational Biology/EBI hackathon on September 4, 2015 for details. -- Daniel Mietchen (talk) 17:08, 8 June 2015 (UTC)
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)
Arewrite 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)
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)
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)
The International Society for Computational Biology (ISCB) is hosting a Wikipedia and Wikidata editathonatISMB 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)
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! Headbomb {talk / contribs / physics / books} 22:17, 7 September 2016 (UTC)
The draft of a new PLOS Computational Biology Topic Pageontranscriptomics is now ready for review at http://compbiolwiki.plos.org/wiki/Transcriptomics. -- Daniel Mietchen (talk) 15:38, 10 October 2016 (UTC)
See
Headbomb {talk / contribs / physics / books} 16:58, 29 October 2016 (UTC)
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, Stevietheman — Delivered: 17:57, 7 December 2016 (UTC)
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
Authors
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.
|
T.Shafee(Evo&Evo)talk 23:08, 13 February 2017 (UTC)
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)
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)
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:
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)
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)
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)
Alist 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 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)
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)
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.
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)
Hi,
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
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)
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)
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)
PLOS Genetics has now joined PLOS Computational Biology in its Topic Pages initiative. As part of this, an article was drafted, peer reviewed and publishedinPLOS 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)
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.
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)
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)
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)
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)
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)
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)
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)
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)
Hello and greetings from the maintainers of the WP 1.0 Bot! As you may or may not know, we are currently involved in an overhaul of the bot, in order to make it more modern and maintainable. As part of this process, we will be rewriting the web tool that is part of the project. You might have noticed this tool if you click through the links on the project assessment summary tables.
We'd like to collect information on how the current tool is used by....you! How do you yourself and the other maintainers of your project use the web tool? Which of its features do you need? How frequently do you use these features? And what features is the tool missing that would be useful to you? We have collected all of these questions at this Google form where you can leave your response. Walkerma (talk) 04:24, 27 October 2019 (UTC)