Wikipedia talk:WikiProject Molecular Biology/Computational Biology/Archive 1

Archive 1

Archive 2

Moving to Wikipedia namespace

Participation in this WikiProject is slowly getting started, so I think it is time to move out of my user page namespace into Wikipedia namespace. I will make the necessary moves later this later this week and have the old pages redirect to the new ones. Hendrik Fuß (talk) 17:12, 19 December 2007 (UTC)

Genetic algorithms

The Genetic algorithms page, which I templated into WikiProj Computer Science, had also been templated WikiProj Molecular and Cellular Biology (!?), but that was recently improved to WikiProj Computational Biology. So, welcome :-) As I mentioned to the CS folks, I now want to build a Genetic Computer, to run a Genetic Algorithm, to optimize a Genetic Simulation, of the Genetic Computer :-) but I'd need a biochemist and a big, big bottle of excedrin. Pete St.John (talk) 17:20, 13 December 2007 (UTC)

Hmmm... I'm not sure myself whether genetic algorithms should be part of computational biology. I always thought of it as a computer science field that is rather independent of biology. After all, computational biology is a biological field, and GAs do not specifically solve biological problems. Hendrik Fuß (talk) 17:01, 19 December 2007 (UTC)

Please define the terms

Unresolved

Is there a difference between bioinformatics, computational biology, and mathematical biology? If so, please clarify on each article, and link to the others as appropriate. If not, merge them. --Adoniscik (talk) 07:44, 20 February 2008 (UTC)

I'd say: Bioinformatics is engineering, Computational Biology is science. It would be pretty easy to go further, and say Mathematical Biology is Mathematics; that would require distinguishing Math from Sci and Eng at such a high level. I wish we said "Mathematics Science" (as opposed to "mathematical sciences") and "Mathematics Engineering" instead of "Theoretical.." and "Applied..." mathematics; but we don't. But fuzzy as it may be, Mathematical Biology applies mathematics (such as systems of partial differential equations) per se, and not computers per se. Of course they all overlap and inter-relate. I don't know if my way of saying this is "clarifying" though :-) However, wow, I just went to bioinformatics and saw what you mean:

• "Bioinformatics and computational biology involve the use of techniques including..."

That's the very first line. So right at the start, Bioinformatics purports to be interchangeable with Compuational Biology. So yes sure that should be clarified. I'm just a hobbyist though. In the area of computers, the distinction between engineering and science is I think blurriest of all. Pete St.John (talk) 23:32, 20 February 2008 (UTC)

Yes, there is a difference, and the first line (or the whole opening paragraph) of Bioinformatics should be changed. The engineering-science distinction is not inappropriate, but remember that bioinformatics was and still is a field of active research, so it should qualify as science, too. I think different people have different ideas about these terms, and sometimes they are stretched to the limit (probably in order to attract funding). So here's my view: All three fields have in common their interdisciplinary location between computer science, mathematics and biology. Bioinformatics is the study of biological information, such as is contained in DNA sequences or protein structures. It deals with discovery, analysis, storage and warehousing of such information. Bioinformatics mostly deals with problems from molecular biology. Computational biology is a more general term and describes scientific approaches which specifically use computational methodology to solve biological problems. Bioinformatics and Systems biology could be seen as subsets of computational biology (but some people may disagree). Mathematical biology is very similar, but the focus is on mathematical methodology, such as mathematical model using e.g. differential equations. Mathematical and computational biology are not necessarily confined to molecular biology, but also cover ecology, physiology, evolution etc.

I chose the title Mathematical and Computational Biology for the WikiProject because it seemed to me to be the broadest description of a field of common interest. I think whatever the outcome of this discussion is, it would be good to have some sort of box or section, or separate article that clarifies the difference. Hendrik Fuß (talk) 14:54, 21 February 2008 (UTC)

I think I have reached the perfect definitions: When one seen a lab one can tell what it does, right? Dry labs (computers, D&D shirts and coffee cups), wet labs (highthroughput cores (noisy machines), Molecular biology (qiagen boxes everywhere and westerns running), physiology (retro look) and Bioengineers (odd machines and are in perpetual space wars with the molbios)). so just group everything into an article called dry lab and noone will complain, most biologist go to sleep as soon as you say a numer!! (Bad joke requiring no answer) --Squidonius (talk) 12:30, 24 April 2008 (UTC)

Definition requestion

Could someone give their opinion on Talk:Mathematical_biology#Merge_of_Computational_biomodeling as it lacks a Good opinion and has just low support speculation. I only known about models made with calculus, so I may be in error. --Squidonius (talk) 18:24, 13 March 2008 (UTC)

I will go ahead and merge. --Squidonius (talk) 11:36, 24 April 2008 (UTC)

List of Systems Biology Research Groups moved

Hi, I am from the WikiProject Systems. I just moved the former "List of Systems Biology Research Groups" to the Wikipedia:WikiProject Systems/List of Systems Biology Research Groups, because some guy nominated that list for deletion. In my experience this is a fight I can't win.

Now the list is no longer in the WikiProject Systems space, these guys 'no longer have anything to say about how we run hour things. I thing this is the 4th or 5th time last year this happened to on of our lists.

I made this move because I consider these list of great importance for the development of the project. These kind of list at the moment are still a great help, to explain about systems science, and to get an impression of what is really going on in the world.

Everybody can still add there information over there. On your project page I read that you have plans to wikify that list. Off cause this still is possible.

If you have any questions or if you want to have this list in your own project space, please let me know. -- Mdd (talk) 23:30, 8 April 2008 (UTC)

Sorry you've had trouble with people voting to delete your contributions. I remember looking at the page you mentioned. I believe the trouble is that Wikipedia doesn't encourage directory-style pages. Therefore, they're excluded by policy. While I agree that having such a directory may be useful, I can also see why Wikipedia does not want to provide such content. I can image that a complete list of systems biology groups (which are sprouting everywhere these days) would mainly consist of a collection of web links and may contribute little to the encyclopedic content of Wikipedia.

In my view, in order to preserve the work on that page, there are two options:

1. Host the list on a different site. There are plenty of directory sites in the web, and some specifically for systems biology. The Systems biology article could then link to that site.
2. Use the current article content to create a different article in accordance with Wikipedia's standards. For example, such an article could discuss historically important contributions by systems biology groups.

User:Hendrik Fuß 14:39, 30 May 2008 (UTC)

Thanks. The situation is kind of resolved here. I updated the list, and renamed it back to List of systems biology research groups. The people of the WikiProject Lists argreed with those changes. --14:53, 30 May 2008 (UTC)

System biology images

Some new images are avalible here people might find useful.

I have uploaded most of those images from a government source, which I think, is very interesting also. I am however not very familair with the field of systems biology myselve. I wonder though if some of these images or others could be used to illustrated the systems biology article. Could anybody give me some suggestions are give it a try. Thanks. -- Mdd (talk) 00:11, 9 April 2008 (UTC)

Category:Systems biologists

I created a Category:Systems biologists two weeks ago. I wonder if one of you noticed and has some more ideas about this. -- Mdd (talk) 14:35, 11 April 2008 (UTC)

New template for talk pages, expecially the larger ones

Unresolved

Some pages, such as this one have lots of post and it requires some work to see what has been answered or acknowledged. therefore I made the {{Unanswered}} template that can be put above a section allowing one to quickly glimpse what has been answered. For now I will tag mine and any post I am 100% sure is unanswered. If you were waiting for an answer but never got one as the post in somewhere in the middle tag it! please voice any queries or comments in the talk Template:Unanswered (links, talk) and not here. Cheers --Squidonius (talk) 14:03, 13 April 2008 (UTC)

Proposed merger of mathematical and theoretical biology

We currently have mathematical biology and theoretical biology as two separate articles. There seems to be significant overlap in scope. Please help find a strategy for dealing with this at Talk:Mathematical biology#Merge with Theoretical biology? Hans Adler 07:40, 21 November 2009 (UTC)

Looks like this merge has now been carried out. Alexbateman (talk) 14:46, 3 February 2011 (UTC)

Please review seriousness v. proposed deletion as parody of new article Names of small numbers at Wikipedia:Articles for deletion/Names of small numbers

Mathematical and Computational Biology WikiProject members, please, this is being discussed at:

Wikipedia:Articles for deletion/Names of small numbers http://en.wikipedia.org/wiki/Wikipedia:Articles_for_deletion/Names_of_small_numbers#Names_of_small_numbers

Please also consider what additions from binary and other numbering systems relevant to computational biology, nanocircuitry, math theory, number theory, statistics, subcellular and biochemical work should be made to this topic as a kept article.

Thank you. Pandelver (talk) 00:26, 12 March 2011 (UTC)

I think this article is irrelevant to the scope of Mathematical and Computational Biology. Here we deal with Biological problems that require computational methods for their solution. Please consider to add this article in a more mathematical project Manuelcorpas (talk) 09:04, 1 June 2011 (UTC)

Involvement with International Society for Computational Biology (ISCB)

There is a wikipedia user group at Hinxton, a bunch of geeks who are interested in disseminating Computational Biology to the wider public. We have recently featured in Nature. [1] We would like to create a subcommittee at ISCB that deals with dissemination, public engagement and widening of access of anything to do with Computational Biology, from Biological Databases to algorithms, techniques and so on. I think development of this wikiproject could be a great start. Please let me know your thoughts. Manuelcorpas (talk) 15:12, 23 November 2010 (UTC)

The ISCB has now endorsed the initiative to promote and encourage editing of Wikipedia to their membership. Although this project is inactive (or has very low activity - I count 5 active editors outwith those associated with the ISCB initiative, and only 8 edits in the last year), it seems like the natural home to co-ordinate editing from the wider computational biology community. An association between a learned society and a Wikiproject as an exciting and novel experiment in encouraging experts to engage with Wikiproject in academic areas. One would hope, if the initiative is successful, that it would serve as a paradigm for other Wikirojects to follow suit. We would also consider publishing a report, with the assistance of active editors, to disseminate the results of the collaboration.

To relaunch the project to make it welcoming to (hopefully) a new contingent of editors interested in computational biology I propose the following, prior to the lauch of the initiative at the 2011 ISCB annual meeting:

• Rename the project to simply WikiProject Computational Biology. Experience shows that multiple-focus groups are less successful from specific ones. "Computational biology" is 5 times the Ghits of "Mathematical biology" and the major focus of the project seems to be Computational biology anyway.
• Begin a systematic programme of article tagging, to grow the number of articles the fall within the projects remit and consider whether to create a Wikiproject categorization system. Thsi should creat a list of articles for new editors to get stuck into.
• Update the Wikiproject's page, filter the participants for activity and organize the structure of the projects goals.

I urge the active or past members to comment on this proposal, as obviously their input and guidance is most welcome. If no comments are forthcoming, I will individually contact each active member to see if there are any objections before enacting these proposals. Rockpocket 18:12, 3 February 2011 (UTC)

I don't see myself as a project member, so this is advice, not an objection. I have some doubts that even the present scope of the project is sufficiently wide in the long run. To stay alive, a project needs activity on its talk page, and the smaller projects generally have serious difficulties with that. Some examples:

• The last time that someone other than the original poster posted to a section on WT:WikiProject Mexico was two months ago on 5 December.
• The last message on WT:WikiProject Luxembourg that was not a broadcast message to all WikiProjects was by me, almost a year ago, and did not get a response.
• Even WT:WikiProject Biology is not very active.
• When I proposed merging two key articles for this project, mathematical biology and theoretical biology, I hoped to get input from editors who work in the field[s], or close to it/them. However, the only response was today, more than two months later and long after the merge was completed. No wonder, since this page is watched by less than 30 editors.

For WikiProjects it's important to get the trade-offs right. For academic WikiProjects this means that editors should feel that they are among colleagues, perhaps even colleagues they have met at conferences. But it is still important that editors don't feel alone. Obviously the scope should be natural. If the present scope is natural in the sense that it describes a community, or a bunch of closely related communities, then I propose leaving it as it is. This does not come with an obligation that you have to deal with articles you are not interested in. It just means that you should treat any mathematical biologists who want to join as welcome new colleagues. If they should ever feel that they are not at home here because they are outnumbered, they can still split off. But I think it's more likely that the project will be grateful for anybody who makes it more lively (and isn't a moron who tries to rewrite all articles according to some crank ideas). Hans Adler 18:46, 3 February 2011 (UTC)

The reason for wanting to have our own Wikiproject for Computational Biology is because we believe that Computational Biology has enough scope on its own. We do not think that Mathematical Biology is directly relevant to Computational Biology. This initiative to engage the community for annotation of Wikipedia articles in Computational Biology comes from the International Society for Computational Biology. I am not an expert in Mathematical Biology myself, but the problems we are dealing with in Computational Biology are pretty unique: Databases, Annotation, Genomics, Metabolomics, Proteomics. These topics are already quite extensive to even add more unrelated topics coming from Mathematical Biology. I do not think that this Wikipedia Project should have been created including Mathematical Biology with Computational Biology, simply because this Wikiproject _does not_ reflect a community here: it reflects Two. Is there such a thing as the Society for Mathematical and Computational Biology? No. If you search for it you find a Society for Mathematical Biology and an International Society for Computational Biology but they are not mixed. Manuelcorpas (talk) 09:21, 1 June 2011 (UTC)

Hans' comments are well taken, and one of the major reasons I propose rebranding is to encourage more editors to embrace the project, which is clearly all but dead currently. I don't think there is much to lose by focusing the scope on CB and encouraging more expert editors to join through the ISCB, and it might prove an innovative way to bring expertise to technical subjects on WP. With that in mind, I - and a few other editors - have gone ahead and renamed the project as part of a relaunch. Over the coming weeks and months, we hope to use this as a way of introducing computational biologists to become new editors to WP. Rockpocket 12:32, 7 June 2011 (UTC)

What you lose by focusing the scope on CB is the math biologists that would be willing to contribute to the work. I agree that there are some topics firmly within computational biology (such as those listed by Manuelcorpas), and others firmly within math biology, but there is also a huge overlap. I recently rewrote the Michaelis–Menten kinetics article, and wouldn't like to pigeonhole it in either field. By instead writing "Simulation, modelling and analysis of biological systems (as in systems biology or Mathematical and theoretical biology)" in the scope you can keep those editors onside. U+003F^? 13:03, 7 June 2011 (UTC)

Thanks U+003F for the comments. I think that for the project to be successful we should try to keep the scope quite open. We certainly don't want to turn people off. I think that you should feel free to tweak the scope described in the Project page. As you say there is a large overlap between math biology and computational biology. BTW I have been trying to add the project template to some more article discussion pages such as at: BLAST. It would be great if you were able to add this to other relevant articles if you had some time. This will help us to track what articles do fall in scope. Alexbateman (talk) 13:50, 7 June 2011 (UTC)

Notwithstanding my concerns about keeping all relevant contributors on board, I really like that you geeks are getting this Wikiproject up and running again. Keep it up! As a matter of priority, I'd put work into the banner. Not because I think the branding is terribly important, but rather because the assessment and importance tags provide an easy and inbuilt way of organising the project. U+003F^? 16:08, 7 June 2011 (UTC)

Assessment and improvement

Now that the project stats are available, two to-dos jump out:

• Assessment work through the 240 unassessed articles. I imagine a lot of these are lower-than-low-importance false positives, for which the banner should be removed.
• Improvement: there are five articles marked as top importance of that are of lower than B standard. We should try to improve these articles as a matter of priority.
  • Computational biology
  • BLAST
  • Sequence analysis
  • Mathematical and theoretical biology
  • Systems biology

I am slowly thinking about how to make the Systems biology one good; would anyone be interested in taking on one of the other four? U+003F^? 10:03, 13 June 2011 (UTC)

Lookingat the unassessed list they largely look within scope. I agree they are probablyalmost all of low improtance. But its still good to tag them. I'll start to work on some of them. I also think that there are probably some other articles that I marked as high importance that might be better as top importance. Alexbateman (talk) 10:34, 13 June 2011 (UTC)

I will take on Sequence analysis Alexbateman (talk) 07:37, 14 June 2011 (UTC)

Scope of Wikiproject Computational Biology

The page says:

"Simulation, modelling and analysis of biological systems (as in systems biology) of any scale (molecular structure, gene regulation, metabolism, protein interactions, cell physiology, cell populations, tissue organisation, organ modelling)"

Does-that include computational neurosciences? (I assume it is included in cell physiology, cell populations etc.)Nicolas Le Novere (talk) 21:06, 15 June 2011 (UTC)

Hi Nicolas Le Novere. The scope of the project is still very much open for debate. From my perspective, yes, yes, yes, computational neuroscience is within the scope of computational biology. I think it would be reasonable to add coputational neuroscience into the scope explicitly. What do others think? Are there other large areas we should include explicitly such as immunoinformatics etc. Alexbateman (talk) 08:06, 16 June 2011 (UTC)

Yes, thinking logically, all of that belong to computational biology. Of course one could reasonably argue that terms like "computational biology", "mathematical biology" and "theoretical biology" are questionable (just like theoretical, mathematical and computational Physics), because using a few equations to describe population genetics or enzymatic catalysis does not make it a separate field (this is still population genetics, enzymology, etc., rather than theoretical/mathematical/computational biology). However, "computational biology" is widely used and therefore has every right to exist per WP:Common name. Biophys (talk) 13:53, 16 June 2011 (UTC)

Systems biology help

Systems biology is identified as one of our most important articles, but is currently very confusing. I've been working on overhauling the piece to a good standard, but progress has been slow. Anyone willing to chip in and (re)write a paragraph or two? U+003F^? 09:44, 21 June 2011 (UTC)

WikiProject banner

I have been adding the WikiProject banner to relevant pages. I've started working on anything with the Category:Bioinformatics. I'm working through the list in my Sandbox User:Alexbateman/Sandbox/foo. Do feel free to either work through this list or make lists of your own. To add the template add the following text to the talk page for the article:

{{WikiProject Computational Biology}}

If you can add the importance and class tags to assess the article so much the better. This will display the following

Alexbateman (talk) 10:55, 8 June 2011 (UTC)

We're almost through the first list of articles! I just created a new list of articles to tag based on the category Category:Biological databases. I've created a list to work through at: User:Alexbateman/Sandbox/database list. Again feel free to edit. Alexbateman (talk) 15:14, 8 June 2011 (UTC)

OK we have over 300 articles with banners now! I've just created a new list of articles that might be added to our WikiProject at User:Alexbateman/Sandbox/banner_list Alexbateman (talk) 09:08, 9 June 2011 (UTC)

Is there a way to list all articles in the project? Sorry if this is a dumb question, I'm new to WikiProjects... Duncan.Hull (talk) 17:54, 9 June 2011 (UTC)

Special:WhatLinksHere/Template:WikiProject_Computational_Biology is a crappy way to do it U+003F^? 18:01, 9 June 2011 (UTC)

Scratch that. I've set up a stats section on the main page. Purdy, huh? U+003F^? 18:29, 9 June 2011 (UTC)

Great thanks U+003F, have you finished editing Systems Biology yet? :-) Duncan.Hull (talk) 19:14, 9 June 2011 (UTC)

Great work U+003F! I expect that the stats will hopefully change quite rapidly at the beginning. Alexbateman (talk) 08:09, 10 June 2011 (UTC)

We now have over 900 articles tagged and assessed for quality and importance. Yay!!! Lets push on towards 1000. Alexbateman (talk) 17:36, 23 June 2011 (UTC)

Presence at ISMB conference

Dear all,

I will be attending the ISMB conference at the end of the week and plan to advertise theis WikiProject as much as possible. There will be a Birds of a Feather group meeting on Sunday at 5:30pm and I will be giving a short talk in the Education track about the WikiProject. If you are there please do come and find me. Alexbateman (talk) 10:56, 12 July 2011 (UTC)

We'll be in Hall F1 of the Vienna International Centre.Alexbateman (talk) 10:18, 17 July 2011 (UTC)

Thanks to everyone who came to the meeting. There was a variety of discussion about theWikiproject. One theme that emerged was that severl editors did not check on Wikipedia often and so would want to be kept informed of changes to the project by e-mail. Ben Good mentioned the GeneWikiPulsenntwitter feed that could be modified for the WIkiProject. Many of the people who came to the meeting had not eited WIkiPedia before and so there seems to be scope to run a training tutorial on WikiPedia at the coneference next year. Any volunteers to help organise such an event? Alexbateman (talk) 13:12, 18 July 2011 (UTC)

I nominate you and Magnus Manske. Altho, it is at Long Beach, California. Perhaps a few more 'pedians could be persuaded to attend. --Paul (talk) 03:56, 19 July 2011 (UTC)

Can you share the talk for those of us who were not able to attend? U+003F^? 16:00, 19 July 2011 (UTC)

Happy to do that. Any ideas of a good way to share the powerpoint file? Alexbateman (talk) 11:54, 22 July 2011 (UTC)

My colleagues are fans of SlideShare. U+003F^? 13:26, 22 July 2011 (UTC)

Michaelis–Menten

Michaelis–Menten kinetics is currently under peer review, in an attempt to get it to a good standard. The reviewer had lots of suggested improvements. Anyone here have the expertise to help out? U+003F^? 22:59, 25 July 2011 (UTC)

1,000 articles now assessed

We have now reached 1,000 articles that have been tagged as part of this WIkiProject! Congratulations everyone! There are still more to be tagged and assessed. If you want to find more then this list is a good start: click this link. Alexbateman (talk) 15:01, 16 August 2011 (UTC)

Things that need doing

I've been thinking of a few things that need to be one. Please add to the list and note if you are working on any of them to avoid clashes. Alexbateman (talk) 08:22, 9 June 2011 (UTC)

• Find articles that need WikiProject banner adding

To get an automated list of candidates, try this link. 1037 pages at the time of writing, but many false positives. --Magnus Manske (talk) 18:03, 12 June 2011 (UTC)

• Assess articles with existing banner
• Create table showing assesments of computational biology articles like the one at MCB: [2]

Done. The table is automatically updated every few days, or you can go here to update immediately U+003F^? 18:34, 9 June 2011 (UTC)

• Rebrand WikiProject home page. Its been suggested that WikiProject Computing is a good template for this. [3]
• Archive old discussions which are cluttering this page

Autoarchiving set up, currently at 180 days but this can be decreased if activity picks up Jebus989^✰ 18:38, 9 June 2011 (UTC)

Do you know why the earliest threads are still there? U+003F^? 18:47, 9 June 2011 (UTC)

The bot runs once a day so it took a while to kick in, there is a problem though. I've manually archived the threads the bot removed but will try to fix archiving Jebus989^✰ 09:32, 10 June 2011 (UTC) Fixed now, parameters must be on new lines Jebus989^✰ 09:41, 10 June 2011 (UTC)

• Find willing editors to help out with tasks for the WikiProject

I just saw an invitation template and copied it for our WikiProject. Please take a look and fix any bugs you notice. Please do add this to the user talk page of people who you think might be interested to join us! Alexbateman (talk) 15:35, 18 June 2011 (UTC)

To add this yourself use this code {{WikiProject Molecular Biology|COMPBIO=yes invite|Signature=~~~~}}

• Threw together a Userbox and updated the templates box. Feel free to fix or toss as you please. Code is: {{User WikiProject CompBio}} Estevezj (talk) 01:13, 13 December 2011 (UTC)

This user is a member of WikiProject Computational Biology.

[announcement] The data for Template:Infobox_biodatabase have been released in DBPedia 3.7.

The data from Template:Infobox_biodatabase have now been integrated into DBPedia 3.7. See:

• http://en.wikipedia.org/wiki/Wikipedia:WikiProject_Molecular_and_Cellular_Biology/Announcements#Infobox_biodatabase (for reference)
• http://dbpedia.org/page/Template:Infobox_biodatabase
• http://dbpedia.org/ontology/BiologicalDatabase
• http://dbpedia.org/page/L1Base

those data can now be searched through a SPARQL query --Plindenbaum (talk) 09:55, 11 September 2011 (UTC)

Folding@home importance

Hi. I would like to know what importance Folding@home sits on the Importance Scale for this WikiProject. I believe it's either going to be high, or mid. I would argue that it is high because Folding@home is an extremely powerful distributed computing system that performs protein folding and protein structure prediction, which have obvious impacts into understanding cellular communication, disease research, and how molecules work in general. In a well-cited statement, it says that Folding@home has caused "paradigm shifts in protein folding theory". While providing thorough sampling of the aspects of protein folding, its simulations remains accurate experimentally comparable, which is considered a "holy grail" of computational biology. At the same time, it could be argued that Folding@home is of mid importance, because it only concerns itself with proteins and to a lesser degree other molecules such as the ribosome and protein aggregation, but does not simulate other aspects of computational biology. It's currently marked as mid importance, and I wanted to make sure that was correct. Thoughts? Jessemv (talk) 16:49, 4 November 2011 (UTC)

Hi, I added it as mid importance I think. That seemed about right to me. Its certainly above low importance. It has gained a lot of press and shown that the distributed model can work well. But I'm not sure that among computational biologists it is widely used in the way that BLAST or ClustalW are used. Alexbateman (talk) 14:40, 12 December 2011 (UTC)

Thanks so much. Yes, it does a very specific job, so in that sense it's limited. Glad to know the rating is correct. Jessemv (talk) 15:45, 12 December 2011 (UTC)

Difference between subdisciplines

Does anyone have any reputable sources that attempt to define the differences between the various disciplines represented here? The overlap between computational/mathematical/systems/theoretical -biology and bio- informatics/statistics is high, but their differences are not clear. Their individual articles would, I think, benefit from setting this out. The NIH defines the difference between computational biology and bioinformatics, but the other fields are not mentioned. Cheers! U+003F^? 12:51, 30 December 2011 (UTC)

I think mostly the differences are operational rather than theoretical. It just so happens that a group involved in topic x happens to describe them self as working in the domain of y... Perhaps a survey of topics / domains would help? --Dan Bolser (talk) 13:52, 12 February 2012 (UTC)

Article request: sequence feature

Perhaps I'm missing this article under a different name, but a redirect would be nice. AFAICT, there isn't any info on 'sequence features'. Its tricky, because of course its a rather abstract topic. In biology, there is no such thing as a 'sequence feature', it only exists as an abstract (and very useful) convention in computational biology. To further complicate issues, the topic is mostly practical, heavily dependent on various 'sequence feature formats', that further increases the abstract nature of the topic (you can describe anything you like within the scope of the format). Anyway, something would be nice! Cheers, --Dan Bolser (talk) 13:50, 12 February 2012 (UTC)

Some links:

• http://www.google.com/search?q=sequence+feature
• http://www.bioperl.org/wiki/HOWTO:Feature-Annotation
• http://www.uniprot.org/manual/sequence_annotation
• ... — Preceding unsigned comment added by Dan Bolser (talk • contribs) 13:56, 12 February 2012 (UTC)

Wikipedia:WikiProject Unique Identifiers

So, there's a new project which may be of interest to some here. It arises out of Wikipedia:Village_pump_(proposals)#UID_interface_to_Wikipedia, a proposal to make wikipedia articles available by their UID - for instance by their UNIPROT number. Umm. For reasons which should be all to obvious to anyone interested in computational biology. And those two pages are all I have to show you, but I live in hope of input from you to take it all further. --Tagishsimon (talk) 20:49, 14 February 2012 (UTC)

Method for assigning article class and importance

When adding the project banner to new pages, what's the procedure for choosing class and importance? Should I just use my judgment according to the quality scale and importance scale? Or should the assessment take user ratings into account? --Quantum7 01:30, 11 March 2012 (UTC)

I'd say to use your own judgement. If you have any questions or would like followup, please post here. Jesse V. (talk) 01:41, 11 March 2012 (UTC)

Just use your best judgement. In terms of importance almost everything is low importance, the subject area is almost never mainstream enough. I only assign mid, high or top for quite significantly important topics to computational biologists. I did use http://stats.grok.se/ to identify highly viewed articles in the Wikiproject and move these to higher importance ratings. Thanks for helping out with adding the templates and assessing articles! Alexbateman (talk) 17:27, 23 March 2012 (UTC)

Translation into layman's terms

The article DNA microarray experiment is written in technical language such that a friend with background in the topic complained to me about it. Would any of you all who are more experts than I be willing to step in and clarify it? Danger ^{High voltage!} 16:36, 23 March 2012 (UTC)

Wow that is very dense, and I'm barely making headway in understanding what the article is even about! I know very little about the subject, but I would also like to add my support for seeing its improvement. Thanks for bringing it to our attention. Jesse V. (talk) 16:44, 23 March 2012 (UTC)

PLoS Computational Biology to Contribute Wikipedia pages?

We would like to solicit your feedback on a proposal from PLoS Computational Biology (PCB). The journal proposes to help establish new Wikipedia pages in the field of computational biology that are not currently covered, either at all, or exist only as a stub. The pages would be created in the Wikipedia sandbox. When complete they would be reviewed by a newly appointed PCB Topic (aka Wiki) Pages Editor and folks s/he solicits, and if suitable the authors would be given the opportunity to publish it as a PCB Topic Page which would appear as part of the Education section of the journal. The page would be available from PLoS under a Creative Commons Attribution License. The PCB page would be indexed in PubMed and would provide a service to journal readers. As such it provides author incentive. PCB would only publish the Topic Page when it has been released into the public Wikipedia and the PCB page would become the copy of record. The community would make further enhancements to the Wikipedia page on an on-going basis as per usual. The upside is that authors would be inclined to provide an initial starting point of high quality material as they get a PLoS publication and are indexed in PubMed. Wikipedia gains good content. The downside is that if this became popular (more than 2-3 per month) PLoS would need to charge to recover publishing costs, but this would not be the case initially.

Phil Bourne EIC PLoS Computational Biology — Preceding unsigned comment added by Pebourne (talk • contribs) 19:50, 7 September 2011 (UTC)

I think it is important to find ways to give incentives for domain area experts to contribute to Wikipedia and I would welcome such an initiative. I would be happy to provide reviews of such contributions to Wikipedia if it would help. Alexbateman (talk) 15:30, 8 September 2011 (UTC)

Excellent proposal. I have long thought that very much like this is how we should get experts involved in "original research" writing that doesn't create problems with our policies. In the unlikely event that something goes terribly wrong with an article (there were some infamous problems at Citizendium), we can still treat it the same way as any other article and don't have to treat it as privileged in any way. Hans Adler 15:38, 8 September 2011 (UTC)

Excellent initiative ! and it could be an interesting example for the other journals (not necessarily about Bioinformatics)--Plindenbaum (talk) 18:51, 8 September 2011 (UTC)

I fully support this proposal, as it seems to be of benefit to all parties. However, rather than your idea of writing a page in a sandbox, why not write the page directly and utilise the existing mechanisms for peer review and good article nominations? These processes could be sped up through contacting potential referees directly or through this project, and would result in an article considered "good" in both your and Wikipedia's interpretation of the word. On a boring-but-important note, any text released to Wikipedia must have both CC-BY-SA and GDFL licensing. U+003F^? 09:00, 11 September 2011 (UTC)

Update: The project (see Signpost coverage for overview) has now progressed such that the first article to be posted has passed peer review and is in production at PLoS Comp Biol. One of the issues that remain to be addressed (apart from format conversions) is that of how to post the articles and associated image and media files. While we intend to automate the process eventually (help with that is welcome), we will initially have to start out posting manually. In order to facilitate tracking of PLoS Comp Biol contributions, it would make sense to use an account like User:PLoS Computational Biology (which we reserved) but this runs afoul of WP:ORGNAME as it stands. On the other hand, some PLoS Comp Biol authors do have an account here that they could use for this purpose (or would this fall under WP:COI?), others don't, and in any case, such an approach would make it rather cumbersome to track - other than by way of categories - contributions made through PLoS Comp Biol. As another alternative, an individual user here could post the materials on behalf of the journal. I am ready to do that but would like to invite some community feedback before getting started. -- Daniel Mietchen - WiR/OS (talk) 16:11, 17 January 2012 (UTC)

For copyright reasons, anything added to Wikipedia ought to trace back to a single person. A role account such as User:PLoS Computational Biology would not resolve to a specific person. If that account were to add material for which it was not the author, it would then need to supply confirmation via WP:OTRS that it was authorized by the copyright owner. Some of these problems might be overcome, so a discussion would be good. In principle it's a great idea for PLoS Computational Biology be helping to create useful articles for Wikipedia. In the short run, it's more persuasive if creators of such articles have their own Wikipedia accounts and prepare themselves to deal with the back-and-forth of Wikipedia feedback. Expecting the off-line review by the journal editors to cover all of the requirements is probably too optimistic. Making a category for articles that were contributed (or enhanced) by collaboration with PLoS Computational Biology should be fine, in my opinion. EdJohnston (talk) 18:20, 17 January 2012 (UTC)

I look forward to seeing the first article! I agree this should be an individual posting the article. I don't see any problem with that person being a PLOS CB employee though. I guess it would be preferable that the content was posted by one of the authors into Wikipedia. I like the idea of the content being placed into the users sandbox to undergo any reviewing and then the user can move the content across with publication. Alexbateman (talk) 15:56, 19 January 2012 (UTC)

I agree with the sandbox idea. When you do something new on this rather old and encrusted wiki you always risk furious responses by some. I would be shocked if anyone posting a high-quality peer-reviewed scientific article specifically prepared for Wikipedia in this way would not be accused by someone of spamming for the journal or some similar crime. We must plan it advance how to deal with such overreactions. It's also quite possible that the first article(s) will not quite fit into what we need here and need a bit of work. By doing this work outside article space we are probably going to avoid a lot of pressure. Hans Adler 17:53, 19 January 2012 (UTC)

On the other hand, perhaps the new material will fit perfectly. Any chance of a preview of the piece, so we can comment more concretely? U+003F^? 18:15, 19 January 2012 (UTC)

A preview woud be really useful to get an idea of the overreaction potential :) If the current article is just a stub or non-existant I think there will be fewer problems. If its got more content more diplomacy may be required. Alexbateman (talk) 21:32, 19 January 2012 (UTC)

We have been editing the article at this external mediawiki instance, so we can dual license the text. This is an extension of an article that is currently a stub and which was mainly drafted by myself. --Andreas (talk) 06:44, 20 January 2012 (UTC)

Looks great to me, I don't see any problem in its immediate uploading by you. A few minor changes are needed; the authors and acknowledgements sections should be removed, the wp: tags are not required on here, you'll have to use {{cite PMID}} rather than <pubmed>, and those refs should come after the full stops. I've knocked up a {{PLoS Computational Biology}} template; adding {{PLoS Computational Biology |source=http://pisaster.ucsd.edu/wiki/index.php/Circular_permutation_in_proteins}} to the bottom of your article will display

{{PLoS Computational Biology |source=http://pisaster.ucsd.edu/wiki/index.php/Circular_permutation_in_proteins }}

and also add Category:PLoS Computational Biology articles. Please edit this for the correct license. Perhaps you might consider adding the figures to Wikimedia Commons too. Cheers! U+003F^? 13:16, 20 January 2012 (UTC)

The talk page contains a list of changes which will be made for transition to wikipedia. Thanks for providing the attribution template! -Spencer Bliven (talk) 20:16, 20 January 2012 (UTC)

The template now uses doi as a parameter pointing back to the source:

{{PLoS Computational Biology|doi=10.1371/journal.pcbi.0010004}}

thus gives

{{PLoS Computational Biology|doi=10.1371/journal.pcbi.0010004}}.

-- Daniel Mietchen - WiR/OS (talk) 23:56, 29 January 2012 (UTC)

Update: PLoS comp biol now accepts a new type of articles, Topic Pages, see this editorial. The first article has been published today. We have also updated the wikipedia article on Circular_permutation_in_proteins to reflect the newly published content. At this stage I would like to request a re-evaluation of that article and we welcome any feedback! --Andreas (talk) 23:19, 29 March 2012 (UTC)

I saw the post on Wikiproject MCB as well, so I put down what I think the ratings should be. Jesse V. (talk) 00:10, 30 March 2012 (UTC)

Would it make sense to use Wikipedia as the sandbox, removing conversion and author mapping issues? (Sorry if I already missed that suggestion being made above, but I didn't see it). --Dan Bolser (talk) 21:37, 21 April 2012 (UTC)

Hi Dan, there is a license issue with using wikipedia as a sandbox for those articles. PLoS is publishing all articles under a very liberal license, the Creative Commons Attribution License. This means, you can do with the article what you want, even change the license, as long as you credit the original sources. This license is in fact more liberal than the wikipedia license, which is Creative Commons Attribution Share Alike. This means we can take a PLoS comp biol article and publish it on wikipedia, as long as we cite the original source of the text, but we can not do this in the opposite direction. To avoid any conflict editing is done in an external mediawiki instance which is using the PLoS style license. See http://topicpages.ploscompbiol.org/ --Andreas (talk) 06:31, 23 April 2012 (UTC)

Could we bring in a 'back catalogue' of CC-BY-SA and GDFL review articles where the exiting page in WP is small / missing? I haven't done a search, but I'd imagine that there are at least a few articles that could qualify. Cheers, --Dan Bolser (talk) 21:37, 21 April 2012 (UTC)

Bit of help with diseases and Folding@home

Hey everyone, I've been heavily editing Folding@home in an effort to get it up to Good Article status. I'm feeling fairly done with the latter half of the article, but I'm having a bit of difficulty in describing the various diseases studied. This is basically the stuff under the "Biomedical research" section. Thing is, I'm learning the molecular processes essentially from scratch, which makes things time consuming since I have to read scientific publications several times before I can understand it enough to cite it. So I'm asking, can someone check my work in that section and let me know if I've incorrectly described the formation of a disease, or if I could say things better? It'll be much easier to tie in F@h's research if I know how the disease develops in the first place, but I'm not a biochem major and I know there are experts here. Any assistance would be appreciated. I'll be watching this page of course. Best, Jesse V. (talk) 06:56, 7 March 2012 (UTC)

I've taken care of several of the diseases, and I'm trying to figure out the rest. There's a checklist on the Talk page. Advice/comments on them and the rest of the article would be greatly appreciated, now more than ever. I feel that GA nominations are very close! Please let me know what you think or if there's issues that need to be addressed. Jesse V. (talk) 19:22, 17 March 2012 (UTC)

Now a GA nominee. I'd appreciate it if someone could review it. :D Jesse V. (talk) 20:44, 5 April 2012 (UTC)

Peer review of Folding@home

Just wanted to let everyone know that I've opened a peer-review on the Folding@home article. It's already achieved GA status, but I'd like to take it further, maybe even meet FA standards if I can. Comments and suggestions would be very much appreciated. Thanks. Jesse V. (talk) 22:51, 14 May 2012 (UTC)

Help with Computational biology article

I have just gone through a cleanup of the Computational biology article to move its many lists into new or existing list articles. However, the content of the article is still a long way from a good description of the field. Given that this is our namesake article I think it would be good to bring its standard up. I'd appreciate any contributions to the main body of the text. Thanks Alexbateman (talk) 16:52, 16 July 2012 (UTC)

ISCB Wikipedia Computational Biology article competition

The ISCB announced that it is going to hold a competition for students and trainees to improve Wikipedia articles in the area of computational biology:

http://www.iscb.org/iscb-news-items/1453-2012-july15-iscb-announced-competition-wikipedia-computational-biology-articles

I'll post more details as they become available. Alexbateman (talk) 16:55, 16 July 2012 (UTC)

"Cite on Wikipedia" tool at National Center for Biotechnology Information website

I am in contact with the National Center for Biotechnology Information (who run web services like PubMed Central) over them providing references in a way that allows for easy copy-pasting into Wikipedia articles (similar to what Europeana does or the Biomedical citation maker). Where would be the best place to discuss what Wikipedia template formats (e.g. {{Cite web}}, {{Cite journal}}, {{Citation}}, {{Cite book}}) would be best to implement at what NCBI projects? Thanks for any pointers. Please reply at WikiProject NIH. -- Daniel Mietchen - WiR/OS (talk) 03:48, 18 July 2012 (UTC)

WikiPedia tutorial at ECCB conference

Dear All,

Daniel Mietchen - WiR/OS (talk) and I will be organising a tutorial to teach people about WikiPedia editing at the ECCB conference in September in Basel.

http://www.eccb12.org/t6

Do please advertise this to anyone or mail lists etc you know who may be interested. Also if you are attending the conference and want to help us out. Please do let me know. Alexbateman (talk) 13:43, 26 July 2012 (UTC)

The tutorial has a rather stiff fee by wiki standards, but we have arranged for some fee waivers. -- Daniel Mietchen - WiR/OS (talk) 06:41, 17 August 2012 (UTC)

Topic Page on Detection of horizontal gene transfer

A Topic Page on Detection of horizontal gene transfer has been drafted and has entered the process of wikification and peer review. Comments and suggestions most welcome. -- Daniel Mietchen - WiR/OS (talk) 07:04, 17 August 2012 (UTC)

Topic Page on Viral phylodynamics

A Topic Page on Viral phylodynamics has been drafted and wikified. It is currently undergoing peer review. Comments and suggestions most welcome. -- Daniel Mietchen - WiR/OS (talk) 07:04, 17 August 2012 (UTC)

Should Topic Pages be covered on a subpage of WP:COMPBIO?

About half of the threads on this talk page currently relate to the Topic Pages initiative at PLoS Computational Biology. Should the matter thus be moved to a dedicated subpage? -- Daniel Mietchen - WiR/OS (talk) 07:09, 17 August 2012 (UTC)

I think it's fine for now. This page hits more potential referees than a subpage would. Cheers, U+003F^? 08:27, 17 August 2012 (UTC)

It's good to have the review requests on this page. Alexbateman (talk) 07:42, 19 August 2012 (UTC)

Help with Folding@home

For months now, I've been working on improving the quality of the Folding@home article. However, I'm having an increasing amount of difficulty finding things to fix or things to add, and I'm running out of what little technical knowledge I have. I hope there are some experts here who can offer an insight on what the article needs next and how to go about taking care of it. Any ideas? • Jesse V.^(talk) 05:59, 28 August 2012 (UTC)

Also, can someone please review it and see if it qualifies for A-class? If it's not A-class, please advise on how I can get it up there. • Jesse V.^(talk) 14:34, 28 August 2012 (UTC)

I'm no expert, but maybe you can use some of the images from Commons? I like this one, but it's from 2010. jonkerz ♠talk 06:11, 28 August 2012 (UTC)

Hmm. The article already has a number of illustrative images, and that one was used on the article at one point but it was later removed. I do describe the breakdown of FLOPS from each platform, and there's a line where I describe what fraction comes from GPU clients. But FLOPS aren't everything, and they're not the most accurate measurement of scientific productivity. For those reasons, although I also like the image, I personally don't feel that it would be helpful to add in. • Jesse V.^(talk) 14:34, 28 August 2012 (UTC)

Folding@home nominated for FA class

I just wanted to let everyone know that I've nominated Folding@home as a Featured Article candidate. Comments or editing assistance would be most welcome. • Jesse V.^(talk) 02:36, 17 September 2012 (UTC)

Disambiguating links

Over the past couple of days I've been working on fixing ambiguous links in WP:CompBiol - it's currently at 25 (from over 100) but I could use some extra help from people more knowledgeable than myself. If anyone has a spare moment it would be appreciated. Thanks! Amkilpatrick (talk) 07:13, 24 September 2012 (UTC)

Circular permutation in proteins

What do you think about nominating this as a Good Article? Given the earlier peer review, I imagine it can't be far off the required standard. Going through a Wikipedia review might also give us some pointers as to how the PLoS articles can be aligned better with protocols here. U+003F^? 17:31, 10 September 2012 (UTC)

That sounds like a great idea. Go for it! Alexbateman (talk) 09:58, 12 September 2012 (UTC)

Done. Anyone who hasn't been involved in the article is welcome to undertake the review. U+003F^? 16:33, 12 September 2012 (UTC)

This went through GA without much trouble (see the review). The main complaint was about the lead: it looked more like a general introduction than WP:LEAD. An issue that (surprisingly) didn't come up was the article's use of WP:PRIMARY sources, rather than referring to secondary review papers. I think this is a real difference in stance with typical scientific literature. Hope this helps with future Topic Pages. U+003F^? 18:09, 6 October 2012 (UTC)

Providing data and links automatically for anatomical development

We've recently launched LifeMap Discovery (discovery.lifemapsc.com), a database of embryonic development, stem cell research and regenerative medicine for developmental biologist and stem cell researchers. In our database, we describe the development of organs, anatomical compartment and cells and have created images and developmental trees that describe these processes. We would like to share our content with WikiPedia by adding to existing developmental biology articles (like Lung Development) and by adding new articles. I would very much appreciate your direction regarding our contributions as well as any ideas about automation processes if any exist. Thanks Yaron Guan-Golan LifeMap Sciences — Preceding unsigned comment added by Mr8Bit (talk • contribs) 03:41, 9 January 2013 (UTC)

You might want to read our guideline on external links. Our goal here is to build an encyclopedia, so it's far better to add content here than to link to external content - the latter doesn't serve the encyclopedia very well unless it provides compelling value that can't be added directly. So, I suggest you consider that guideline and then decide whether you still think links to your resource are likely to be accepted. If so, go to the Talk page of an article to which you'd like to add a link, and ask there for comment. If you have not read WP:COI yet, you should. -- Scray (talk) 04:46, 9 January 2013 (UTC)

Hi Scray. I completely agree about conflict of interest here - which is why I raised the issue. We believe we have a unique resource that could add value to people interested in developmental processes, and that as such we can enrich Wikipedia. However, we believe it would only be fair if our content would be attributed to us as a source. Please note that our purpose here is not just to add links, rather to add content, new articles, and visualizations. We would be of course referencing our database as a source or external link so users that are interested in seeing more information could direct access to our database. Thoughts? — Preceding unsigned comment added by Mr8Bit (talk • contribs) 05:11, 9 January 2013 (UTC)

Topic Page on Approximate Bayesian computation

As part of the Topic Pages initiative of PLoS Computational Biology, a draft for Approximate Bayesian computation has now been peer-reviewed and wikified. Comments and suggestions welcome. -- Daniel Mietchen - WiR/OS (talk) 06:52, 17 August 2012 (UTC)

The paper has now been published in PLOS Computational Biology, and the Wikipedia article has been updated accordingly. -- Daniel Mietchen - WiR/OS (talk) 03:00, 12 January 2013 (UTC)

ISCB Wikipedia Computational Biology article competition

The ISCB Computational Biology article competition is now open for entries. Please pass the announcement around to anyone you think may be interested in entering. The competition is open to all students and trainees.

http://en.wikipedia.org/wiki/Wikipedia:WikiProject_Computational_Biology/ISCB_competition_announcement

Thanks. Alexbateman (talk) 09:57, 12 September 2012 (UTC)

It was great to see so many entries in the competition! The competition has now officially closed. That doesn't mean you should stop editing though :-) Now its over to the judging panel. Alexbateman (talk) 15:58, 11 January 2013 (UTC)

Topic Page on Evolving digital ecological networks

As part of the Topic Pages initiative of PLoS Computational Biology, a draft for Evolving digital ecological networks has now been peer-reviewed and wikified. Comments and suggestions welcome. -- Daniel Mietchen - WiR/OS (talk) 06:47, 17 August 2012 (UTC)

Meanwhile, the draft has entered production and is scheduled for publication in a month or two. -- Daniel Mietchen - WiR/OS (talk) 02:57, 12 January 2013 (UTC)

The article has now been published in the journal and copied over to Evolving digital ecological networks. -- Daniel Mietchen - WiR/OS (talk) 01:20, 12 March 2013 (UTC)

Topic Page on Viral phylodynamics now published

As part of the Topic Pages initiative of PLoS Computational Biology, an article was published in the journal that served as the basis for the new article viral phylodynamics here. -- Daniel Mietchen - WiR/OS (talk) 11:37, 25 March 2013 (UTC)

Topic Page on Flow cytometry bioinformatics

The article has been drafted at http://topicpages.ploscompbiol.org/wiki/Flow_cytometry_bioinformatics and is now going to peer review. Comments and suggestions most welcome. -- Daniel Mietchen - WiR/OS (talk) 10:24, 3 May 2013 (UTC)

This looks to be the basis for a very nice Wikipedia article! The only suggestions I would have are (1) the level of detail of the article is such that the lead could be expanded to provide a summary of the article content, per MOS:LEAD, and (2) just a small typo: in the Gating subsection, there is a malforrmed 'dimension|dimension reduction' wiki link. I know little of flow cytometry, but found the article very readable. Thanks, --Mark viking (talk) 11:14, 3 May 2013 (UTC)

Thanks. I fixed that link and forwarded your comment on the lead. -- Daniel Mietchen - WiR/OS (talk) 00:05, 6 May 2013 (UTC)

Thanks Mark and Daniel -- that's encouraging to hear. We'll work on expanding the lead as part of the process of addressing the reviewers' comments. -Kieran (talk) 18:25, 17 May 2013 (UTC)

commons:Category:Bioinformatics needs diffusion

There are currently over 1000 files in this category, mostly videos brought in there by my bot. The majority of these files shouldn't actually be in there, but the existing sub-categories do not cover the ground systematically yet, so I would appreciate if some of you could take a look and comment. Thanks! -- Daniel Mietchen - WiR/OS (talk) 23:54, 5 May 2013 (UTC)

Proposed Topic Page on ancestral reconstruction

It has been proposed to expand ancestral reconstruction as part of a Topic Page in PLOS Computational Biology. Community feedback is invited here. -- Daniel Mietchen - WiR/OS (talk) 00:26, 11 May 2013 (UTC)

Topic Page on Cooperative binding

As part of the Topic Pages initiative of PLoS Computational Biology, a draft for a much expanded article on Cooperative binding has received its first peer review. Comments and suggestions welcome. -- Daniel Mietchen - WiR/OS (talk) 01:57, 12 March 2013 (UTC)

Great work. Just looking through the two recently accepted ones - Approximate Bayesian computation and Evolving digital ecological networks - I see that the peer reviews weren't also moved to the discussion – unlike in the Circular permutation in proteins article. Was this a deliberate change?

Thanks for the pointer. Fixed for both. -- Daniel Mietchen - WiR/OS (talk) 20:32, 12 March 2013 (UTC)

The article has now been published in PLOS Computational Biology and transferred to Cooperative binding. -- Daniel Mietchen - WiR/OS (talk) 09:04, 28 June 2013 (UTC)

ISCB Wikipedia Computational Biology article competition 2013

I'm pleased to announce that we are going to run the ISCB Computational Biology article competition in 2013. The competition supported by the International Society for Computational Biology is designed to help improve the quality of articles in the area of Computational Biology. There will be three monetary prizes awarded for the most improved articles. Please pass the announcement around to anyone you think may be interested in entering. The competition is open to all students and trainees. Further details will be posted in the next few days. Alexbateman (talk) 09:04, 20 July 2013 (UTC)

You can find out more about the competition here: http://en.wikipedia.org/wiki/Wikipedia:WikiProject_Computational_Biology/ISCB_competition_announcement_2013 Alexbateman (talk) 15:53, 5 August 2013 (UTC)

I am also pleased to announce the winners of the 2012 competition were:

* 1st Prize Estevezj for his improvements for the Genomics article.

* 2nd Prize Jebus989 for his contribution to the European Nucleotide Archive article.

* 3rd Prize LuisPedroCoelho for his contribution to the Bioimage informatics article.

As chair of the judging panel I'd like to thank all the other entrants for their contributions.Alexbateman (talk) 16:02, 5 August 2013 (UTC)

How WikiProject Computational Biology has grown over time

I was just looking at some historical data showing the number of articles at each quality level in our Wikiproject. Basically I have a screengrab of the articles by quality and importance from 2011, 2012 and 2013.

Class	17th July 2011	14th July 2012	21st August 2013
FA	1	1	2
GA	1	3	6
B	74	92	95
C	54	69	73
Start	380	444	472
Stub	382	461	464
List	30	32	35
Total	922	1102	1147

For the best classes of article, FA and GA we have consistently been doubling the quantity each year. So we need to get 8 more FA and GA articles in the coming year to keep this up :-) Alexbateman (talk) 15:01, 22 August 2013 (UTC)

New Article Request - Variant Calling and Genotyping

Hi, I am looking to create a new article on Variant calling and genotyping for the computational biology wiki project and would like to confirm entry for this article with ISCB?

Vongap (talk) 03:48, 27 September 2013 (UTC)

Hi Vongap. There are several articles in Wikipedia that already exist such as SNP genotyping and Genotyping. But those are not really in scope of computational biology directly. I cannot see anything about Variant calling (genetics) so that could be a new article. I would not include the word genotyping in the article title though. One user is creating a new article Software for identifying structural variation. You could consider creating a new article for Software for identifying SNP variation. Thanks for your contributions. Alexbateman (talk) 07:23, 3 October 2013 (UTC)

With regard to variant calling, we have Copy number analysis which is a short article that could be good for expansion. Structural variation has a software section with programs for structural variant calling. --Mark viking (talk) 04:39, 10 October 2013 (UTC)

Hi, I am working with Vongap in this competition. We are wanting to write about the detection of single nucleotide variations from next-generation sequencing data. I have proposed the title of "SNV detection from NGS data" in the competition entries page for this article. Would this be an appropriate name for such an article? (To get a better idea of what we are looking at creating, check out my sandbox page, which contains a partially completed skeleton for this article). Benno89 (talk) 12:38, 16 October 2013 (UTC)

New Article Request - SBOL

Hi, I am looking to create a new article on the Synthetic Biology Open Language standard for the computational biology wiki project and would like to confirm entry for this article with ISCB? Badgeriger (talk) 04:31, 10 October 2013 (UTC) Actually, never mind. I have found another article to work on Badgeriger (talk) 04:32, 17 October 2013 (UTC)

NCBI traffic data

If you have ideas or suggestions as to which data NCBI should make available about traffic they get from Wikimedia servers, please list them here. Thanks! -- Daniel Mietchen (talk) 21:21, 25 October 2013 (UTC)

Topic page on Flow cytometry bioinformatics

The article has now been published in PLOS CB and transferred to Flow cytometry bioinformatics. -- Daniel Mietchen (talk) 16:34, 9 December 2013 (UTC)

Archived a few threads

I've archived some inactive threads to subsections which were notifications about discussions that have since been closed. — Cirt (talk) 19:20, 8 February 2014 (UTC)

HARMONY

As part of the HARMONY 2014 hackathon, we hope to create and improve articles under the COMBINE/HARMONY umbrella. This involves creating stubs for any missing articles, and improving existing articles to B class. Please add to and amend the following list:

• BioPAX (start)
• SBGN (start)
• SBML (B)
• SED-ML (does not exist)
• CellML (?)
• MIRIAM (start)
• SBO (start)
• KiSAO (does not exist)
• BioModels.net (BioModels Database: start, BioModels.net: does not exist)
• TEDDY (does not exist)

(article quality on 23 Apr 14 in brackets)

U+003F^? 09:08, 23 April 2014 (UTC)

Royal Society journals - subscription offer for one year

I'm delighted to say that the Royal Society, the UK’s National Academy for science, is offering 24 Wikipedians free access for one year to its prestigious range of scientific journals. Please note that much of the content of these journals is already freely available online, the details varying slightly between the journals – see the Royal Society Publishing webpages. For the purposes of this offer the Royal Society's journals are divided into 3 groups: Biological sciences, Physical sciences and history of science. For full details and signing-up, please see the applications page. Initial applications will close on 25 May 2014, but later applications will go on the waiting list. Wiki at Royal Society John (talk) 02:56, 29 April 2014 (UTC)

Leaflet For Wikiproject Computational Biology At Wikimania 2014

Hi all,

My name is Adi Khajuria and I am helping out with Wikimania 2014 in London.

One of our initiatives is to create leaflets to increase the discoverability of various wikimedia projects, and showcase the breadth of activity within wikimedia. Any kind of project can have a physical paper leaflet designed - for free - as a tool to help recruit new contributors. These leaflets will be printed at Wikimania 2014, and the designs can be re-used in the future at other events and locations.

This is particularly aimed at highlighting less discoverable but successful projects, e.g:

• Active Wikiprojects: Wikiproject Medicine, WikiProject Video Games, Wikiproject Film

• Tech projects/Tools, which may be looking for either users or developers.

• Less known major projects: Wikinews, Wikidata, Wikivoyage, etc.

• Wiki Loves Parliaments, Wiki Loves Monuments, Wiki Loves ____

• Wikimedia thematic organisations, Wikiwomen’s Collaborative, The Signpost

For more information or to sign up for one for your project, go to:
Project leaflets
Adikhajuria (talk) 16:50, 13 June 2014 (UTC)

Redesign of landing page

Our landing page looked quite bare and boring so I've made some changes:

• Now has a body / sidebar design, modelled on WP:MCB. I think this looks nicer but also will inevitably sometimes cause spacing issues on smaller screens or low-res displays. It's done with simple Wikimarkup rather than html divs etc. to minimise issues.
• Includes panels about PLOS topic pages and the ISCB competition, while these are a little unusual for a WikiProject and mostly down to a few individuals rather than specifically the WikiProject, I still think it's a good idea to showcase them. Remove if you disagree.
• Some reordering/tweaking of stuff, participants now scroll within a div rather than take up lots of space.

I've also made some changes to the text which would benefit from further editing. I think it looks a bit nicer and has some more useful info now, if you disagree by all means revert and/or discuss! benmoore 00:52, 15 July 2014 (UTC)

Thoughts on Template:Bioinformatics?

I've just come across Template:Bioinformatics, which seems pretty sparse and only used in ~25 articles - not sure how useful this is, though. Is it worth thinking about a Bioinformatics/Compbio template that could be used more widely amongst relevant articles? Or having several, e.g. Bioinformatics institutions, Bioinformatics people, etc? --Amkilpatrick (talk) 12:24, 25 July 2014 (UTC)

Stub contest next month

May be of interest: Next month there's a stub contest awarding prizes for editors who expand the most stubs, also considers the oldest stubs, most visible, funniest etc. This WikiProject currently has 128 articles tagged with the stub template, as well as 448 currently assessed as such (though some ratings are likely inaccurate) — would be great to chisel away at some of these! Amazon voucher prizes are up for grabs too. benmoore 15:18, 15 August 2014 (UTC)

Sounds good - I would guess the number of WP:CompBio stubs is closer to 448 than 128 so it would be good to make some impact on that (unfortunately it seems like the stub template is not linked with the assessments). Just a couple of thoughts: Are there any tools for listing articles within a wikiproject/category by age/length? A quick google didn't bring up anything obvious. Also, I wonder if the contest could be linked with the ISCB competition in some way? Amkilpatrick (talk) 08:20, 16 August 2014 (UTC)

You can probably do the search with CatScan. Maybe a plan B for if other language / multimedia competitions don't work out would be something like this, i.e. points-based and awarding for quantity rather than quality of a specific article. benmoore 11:58, 18 August 2014 (UTC)

Hi. I think that I probably did a lot of the assessments for WP:CompBio. I didn't think to add the stub template as I was going. Alexbateman (talk) 11:50, 1 September 2014 (UTC)

Does WP:CompBio have specific criteria for assessing articles within its scope? Alistairirvine (talk) 18:46, 1 September 2014 (UTC)

Alistair, I don't think WP:CompBio has any specific criteria for assessment - WP:Quality is useful for assessing quality, importance is a bit trickier, though. If you've a particular article/articles in mind, someone on the talk page should be able to help out with assessing. Hope that helps, Amkilpatrick (talk) 09:07, 3 September 2014 (UTC)

Claiming new articles for ISCB competition 2014

Hi there, I would like to participate in the ISCB competition 2014. It is stated in the competition page that "If you plan to start a new article, please contact WikiProject Computational Biology to make sure the article would be considered within the scope of the project". In this regard, may I start the article "Gene co-expression networks"?

Smh.oloomi (talk) 13:00, 17 August 2014 (UTC)

(Pinging judges @Alexbateman and Daniel Mietchen should they wish to comment.) I can confirm that an article on gene co-expression networks would fall within the scope of WikiProject Computational Biology and as such is acceptable as a competition entry. benmoore 11:49, 18 August 2014 (UTC)

Such an article would be within scope. Its worth seeing what related articles in exist in Wikipedia already. For example, Weighted correlation network analysis is quite related and you may consider whether you might want to improve the existing articles. Or perhaps you may wish to work on both :) Alexbateman (talk) 07:26, 31 August 2014 (UTC)

Hi, I am wanting to create a new article for the ISCB competition 2014, we are wanting to create the article on "Epigenome-wide association studies". Is this within scope of the project? (Taarguss (talk) 06:53, 5 September 2014 (UTC))

Yes, such an article would be in scope for the WikiProject, as per GWAS. Notability is an important consideration with new articles but in this case there appears to be sufficient sources available to establish EWAS as a notable approach and one worthy of inclusion in the encyclopaedia. benmoore 11:27, 11 September 2014 (UTC)

Some new users turning an article into a textbook under Wikipedia:WikiProject Computational Biology/ISCB competition entries 2014 ‎

I've been watching Pharmacogenomics get developed into what looks to me like a textbook or manual, which would be a violation of WP:NOTHOWTO. Whoever is guiding the students (? not sure they are, but they are WP:SPA for sure and have signed up under Wikipedia:WikiProject Computational Biology/ISCB competition entries 2014 ‎) should consider stepping in... Jytdog (talk) 09:15, 12 September 2014 (UTC)

Topic-page on multi-state modeling of biomolecules

A PLOS Computational Biology Topic Page on Multi-state modeling of biomolecules has now received peer reviews after revision. Comments are still welcome, especially on matters of style. -- Daniel Mietchen (talk) 09:46, 15 April 2014 (UTC)

The article is now live at Multi-state modeling of biomolecules. -- Daniel Mietchen (talk) 01:43, 28 September 2014 (UTC)

ISMB article GA nomination

I've nominated the ISMB article for Good article status - hopefully it shouldn't take too much further editing to upgrade it from B-class. I'd suggest the other B-class ISMB Wikipedia Competition award winning articles could also be good candidates for nominating:

• Genomics
• Point accepted mutation
• SNV calling from NGS data

Also,

• Michaelis–Menten kinetics,

which was nominated in 2011, but eventually not given GA status. --Amkilpatrick (talk) 13:04, 21 July 2014 (UTC)

Pinging @Estevezj: are you interested in nominating Genomics? If so I'd be up for reviewing and it looks great from a distance. Else if you don't have the time I could tweak and nominate — would be a nice article for the WikiProject to get to GA! benmoore 14:28, 21 July 2014 (UTC)

I think that's a good idea. As an editor, I've been much less active this year, so it'd be nice to do some work. The assembly section is a bit thinner than I'd like before submitting the nomination. I'll take a look at it this weekend and ping you once I've nominated the article. — James Estevez (talk) 22:18, 23 July 2014 (UTC)

Cool sounds good to me, no pressure of course. Cheers, benmoore 10:28, 24 July 2014 (UTC)

Update: following review, Intelligent Systems for Molecular Biology is now a Good Article! --Amkilpatrick (talk) 16:55, 30 September 2014 (UTC)

Comment on the WikiProject X proposal

Hello there! As you may already know, most WikiProjects here on Wikipedia struggle to stay active after they've been founded. I believe there is a lot of potential for WikiProjects to facilitate collaboration across subject areas, so I have submitted a grant proposal with the Wikimedia Foundation for the "WikiProject X" project. WikiProject X will study what makes WikiProjects succeed in retaining editors and then design a prototype WikiProject system that will recruit contributors to WikiProjects and help them run effectively. Please review the proposal here and leave feedback. If you have any questions, you can ask on the proposal page or leave a message on my talk page. Thank you for your time! (Also, sorry about the posting mistake earlier. If someone already moved my message to the talk page, feel free to remove this posting.) Harej (talk) 22:47, 1 October 2014 (UTC)

Topic Page on Inferring horizontal gene transfer

Reviews have now come in for the Topic Page on Inferring horizontal gene transfer. Comments still welcome. -- Daniel Mietchen (talk) 11:43, 2 October 2014 (UTC)

Topic Page on Ancestral reconstruction

The Topic Page on Ancestral reconstruction has been reviewed. Comments are still welcome, especially since the WP article Ancestral reconstruction has developed quite a bit since the drafting of the Topic Page started. -- Daniel Mietchen (talk) 11:49, 2 October 2014 (UTC)

Expert attention

This is a notice about Category:Computational Biology articles needing expert attention, which might be of interest to your WikiProject. It will take a while before the category is populated. Iceblock (talk) 16:19, 28 October 2014 (UTC)

Pageview stats

After a recent request, I added WikiProject Computational Biology to the list of projects to compile monthly pageview stats for. The data is the same used by http://stats.grok.se/en/ but the program is different, and includes the aggregate views from all redirects to each page. The stats are at Wikipedia:WikiProject Computational Biology/Popular pages.

The page will be updated monthly with new data. The edits aren't marked as bot edits, so they will show up in watchlists. You can view more results, request a new project be added to the list, or request a configuration change for this project using the Tool Labs tool. If you have any comments or suggestions, please let me know. Thanks! Mr.Z-man 01:28, 2 November 2014 (UTC)

Thanks for this, very cool! benmoore 08:40, 2 November 2014 (UTC)

Late to this, this is pretty interesting, the assessment and importance ratings are a good starting point for identifying where the WikiProject should be making improvements. Ben Moore, Daniel Mietchen - maybe worth mentioning when the curriculum project restarts? Amkilpatrick (talk) 04:17, 5 December 2014 (UTC)

Thanks! Just added an item on this to the upcoming Tool testing report. Textbits welcome. -- Daniel Mietchen (talk) 04:22, 5 December 2014 (UTC)

What do you mean by the "curriculum project"? U+003F^? 08:25, 5 December 2014 (UTC)

It's an ISCB taskforce for refining their draft bioinformatics curriculum guidelines, seems to be on hold at the moment, though. Amkilpatrick (talk) 16:28, 5 December 2014 (UTC)

Launch of WikiProject Wikidata for research

Hi, this is to let you know that we've launched WikiProject Wikidata for research in order to stimulate a closer interaction between Wikidata and research, both on a technical and a community level. As a first activity, we are drafting a research proposal on the matter (cf. blog post). Your thoughts on and contributions to that would be most welcome! Thanks, -- Daniel Mietchen (talk) 02:15, 9 December 2014 (UTC)

WikiProject X is live!

Hello everyone!

You may have received a message from me earlier asking you to comment on my WikiProject X proposal. The good news is that WikiProject X is now live! In our first phase, we are focusing on research. At this time, we are looking for people to share their experiences with WikiProjects: good, bad, or neutral. We are also looking for WikiProjects that may be interested in trying out new tools and layouts that will make participating easier and projects easier to maintain. If you or your WikiProject are interested, check us out! Note that this is an opt-in program; no WikiProject will be required to change anything against its wishes. Please let me know if you have any questions. Thank you!

Note: To receive additional notifications about WikiProject X on this talk page, please add this page to Wikipedia:WikiProject X/Newsletter. Otherwise, this will be the last notification sent about WikiProject X.

Harej (talk) 16:57, 14 January 2015 (UTC)