Wikipedia talk:WikiProject Molecular and Cellular Biology/Archive 2

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Archive 1 Archive 2 Archive 3

Contents

comments on new PDB galleries on gene pages

Any comments/suggestions for the PDB gallery prototype on ITK (gene)? If/when we get something with broad consensus, we can roll this out for all gene pages with corresponding protein structures... Cheers, AndrewGNF (talk) 20:08, 25 January 2009 (UTC)

Looks great! Of course, some upper limit needs to be placed on the number of structures displayed per article (~10?). If the number of available structures exceeds this limit, ideally the structures selected should be:
  • most informative (i.e., largest fragments of the protein, include biologically relevant co-factors, endogenous ligands, highest resolution, etc.) and
  • maximally diverse (e.g., making sure that at least one structure from each of the available domains for multi domain proteins is included)
but it is probably not possible to automate this. Lacking any automatic mechanism, if all the structures EMBL-EBI are uploaded into Wikipedia, then editors could manually change the selection if needed. Boghog2 (talk) 22:37, 25 January 2009 (UTC)
Yes, I should have mentioned that this is part of a parallel project to load images for all PDB files into wikicommons. I'm very interested to hear how people think we should handle gene for which there are many structures (e.g., Cyclin-dependent kinase 2). Perhaps we should embed the gallery in one of those javascript show/hide bars? AndrewGNF (talk) 06:16, 26 January 2009 (UTC)
I hadn't thought about javascript show/hide bars. That would be an elegant way of handling the problem of band width and screen real estate. However this doesn't address the more fundamental issue of what the purpose of these graphics is. The first figure added has very high value, if for no other reason to add eye candy to entice the viewer to read the rest of the article. In addition, one representative figure gives a quick impression of the tertiary structure of the protein (i.e., All-α proteins vs All-β proteins vs Α/β proteins, etc.). Furthermore displaying only one structure can be very misleading in the case of multi-domain structures where each of the structures may only correspond to one domain and not contain the entire protein. On the other end of the spectrum, there are certain drug targets (e.g., PPAR-γ) for which there are close to 100 structures in the PDB (please note that the list of PDB structures in the PPAR-γ article is a small fraction of what is currently available), but the overall tertiary structure is almost unchanged. There are differences in the ligand binding cavity, but these differences are not obvious when looking at static images of the entire PPAR-γ ligand binding domain. In the case of PPAR-γ, I would argue that showing 3dzy (entire structure), one of the DNA binding domain structures, and one of the ligand binding domain structures would be sufficient. Additional structures would add very little extra. Selecting the appropriate structures would be extremely difficult if not impossible to automate. Hence I think the best solution would be to place an upper limit on the number of figures the bot adds and leave it to human editors to prune, expand, or alter the selection as appropriate. Cheers. Boghog2 (talk) 20:00, 26 January 2009 (UTC)
I like it, let's set an upper limit (say five?) and let human editors expand/replace as necessary. As a default selection, how about we choose the five longest sequences? (I think we can easily get this...) Unless there are any structural biologists in the room who have a better idea of how to define the criteria for "most useful"? AndrewGNF (talk) 22:19, 26 January 2009 (UTC)
Five as an upper limit sounds reasonable. However instead of choosing the five longest sequences, it might be better to choose the longest, the shortest, and several in between. In the case of PPAR-γ, choosing the five longest would select three holo structures, two ligand binding domain (LDB) structures, and no DNA binding domain (DBD) structures. Using a sequence length spread would increase both the diversity of structures displayed and the probability that structures representing all of the domains were displayed (e.g., holo + LBD + DBD). I noticed that you included the SCOP classification with each of the structures. Perhaps this could be parsed in order to make sure that each of the available domains were covered, although this may be misleading in the case of structures which are complexes of two or more proteins. Does the procedure used to select the SCOP classification insure that the classification is based on the protein of interest and not other proteins that may be co-crystallized with the target protein? Ditto for the calculation of the sequence length. Boghog2 (talk) 22:55, 26 January 2009 (UTC)
I agree with Boghog2 on picking a diversity of domains if it is possible to automate that. I also wondered, purely as an asthetic thing, whether the label under each image may include the protein/domain description rather than just a PDB accession number? ~ Ciar ~ (Talk to me!) 23:46, 26 January 2009 (UTC)
If some structural biologist can propose a reasonable way to pick diverse examples, we can work on implementing it. But, this may be a difficult enough problem to require human intelligence. On the label issue, I'm happy to label it with whatever field we decide on. The challenge is figuring out which one, as most relevant fields are quite long. Check out [1] or [2] (and links), for example. Do you see a field you think would be appropriate? BTW, anyone is free to play around with ITK (gene), which will be the prototype for our implementation... Cheers, AndrewGNF (talk) 02:10, 27 January 2009 (UTC)
H'mmm, just looking at these 2 examples, what about (under the PDB header link) the line beginning
"COMPND 4 FRAGMENT:""
I don't know if this rule will hold up in all the PDB files, but maybe the text following "FRAGMENT:" could be grabbed? The actual protein name won't be needed since the entire page is about one protein. What do you think? ~ Ciar ~ (Talk to me!) 02:47, 27 January 2009 (UTC)
Sure, that seems like a pretty good idea. Just heading out now, but I'll try to mock that up tomorrow... Cheers, AndrewGNF (talk) 03:00, 27 January 2009 (UTC)
My preference would be to use the PDB TITLE field for the figure caption. The title field contains other potential useful information (e.g., experimental method) and also information about the domain (although less detailed). A complication with the FRAGMENT field is how to handle heteromultimeric structures such as PDB 3dzy. In this particular example, there are two fragment fields which are difficult to interpret without also looking at the corresponding MOLECULE fields. For this structure, one would need some how parse and combine four different fields (two fragment and two molecule fields). It would be much simpler to use the single title field.
I have taken the liberty to add the PDB title fields to the figure caption in the ITK (gene) article. How does this look? Cheers. Boghog2 (talk) 15:18, 27 January 2009 (UTC)
I was worried that the title field would be too long, but I actually like how it looks now. Multi-line caption doesn't bother me at all, and it gives a bit more context that might bring the gallery beyond eye candy. Nice! Do you all think we should still look at the hide/show bar, or not? AndrewGNF (talk) 16:58, 27 January 2009 (UTC)
Agree, looks good, and likely more consistent than the fragment thing! ~ Ciar ~ (Talk to me!) 21:01, 27 January 2009 (UTC)

Capsaicin/vanilloid/TRPV mess

There needs to be a single article on this family, and it needs to give the (former) synonyms. Also it should start with mentioning its discovery, i.e. PMID 9349813. If nobody else volunteers I'll do it at some point. Xasodfuih (talk) 19:54, 27 January 2009 (UTC)

Vanilloids are actually a class of compounds which contain a vanillyl group ([3]), such as capsaicin and olvanil; I really don't know why the vanilloid page was about TRPVs and not their ligands. As for the merge, I don't think there's anything on the Vanilloid Receptor article that isn't already in the TRPV article. I'd propose just making a redirect from Vanilloid receptor to TRPV, and from Vanilloid to Vanillyl. This seems fairly non-controversial - thoughts? St3vo (talk) 20:20, 27 January 2009 (UTC)
Sounds good. I think the vanillyl/vanilloids article could be easily expanded for a DYK. I'm working on something else right now. I'll add the historical info to the TRPV and TRPV1 articles later; TRPV also has DYK potential. Xasodfuih (talk) 20:35, 27 January 2009 (UTC)

more comments on proposed gene stub enhancements

Hello, I've prototyped two more gene stub enhancements for comment. The first is shown here, which adds a section for well-established protein interactions. Adding this systematically will help our underlinking problem on gene pages. Second, I've added an additional optional parameter to add the protein domain structure to the infobox (diff). Both enhancements were previously requested from the community (as noted on our ideas page). Feedback on either/both is welcome (and feel free to tweak the pages yourself). Cheers, AndrewGNF (talk) 02:06, 29 January 2009 (UTC)

Both additions look great and add useful information! My only suggestion is perhaps the domain diagram should be made collapsable. These protein boxes are getting very long. Cheers. Boghog2 (talk) 20:17, 29 January 2009 (UTC)
Good suggestion. I'm knee deep in grant writing at the moment, but I'll try to make that change in the next week or so. (BTW, is it just me, or does firefox not render the Gene Ontology section as collapsible anymore?) AndrewGNF (talk) 20:42, 29 January 2009 (UTC)
Obviously no rush on the collapsible protein domain graphic suggestion. More importantly, best of luck on your grant application! (BTW, the Gene Ontology section is still collapsible using FF or Safari on my computer.) Boghog2 (talk) 23:41, 29 January 2009 (UTC)

Ankyrin infoboxes

We have 3 infoboxes on that page; can someone replace them with a family infobox? That should prevent further drive-by merge tagging, which I've just removed. Xasodfuih (talk) 01:25, 30 January 2009 (UTC)

Unfortunately I don't think this is possible since there is no Pfam classification specifically for the ankyrin protein family. There is a Pfam classification (Pfam PF00023) for the Ankyrin repeat, but since many proteins besides the ankyrin family contain the ankyrin repeat (TRPV channels for example), it would be a mistake to add this Pfam box to the ankyrin article. Finally I do not see any problem with leaving the three protein boxes in the ankyrin article as is. Boghog2 (talk) 08:54, 30 January 2009 (UTC)

Milestone Announcements

Announcements
  • All WikiProjects are invited to have their "milestone-reached" announcements automatically placed onto Wikipedia's announcements page.
  • Milestones could include the number of FAs, GAs or articles covered by the project.
  • No work need be done by the project themselves; they just need to provide some details when they sign up. A bot will do all of the hard work.

I thought this WikiProject might be interested. Ping me with any specific queries or leave them on the page linked to above. Thanks! - Jarry1250 (t, c) 22:08, 1 February 2009 (UTC)

Chemical warfare FAR

User:Xasodfuih has nominated Chemical warfare for a featured article review here. Please join the discussion on whether this article meets featured article criteria. Articles are typically reviewed for two weeks. If substantial concerns are not addressed during the review period, the article will be moved to the Featured Article Removal Candidates list for a further period, where editors may declare "Keep" or "Remove" the article's featured status. The instructions for the review process are here. SandyGeorgia (Talk) 13:21, 3 February 2009 (UTC)

C. elegans proteins/genes

Looking at OSM-9, it seems we don't have categories for these. Am I right, and should they be created? Xasodfuih (talk) 08:16, 5 February 2009 (UTC)

Lewy body

I am not sure which project should take this... (Nothing in talk page) I am going to add it to the medicine project with a low rating... I suppose this project would also be interested... --Garrondo (talk) 11:17, 11 February 2009 (UTC)

Contradictory info about the Umami receptor(s) and ligands

Various pages on the wiki have contradictory info on which is the receptor for the umami (L-glutamate) taste. The confusion stems from the fact that circa 2000-2002 at least two candidates were identified by the same group: a mGluR4 splice variant (PMID 10649565), and a T1R1+3 heteromer (PMID 11894099). Not making the job any easier, a mGluR1 variant has also been proposed in 2005 (PMID 15738140). I think that a separate article is probably needed to keep track of these hypotheses and just link all the other pages to it. Any other ideas on how to sort out this mess? Xasodfuih (talk) 21:15, 11 February 2009 (UTC)

N.B.: I've managed to find a recent review (PMID 18827337) that suggests multiple pathways based on KO models. I think the article on umami is the best place to discuss this. Xasodfuih (talk) 21:28, 11 February 2009 (UTC)

Like the above wasn't confusing enough there is more contradictory info about the role of:

  • aspartate— some papers, especially those about the T1R1+3 pathway, say that it also elicits umami taste (in humans), some don't mention it, and one explicitly says that it doesn't (PMID 12438213).
  • the role of 5'-ribonucleotides guanosine monophosphate (GMP) and inosine monophosphate (IMP) and salts thereof. While there is agreement on the synergistic effect of these with glutamate (mechanism for that recently proposed in [4]), some sources indicate that these cause umami taste by themselves, but others don't say that.

If somebody else feels like taking a look at this stuff... Xasodfuih (talk) 14:42, 12 February 2009 (UTC)

Looking at this plot, it appears that aspartate elicits a significant response only in the presence of IMP or GMP. That may explain some of the confusion. Xasodfuih (talk) 15:01, 12 February 2009 (UTC)

Phagocyte

Hi, has anyone got the time and inclination to do a peer review? Wikipedia:Peer_review/Phagocyte/archive2. Graham. Graham Colm Talk 20:38, 14 February 2009 (UTC)

Welcome template

Hi everybody, I made a MCB welcome template based on the Wikiproject Medicine example. Any tweaks or suggestions are welcome. Tim Vickers (talk) 20:24, 16 February 2009 (UTC)

Tim, this is very pretty indeed—and I like the idea. But I don't think "MCBGreeting," is needed and looks a little odd. Graham. Graham Colm Talk 12:04, 17 February 2009 (UTC)

"MCBgreeting" is part of the template that takes the name of the user and customises the text. If I put the template on your talkpage it would say "GrahamColm" instead of "MCBgreeting". Tim Vickers (talk) 16:58, 17 February 2009 (UTC)
I've tested it here. Tim Vickers (talk) 17:00, 17 February 2009 (UTC)
Sorry for being thick. It looks great, can I keep it :-) Graham. Graham Colm Talk 17:11, 17 February 2009 (UTC)
Of course, its a good point though, I'll add it to the documentation. Tim Vickers (talk) 17:20, 17 February 2009 (UTC)

Non-human aspects

I've found that - on articles where your project is mentioned together with the medicine project - there often seems to be a lack of consideration of non-humans. Estrogen is the one where I stumbled over it this time, but I've had this before in other cases. The medicine bunch seems to be good enough at covering topics concerning humans. So it falls to you to keep an eye on having a section in the articles applicable (and linkable) for non-humans. Thks. 76.97.245.5 (talk) 23:37, 16 February 2009 (UTC)

There's a lack of editors to do all that, so please be WP:BOLD. Xasodfuih (talk) 00:28, 17 February 2009 (UTC)

Invitation template

We also now have an invitation template Template:MCBInvitation, which I'd encourage everybody to add to the userpage of editors who are adding useful content to our articles. Tim Vickers (talk) 20:57, 17 February 2009 (UTC)

Mitochondrial Eve

Mitochondrial Eve has been nominated for a good article reassessment. Articles are typically reviewed for one week. Please leave your comments and help us to return the article to good article quality. If concerns are not addressed during the review period, the good article status will be removed from the article. Reviewers' concerns are here. Xasodfuih (talk) 14:42, 18 February 2009 (UTC)

Notification of Science FAC symposium

Wikipedia:Article alerts

I was reading this and thought this might be very useful, so I subscribed us to this service. Tim Vickers (talk) 03:18, 25 February 2009 (UTC)

I think it will be created automatically, according to this --hroest 07:44, 25 February 2009 (UTC)
It is up at the top of this page now (although it is still a redlink). Please add it to your watchlists. Tim Vickers (talk) 17:46, 25 February 2009 (UTC)

Anthropocentrism at Fetus, embryo and similar articles?

There's a discussion at WT:BIOLOGY on whether it's appropriate or not for articles like fetus, prenatal development or embryo to be exclusively about human aspects and to just give a hat-tip to the general articles that presumably nobody reads or writes given how bad they look. I'm posting this notice here because WP:BIOLOGY has less than a handful of active editors; please join the discussion there. Xasodfuih (talk) 10:36, 27 February 2009 (UTC)

Coordinators' working group

Hi! I'd like to draw your attention to the new WikiProject coordinators' working group, an effort to bring both official and unofficial WikiProject coordinators together so that the projects can more easily develop consensus and collaborate. This group has been created after discussion regarding possible changes to the A-Class review system, and that may be one of the first things discussed by interested coordinators.

All designated project coordinators are invited to join this working group. If your project hasn't formally designated any editors as coordinators, but you are someone who regularly deals with coordination tasks in the project, please feel free to join as well. — Delievered by §hepBot (Disable) on behalf of the WikiProject coordinators' working group at 06:02, 28 February 2009 (UTC)

Oscillating gene

I just created a new stub article titled oscillating gene. Happy editing! Michael Hardy (talk) 18:57, 11 March 2009 (UTC)

One bit of editing that's easy to neglect is links to the new article from appropriate other articles, so that it won't be orphaned. So far there are only two (not counting redirects, of which I created seven, and also not counting the link from this present WikiProject discussion page). So if anyone knows of other articles that should link to the new one, please add those links. Michael Hardy (talk) 20:55, 11 March 2009 (UTC)

L-form cells

This is a new one for me: bacteria without cells walls doi:10.1038/nature07742. Am I searching wrong, or do we not have an article on this? And if we have no article, is the topic of enough significance to warrant one?[5] I haven't totally mangled a science topic yet, but I could try for this one. ;) Franamax (talk) 21:50, 14 March 2009 (UTC)

Looks a good topic, I'd recommend L-form bacteria as a title. Watch out for crank material, there seems to be a few fringe theories surrounding this topic (eg Trevor Marshall's "Marshall Protocol"). Tim Vickers (talk) 22:28, 14 March 2009 (UTC)

Peer review for 'Homologous recombination'

If anyone could give their input at the peer review for homologous recombination, I'd greatly appreciate it. Emw2012 (talk) 21:44, 20 March 2009 (UTC)

3 weeks of biomembrane madness

I have been recruited by a professor at the University of Florida to assist her graduate-level class to get GA level articles in the topic of their choice. Each of them gave a PowerPoint presentation primarily of visuals and oral explanations. The professor then asked them to translate their presentations into Wiki articles. They don't necessarily have a lot of time to nominate their articles for GA, so the instructor is going to assess their articles and grade them on how close they get to GA criteria. They are, however, urged to nominate their articles for GA even though they may not be in the class by the time it is reviewed.

I gave an hour-long presentation in their class today on the very basics of editing and Wikipedia. The class has a WikiProject here. Students should be choosing their articles today. They may need formatting assistance, particularly with sources. They should be completely responsible for content. The instructor is also requiring them to upload one public domain image. Any assistance anyone can give would be much appreciated. --Moni3 (talk) 23:48, 31 March 2009 (UTC)

Collaboration of the Month

This is now running again, our new collaboration of the month is gene expression. See you there! Tim Vickers (talk) 18:53, 1 April 2009 (UTC)

C.elegans

There are a few articles in this projects scope with the redirect C.elegans, is the organism Caenorhabditis elegans so well known it needs no introduction? cygnis insignis 07:59, 15 April 2009 (UTC)

Using figures from scientific papers

What is the policy with regard to using figures from scientific papers on wikipedia? I noticed that on carboxysome the images have been taken from papers and are licenced under the Creative Commons Attribution 3.0 Unported licence. I'd like to add similar images to acidocalcisome from the referenced paper - can I just copy it and use the same licence? Do I need permission from the paper's author? PS I've asked on the copyright questions page [6] but the answer wasn't much use. Thanks Smartse (talk) 21:47, 15 April 2009 (UTC)

You can't use the figures without the copyright holders releasing them into the public domain or under a Creative Commons licence. The exception is the public library of science journals, here you need to upload them under the journal's CC license and attribute the authors on the upload page, I do this by adding the citation and linking to the article. Tim Vickers (talk) 21:51, 15 April 2009 (UTC)
Great - that'll keep me busy!! Smartse (talk) 21:53, 15 April 2009 (UTC)
(edit conflict) You can't. Pictures need a Creative Commons licence / similar, and that means taking them from the Public library of science (PLoS) or BioMed Central. Nature Press uses copyright. Narayanese (talk) 21:55, 15 April 2009 (UTC)
Ah ok. Smartse (talk) 21:56, 15 April 2009 (UTC)
As a caution, Biomed Central may contains copyrighted articles, unfortunately free-access doesn't mean no copyrights. I have had a lot of success however in getting scientists to contribute images, this page gives you an persuasive argument - particularly in high profile articles. Tim Vickers (talk) 21:58, 15 April 2009 (UTC)
Interesting. I've been using this page for access stats. It produces different results to yours. I've also had success contacting authors directly. Eg. the EM figures on the Spliceosome page.--Paul (talk) 23:15, 15 April 2009 (UTC)

Help please

With influenza high in the popular press at the moment our article on Cytokine storm is now of high importance and visibility. Could some people from this project look this over and watchlist it? Tim Vickers (talk) 16:54, 29 April 2009 (UTC)

Combined gene and protein product articles

It has been proposed to merge the huntingtin protein into the Huntingtin gene article, they are intrinsically linked and would make more sense together but wandered if anyone had any comments. L∴V 11:11, 2 May 2009 (UTC)

I agree with you that these two article should be merged. As discussed here, I think there is a general consensus for the merger. Unless someone has a strong objection, I will go ahead and implement the merger. Cheers. Boghog2 (talk) 13:08, 2 May 2009 (UTC)

Society for Neuroscience

I noticed this page about the Society for Neuroscience undertaking to improve neuroscience-related articles on Wikipedia. The MCB and other WikiProjects might be able to help them — should we try to contact them? Proteins (talk) 20:53, 2 May 2009 (UTC)

There is a discussion on this subject over in Neuroscience L∴V 21:13, 5 May 2009 (UTC)

Ion channel

I found this on User:Adenosine's talk page:

I have made some simple picture for the ion channel for the polish Wikipedia. If you know somebody, who could translate this to english, you can take it and insert in your Ion channel. The link is: http://pl.wikipedia.org/wiki/Plik:Ion_channel.png This is only simple scheme, I hope - correct.
I have also made simple scheme, comparing the chemical and electric synapse, placed here: http://commons.wikimedia.org/wiki/File:Electr_and_chem_synapse.png?uselang=pl
Answers, in any, please put in my polish wiki discussion site: http://pl.wikipedia.org/wiki/Dyskusja_wikipedysty:Outslider (add new section: http://pl.wikipedia.org/w/index.php?title=Dyskusja_wikipedysty:Outslider&action=edit&section=new )
Outslider (talk) 14:41, 3 February 2009 (UTC)

Can anyone label the diagrams? Smartse (talk) 23:13, 10 May 2009 (UTC)

Gene encoding protein of unknown function on AfD

Deletion of recently created article C7orf30 is currently under discussion at AfD. Regards, Qwfp (talk) 14:18, 11 May 2009 (UTC)

Does your WikiProject care about talk pages of redirects?

Does your project care about what happens to the talk pages of articles that have been replaced with redirects? If so, please provide your input at User:Mikaey/Request for Input/ListasBot 3. Thanks, Matt (talk) 02:08, 12 May 2009 (UTC)

I don't think we do. Are there any MCB-tagged redirects you people are aware of? Tim Vickers (talk) 02:20, 12 May 2009 (UTC)
Not specifically, but they are just as prone to being wiped and replaced with a redirect as any other talk page under the scope of any other WikiProject. Matt (talk) 03:43, 12 May 2009 (UTC)

Vacuolation

I need a Wikipedia article about vacuolation; the closest I can find is Vacuole, which is about normal vacuoles. Abnormal vacuoles are a feature of certain metabolic diseases. Would someone here like to expand Vacuole, or start a new article, or ... ? --Una Smith (talk) 15:32, 12 May 2009 (UTC)

A new article would be a bad idea, a section in the existing vacuole article would probably be best. Tim Vickers (talk) 16:03, 12 May 2009 (UTC)
I agree, if you could improve the animal section of vacuole too, even better! Smartse (talk) 16:14, 12 May 2009 (UTC)
Okay, I'll see what I can do to expand Vacuole. --Una Smith (talk) 17:13, 12 May 2009 (UTC)

Mannosidase stubs

Here is a collection of stubs related to mannosidase, that could use some cleanup, expansion, and cross-referencing. An important primary consequence of alpha-mannosidase deficiency is vacuolation. --Una Smith (talk) 17:13, 12 May 2009 (UTC)

Proposal section "Possible merge of wikiproject cell signaling to this project as a taskforce"?

I made a proposal on the proposal section of this talk page here: [7] and I assume not many have had a look at it and/or don't mind either way. If anyone wants to comment, feel free to do so. Also see this [8]. I would be more than happy to do all the merging, I just want to make sure I am not going to annoy someone by doing it, or if anyone would think there would be no point to do so and leave everything as it is. Cheers!Calaka (talk) 04:09, 16 May 2009 (UTC)

In addition to the above, I think the same would apply for Wikipedia:Wikiproject Metabolic Pathways and Wikipedia:WikiProject RNA. Hence we can create something similar to the set up of WP:MED where they have a task force page linking all the task forces and the ability to suggest new task forces in the talk page. Hence this project would have 3 task forces to begin with and any new suggestiosns can be made there. I will post a little note on these 2 other projects as well. Calaka (talk) 03:45, 23 May 2009 (UTC)
In principle, I don't have a problem with this idea. I know WikiProject RNA hasn't been very active recently. In spite our pleas to the RNA community. However, I don't see the advantage of a task-force of MCB versus a daughter WikiProject of MCB. Can you give some further justification/motivation?--Paul (talk) 19:59, 23 May 2009 (UTC)
I would be happy to. Having said that, I will not get angry if there is no push for forming the above into task forces, it was just my oppinion of it being a better way to go. So some reasons I would suggest include:
  1. There will be only one talk page template and would reduce the amount of templates that are to go on one page. Example: Instead of Talk:Cytokine having 4 tags (one for WP:MED, one for WP:MCB, one for WP:Cell signaling and (well I think it should have) one for WP:metabolic pathways), it can just have two, the WP:MED one and the WP:MCB one where there can be an indication of the task forces associated. So the tag would look like this: {{WP:MCB|class=|importance=|cell-signaling=yes|metabolic-pathway=yes}}. This is allready done in many other wikiprojects such as the videogame wikiprojects, military history and of course WP:MED. Examples for each respectivelly: Talk:World_of_Warcraft, Talk:Battle_of_Iwo_Jima and Talk:Dermatology.
  2. There will be one list of participants. They can then select whether they want to be associated with that project or that one, instead of having to write their name each time they want to join a project. This leads on to point 3:
  3. There will be larger activity/discussion on the one talk page (i.e. this one right here) for an overall discussion about certain topics. I.e. if they wanted to talk about cytokines, they can bring up the discussion on this page, which will get the most attention and it applies to all things that they might be interested in. Having said that, there will be nothing stopping them from discussing this in their own task force talk page, but as I have noticed on WP:MED talk page, there tends to be the most viewership/discussion on the one main page. Leading on again from this is point 4:
  4. Users can watchlist only one talk page, instead of having to watchlist one for every wikiproject. So they can focus on this page to discuss, while they can check up on the others less frequently.
  5. In terms of organization/hierarchy, it would be better to have everything under one "umbrella" so to speak so everything comes out under the MCB link. I.e. I have personal trouble finding wikiprojects of a specific nature (e.g. I have trouble searching for devil may cry wikiproject, but wikiproject video games was very easy to find). In this same regard, having MCB as the parent which then directly links to the taskforces increases their exposure c.f. seperate wikiprojects where users might feel overwhelmed with joining other wikiprojects because they think they will be having too much to handle. In this way, it will seem that the projects while not appearing as LARGE, also seem more accessible to them.
  6. This in no way reduces the value of these wikiprojects. Just because they are classified as task forces, does not mean that they reduce their importance that they play in encouraging collaboration between users of a certain interest.
  7. Following on from step 3, the more users in one wikiproject would just be better in general. I will give an analogy: Imagine 5 very very large cities. They are extremelly large in area, but have a small population density. While they might be big in themselves, they are after all quiet due to not having as many people in them. Then think of Singapore. It too is a big city but it has an incredible amount of people in that space! So imagine they had their own little metaphorical talk page. Just by numbers alone, you can imagine/predict there would be more activity in the Singapore talk page than in the 5 individual cities individually or combined. More discussion would lead to more activity and more activity to hopefully more creation/collaboaration in improving the wikipedia articles of interest (in this case MCB type ones).
I had more thoughts, but at the moment they escape me. When I think of a few more I will add some here. If you want, feel free to look at this here: Template:WPMED_Navigation and here Wikipedia:WikiProject Medicine/Task forces which also states reasons on why they chose to go in the "task force" direction. I should have looked at that page first before I wrote all of the above hehe! To make things easier though, we wont be recreating the wheel, but will just take the ideas from the WP:MED people and follow their guidelines in going through this whole process.
At the end of the day, it is my hope that this process of wikiprojects-->taskforces will lead to more activity & hence more editing/working on these articles. Thanks and again, all comments are welcome. Calaka (talk) 04:09, 24 May 2009 (UTC)
I like this idea, mostly since it will make it easier for new editors trying to find an active talkpage to ask questions on. Tim Vickers (talk) 14:39, 24 May 2009 (UTC)
Makes sense to me - it looks stupid having loads of different wikiproject tags on talk pages. I agree that it would also help in aiding discussion on talk pages. (Correct me if I'm wrong) but this project isn't exactly busy at the moment - after all it's a sub project of biology really - so having another tier of projects below this doesn't make sense to me. Smartse (talk) 15:33, 24 May 2009 (UTC)
Glad to know you guys are for it. I will give it a few more days (perhaps until June first?) in case anyone else has any other comments to make and I will do incremental changes (i.e. I will move one wikiproject at a time, make sure it is moved correctly, then go over the next one after a few days, I guess there is no rush in this process). I guess this wikiproject might not be as active as it can be (or as it has been), but with time it should grow and with this addition of the additional task forces, it might lead to an increase in activity. Cheers! Calaka (talk) 11:38, 25 May 2009 (UTC)
Well actually, this project (MCB) seems really inactive to me too... sounds maybe weird for such a big project with so many articles and members. But I am trying to find some articles where several members of this project are working on, but I can't find anything. There might be much people that are working on articles on this project as individuals, but I can't find any group effort to join. Kasper90 (talk) 14:43, 26 May 2009 (UTC)
Very true, considering the thousands of articles tagged by this project. I suppose that when there is a need though, discussion/activity will occur here. Anyway, I am going to give one of these task forces a start now (will do one at a time), so if there are any last minute objections, speak now. :P Calaka (talk) 10:57, 30 May 2009 (UTC)
I have done a bit of the transferring over. A lot of the subpages still need to be moved though (anyone else is more than welcome to do it) since I wont be on Wikipedia for a while now. But hopefully it should all work out. Please see my contributions list if you want to double check to make sure everything is in order/nothing is missing. Calaka (talk) 13:29, 30 May 2009 (UTC)
  • Hi All! Just to let you know I think the metabolic pathways migration is a really good idea. The project as an independent project never really got going, by joining it to the MCB project it should help gather some interest in improving the huge number of articles related to metabolism. - Zephyris Talk 07:30, 31 May 2009 (UTC)

Enzyme induction and inhibition

This article is at AfD here. Enzymes aren't my forte - I'm sure someone here can add something to the discussion. Smartse (talk) 12:31, 27 May 2009 (UTC)

Membrane receptor

A project in a North Carolina university adopted membrane receptor, added a lot of valuable material and then abandoned it again. I have tried to put some Wikipedia touch to it and think it is now rather good. Would like to put it up for GAC, but realize that I am in deep waters here. Would someone be interested in a GAC cooperation where I promise to do the formal editing chores that turn up while this someone takes care of deeper subject matter problems? --Ettrig (talk) 10:52, 29 May 2009 (UTC)

I can help. The first thing I noticed is that the membrane receptor page has a red link to Category:Receptor tyrosine kinases, but other pages such as Receptor tyrosine kinase use Category:Tyrosine kinase receptors. According to my search of the NLM's PubMed data base, "receptor tyrosine kinase" is used more than "tyrosine kinase receptor". --JWSchmidt (talk) 04:33, 31 May 2009 (UTC)
I thought then that this article was close to being a Good Article. When looking further I found that much of it belonged to other articles. I have moved material to Drug design and G protein coupled receptor. So now it is probably too short to put up as GA candidate. --Ettrig (talk) 05:58, 31 May 2009 (UTC)

Administrators needed for updating Talk page TAG MCB

Could an administrator please allow for the addition of |Metabolism-pathways=yes|Metabolism-pathways-importance=| under the Template:WikiProject Molecular and Cellular Biology. See this as an example of how it is done for the WP:MED task forces: Template:WPMED. I will personally change the tag on the previously listed pages so when the update is added, the changes will appear automatically. Cheers.Calaka (talk) 11:39, 30 May 2009 (UTC)

Also to add: In addition to the above parameters, suitable shortcuts can be |mp=yes|mp-importance=|. Hence the above two can look like this within the MCB project template tag:

{{WPMCB|class=|importance=|Metabolism-pathways=yes|Metabolism-pathways-importance=|}} or {{WPMCB|class=|importance=|mp=yes|mp-importance=|}}. Cheers!Calaka (talk) 12:00, 30 May 2009 (UTC)

Aminoacid structure formulae

Hi, I've been browsing the amino acid articles lately, and I noticed the lewis formulae lack a consistent style. At least for those amino acids that allow it, I think it would be a good idea to implement some basic guidelines, like having all structural formulae horizontally aligned, with the amino group showing down and the carboxyl group showing left. This seems to be the tentative standard for most amino acids - take Cysteine or Glutamine for instance if you want to see what I mean. However there are some which do not yet abide to this rule, like say asparagine. Also some α–amino acids show the hydrogen atom bound to the α–carbon, which is redundant even with respect to isomery, since the position of the C-C bonds unmistakably indicates that of the C-H bond.

That being said, I find this would be a considerable improvement, and I would gladly take care of it myself, but I lack any knowledge of how to produce lewis formulae save for painstakingly drawing them out with the gimp :-/ —Preceding unsigned comment added by Chymæra (talkcontribs) 18:29, 30 May 2009 (UTC)

I agree with you but WP:Chemicals is perhaps a better place for this discussion. I have updated the graphic on the Cysteine page. Is this what you had in mind? One complication is that the space filling models would also need to be updated so that both the 2D and 3D structures are drawn in a consistent orientation. Cheers. Boghog2 (talk) 07:02, 31 May 2009 (UTC)

addition of PDB gallery to gene pages

I'd like to start moving forward with systematically adding a PDB gallery section to all gene pages with linked PDB structures. One example prototype is shown at ITK_(gene)#PDB_gallery. The only challenge I can see with this is how to handle genes for which there are very many PDB entries (e.g., Cyclin-dependent kinase 2). My top preference would be to modify {{Gallery}} to add a show/hide button beyond a certain number of images, but so far, no one has replied to the suggestion to add that functionality. If no one volunteers to make that change (it's beyond my technical expertise), then we'll just go ahead and only link nine PDB structures. Unless someone has a rational way to select them, I propose to just take a random set of nine structures. Hopefully individuals will adjust the selection for their favorite genes if different ones are more appropriate. Comments on this plan? Cheers, AndrewGNF (talk) 23:01, 5 June 2009 (UTC)

Maybe you can put large galleries inside a frame that has hide/show. --JWSchmidt (talk) 01:19, 6 June 2009 (UTC)
Nice! I was thinking it would be ideal if just the overflow images (beyond some set threshold) would be hidden/shown, but now that I see it, I think your solution is pretty good. In fact, maybe all galleries should be hidden by default... Other thoughts? AndrewGNF (talk) 16:08, 6 June 2009 (UTC)

More work required

I've just rescued NC ratio from Proposed Deletion. More work is required, though. Immediate concerns are that the article is still an orphan. But it also doesn't yet discuss the use in cancer diagnosis. Uncle G (talk) 11:20, 6 June 2009 (UTC)

Link to where deletion was proposed --JWSchmidt (talk) 16:40, 6 June 2009 (UTC)

Update on merger Metabolic pathways task force.

The merger is essentially complete (I thank the individuals who tidied up the process just recently). Everything is in order, except I am still waiting for an administrator to allow for the addition of the taskforce sign onto the MCB talk page tag. Next week I will begin organizing/preparing for the merger of the other daughter project. I am spacing out the mergers to give enough time/space for anyone and everyone to see this instead of jumping really quickly/rashly into the merging before anyone realized what just happened. Also the Wikipedia:WikiProject Molecular and Cellular Biology/Task forces might need a bit of work so if anyone is willing to have a look at that and fix it up (as I copied it from the WPMED area) so as to reflect the MCB project layout/guidelines, that would be appreciated. Kind regards.Calaka (talk) 03:33, 8 June 2009 (UTC)

Inter/intracellar signal transduction

Does anyone have any good techniques/suggestions/etc for outlining signal transduction outside or inside a cell without using cartoons/diagrams (i.e. some type of all-text approach)? ---kilbad (talk) 01:34, 11 June 2009 (UTC)

Relating gene pages by protein interactions

Since many gene pages were getting tagged with {{orphan}}, I thought a good way to better integrate these pages would be to create interwiki links based on protein interactions. With the help of Plindenbaum, we have two prototypes that we'd like feedback on. One is text-based (e.g., ITK_(gene)#Protein_interactions), and the other is table-based (e.g., GFER#Interactions). In both cases, the data are based on BioGRID, where we require at least two references or two methodologies to list an interaction. We'd like to create a similar section for all gene pages with high-quality interaction data. Any comments on which model is preferable, or how to further improve? Cheers, AndrewGNF (talk) 22:41, 25 June 2009 (UTC)

Great news! According to WP:EMBED, "most Wikipedia articles should consist of prose, and not just a list of links" and "a list style may be preferable to a long sequence within a sentence". I am assuming that the same argument applies to prose vs. tables. So I guess which is preferable depends on the number of interacting partners. For a small number of partners, (< ~ 8) prose is probably preferable whereas for longer lists a table or list is probably preferable. Another advantages of prose over a table is that the former is probably less intimidating and easier edit for new editors. Boghog2 (talk) 23:10, 25 June 2009 (UTC)
Good thoughts... I put up some possibly relevant stats at User:AndrewGNF/Interactions. Cheers, AndrewGNF (talk) 00:12, 26 June 2009 (UTC)

Pageview stats

After a recent request, I added WikiProject Molecular and Cellular 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 Molecular and Cellular 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. If you have any comments or suggestions, please let me know. Thanks! Mr.Z-man 20:31, 9 July 2009 (UTC)

Changes to popular pages lists

There are a few important changes to the popular pages system. A quick summary:

  • The "importance" ranking (for projects that use it) will be included in the lists along with assessment.
  • The default list size has been lowered to 500 entries (from 1000)
  • I've set up a project on the Toolserver for the popular pages - tools:~alexz/pop/.
    • This includes a page to view the results for projects, including the in-progress results from the current month. Currently this can only show the results from a single project in one month. Features to see multiple projects or multiple months may be added later.
    • This includes a new interface for making requests to add a new project to the list.
    • There is also a form to request a change to the configuration for a project. Currently the configurable options are the size of the on-wiki list and the project subpage used for the list.
  • The on-wiki list should be generated and posted in a more timely and consistent manner than before.
  • The data is now retained indefinitely.
  • The script used to generate the pages has changed. The output should be the same. Please report any apparent inconsistencies (see below).
  • Bugs and feature requests should be reported using the Toolserver's bug tracker for "alexz's tools" - [9]

-- Mr.Z-man 00:19, 12 July 2009 (UTC)

Organism groups ???

I notice Bacteria in the trophy case. It is not reasonable to consider each taxon a part of MCB. So how do we choose to include some of the taxa? Some have been especially important in MCB research. Sperm whale in studying the structure of hemoglobin, Humans because this is the subject of Medicine, Drosophila melanogaster for early chromosome studies etc. But I can't see why bacteria should be more central to MCB than animals or plants. Because they have only one cell each? Well isn't there more MCB when there are more cells? ... and bigger more complex cells? To summarize: What are the legitimate criteria for including a taxon article in MCB? --Ettrig (talk) 07:02, 12 July 2009 (UTC)

I see your point, but I suppose I'd argue that the article does dwell in detail on bacterial cellular biology and biochemistry, since this forms a larger proportion of their biology than multicellular organisms. Classifications are not exclusive, and Wiki articles can be maintained by several projects, see Talk:Bacteria for the complete list. Tim Vickers (talk) 16:12, 12 July 2009 (UTC)

Help with Ku (protein) and redundant articles

Not sure what to do about this. There is an article on the Ku heterodimer, but there are also articles on each subunit, Ku70 and Ku80. Would it be best to have the individual subunits redirect to the heterodimer article, or should there be some brief text there along with a link? What is the standard when dealing with members of a complex when there's a separate article for the complex? Compounding the situation is the fact that Ku70 and Ku80 are currently redirected to old gene names that have not been used in the literature in years. Suggestions for how to deal with this? Thanks. Amazinglarry (talk) 21:34, 15 July 2009 (UTC)

I don't think there is a problem having separate articles about the complex and the individual subunits. I have added protein boxes to the parent article to make clearer both the old and new nomenclature. I do agree however that the present naming is both out of date and confusing. I propose that the three pages be renamed as follows:
Does this sound reasonable? Are there other suggestions? Boghog2 (talk) 07:14, 16 July 2009 (UTC)
Thanks for your help. I think the article titles for the subunits should be Ku70 and Ku80, and the heterodimer can probably stay as it is. XRCC5 and XRCC6 were the names of the original CHO cell lines but haven't been used in the literature in over a decade. I'm not even sure where the "ATP dependent helicase" names came from because this protein is not a helicase (it is an ATPase though). Amazinglarry (talk) 11:43, 16 July 2009 (UTC)
The currently accepted official HUGO gene names for Ku70 and Ku80 are XRCC6 and XRCC5 respectively. Hence XRCCn page names is probably preferable to the Ku nomenclature or the full name "X-ray repair complementing defective repair in Chinese hamster cells" which is very long winded and hard to decipher. The name "DNA helicase II" came from this PubMed publication. Has this protein complex been shown since then not to be a helicase? Boghog2 (talk) 12:36, 16 July 2009 (UTC)
After further digging, the currently recommended UniProt protein names are:
  • P12956 – ATP-dependent DNA helicase 2 subunit 1
  • P13010 – ATP-dependent DNA helicase 2 subunit 2
The diversity of names is somewhat confusing. My bias would be to use the UniProt protein names in preference to HUGO gene names since the function is clearer from the protein names. Boghog2 (talk) 13:13, 16 July 2009 (UTC)
I think it makes the most sense to use the name that is used in the literature. Nobody will ever find this article if it's under "ATP-dependent DNA helicase 2 subunit 1" because all of the hundreds of papers on it have been calling it "Ku" for over a decade now. People looking for information on this protein will be searching for "Ku". I feel that calling it by an archaic unused name from a database makes Wikipedia look out of touch with current research. Amazinglarry (talk) 13:31, 16 July 2009 (UTC)
Finding the articles need not be a problem. Just create redirect pages for all the names. --Ettrig (talk) 14:24, 16 July 2009 (UTC)
In searching PubMed, the terms XRCC5 and XRCC6 are used in very recent literature, especially by geneticists (see for example PubMed and PubMed). But I would agree that Ku70 and Ku80 are more widely used, especially when referring to the protein. The Ku70 and Ku80 articles are about both the proteins and the genes that encode these proteins. So I agree that the pages should be named Ku70 and Ku80 but the XRCCn and "DNA helicase 2" aliases should be included in the lead as well as redirects to these subunit articles. Boghog2 (talk) 14:39, 16 July 2009 (UTC)
That sounds great, I think this will make it much easier to locate these articles while avoiding as much confusion as possible. Amazinglarry (talk) 14:59, 16 July 2009 (UTC)

Category renaming proposed

Category talk:Genes by chromosome#Requested move. This cat hierarchy is tagged for WMC. DMacks (talk) 16:22, 16 July 2009 (UTC)

MCB quality vs popularity

Article list. Testosterone seems to be an outlier. Tim Vickers (talk) 16:46, 12 July 2009 (UTC)

A highly accessed article indeed: "This article ranked 2896 in traffic on en.wikipedia.org" I have made some major edits, especially to the organization and the citations. I believe the article is now close to B class, but it certainly could use some additional editing if anyone is interested in helping out. Cheers. Boghog2 (talk) 19:22, 18 July 2009 (UTC)

NIH event

Press release, several people from Wikipedia will be talking at this event and we will be discussing this project. The presentations will apparently be broadcast on the web. See Meta for schedule. Tim Vickers (talk) 12:41, 15 July 2009 (UTC)

Just a note to say that this seemed to go very well indeed. More details at Wikipedia:Academy/NIH 2009. Tim Vickers (talk) 17:32, 17 July 2009 (UTC)

Enzyme templates

alcohol dehydrogenase
Identifiers
EC number 1.1.1.1
CAS number 9031-72-5
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / EGO

WillowW has done a fantastic job creating pages for enzymes which incorporate both the {{enzyme links}} and {{enzyme references}} templates. While these templates are very useful, I think they could be tweaked to make them even better.

As I see it, there are a few shortcomings with the present templates. First, there is some redundancy in that the IUBMB and BRENDA links are contained in both templates and also the EC number is displayed in almost every line of the template generated text. Second, they do not contain internal Wiki links which would give some information on the type data that these external links contain. Based on her work, I have created a new template {{enzyme}} (see the example to the right). This merges the information that is contained in the links and references templates and at the same time address the shortcomings mentioned above.

I am not suggesting that we replace en masse the {{enzyme links}} and {{enzyme references}} templates with this new template, but in certain situations the new template might offer some advantages when updating enzyme articles.

Comments and suggestions are welcome. Boghog2 (talk) 09:29, 19 July 2009 (UTC)

PS: I am quite saddened to see the User:WillowW user page marked as "currently inactive". I wish her well. Boghog2 (talk) 09:29, 19 July 2009 (UTC)
I support. I also think that we should perform an in-mass replacement. --Arcadian (talk) 10:39, 19 July 2009 (UTC)
Thanks for your support. For consistency, an in-mass replacement certainly would make sense, but not before we obtain community consensus. For reference, there are approximately 3000 enzyme articles that transclude the {{enzyme links}} links template. In exploring this further, I noticed that the PUMA2 web site has the posted the following notice:

PUMA2 is not being maintained or updated by Argonne National Laboratory and will be taken down in the near future.

Unless there are strong objections, I propose that this link be removed from the template. Boghog2 (talk) 17:09, 19 July 2009 (UTC)
Can References be renamed to something else, like Search or Articles or something, as the links are not references for anything in the article. Narayanese (talk) 17:12, 19 July 2009 (UTC)
Good suggestion. How does it look now? Boghog2 (talk) 17:25, 19 July 2009 (UTC)
Using a spot check of different EC numbers, the Google Scholar search doesn't appear to return any hits, no matter what the EC number. Therefore I have commented it out for now. Boghog2 (talk) 17:29, 19 July 2009 (UTC)
I noticed that the {{GO code links}} is also transcluded into many enzyme pages. I have therefore incorporated these GO code links into the {{enzyme}} template (see Gene Ontology identifier in example template to the right). Boghog2 (talk) 16:15, 20 July 2009 (UTC)

Serrapeptase is a mess

I've also raised this on the new content board. The article is a mess - markup problems, content problems, accusing a company of illegal activities with no evidence, etc. I really know nothing about the subject and can't recall how it ended up on my watchlist. Thanks. Dougweller (talk) 11:34, 19 July 2009 (UTC)

Silently encoding semantic wikilinks

I made a proposal yesterday over at the village pump (Wikipedia:Village_pump_(proposals)#silently_encoding_semantic_links) to create a template for silently encoding semantic links. From a biological perspective, this could be very useful. Right now we can easily store wikilinks between Gene A and Gene B indicating some relationship, but the nature of the relationship is critically important (activation, repression, enzyme/substrate, physical interaction, transporter/ligand, receptor/ligand, etc.). More details and some mocked-up examples are at the village pump link. Anyway, I thought I'd specifically mention it here because if no one has major objections over there (and there doesn't appear to be any yet), then we will start incorporating semantic wikilinks on gene pages with any future mass edits. Feedback appreciated... Cheers, AndrewGNF (talk) 20:49, 21 July 2009 (UTC)

RfC on swine flu statistics

RfC link, input welcome. Tim Vickers (talk) 19:33, 23 July 2009 (UTC)

Problem with the ELK1 PBB template

What's with the PBB template in ELK1? Clarityfiend (talk) 08:28, 24 July 2009 (UTC)

Someone accidentally added content to the template when it should have been added to the article. This has now been fixed. Cheers. Boghog2 (talk) 09:55, 24 July 2009 (UTC)

FAR Baby Gender Mentor

I have nominated Baby Gender Mentor for a featured article review here. Please join the discussion on whether this article meets featured article criteria. Articles are typically reviewed for two weeks. If substantial concerns are not addressed during the review period, the article will be moved to the Featured Article Removal Candidates list for a further period, where editors may declare "Keep" or "Remove" the article's featured status. The instructions for the review process are here.

Regards, —Mattisse (Talk) 22:33, 28 July 2009 (UTC)

Protein Box Bot to Add PDB gallery to all (most) Gene pages

Hi All, Just wanted to give a heads up that I am ready to have Protein Box Bot update all the gene pages with the new PDB Gallery box. We've already ran a few pages and you can check them out by following the links to them in My Sandbox. Please let us know if there are any concerns or if you like what we've done. JonSDSUGrad (talk) 00:17, 23 July 2009 (UTC)

Update - 2823 gene pages have now been successfully update with the PDB image Gallery. JonSDSUGrad (talk) 22:32, 30 July 2009 (UTC)
Looks great! I do appreciate the effort you are putting into this. Cheers. Boghog2 (talk) 22:35, 30 July 2009 (UTC)

New article: Optical sectioning

I have just written a new article on optical sectioning (in microscopy) after noticing several of the microscopy-related articles referred to it without making any attempt at a definition. Please take a look if you can and check I havn't made any stupid mistakes! - Zephyris Talk 10:16, 29 July 2009 (UTC)

En masse replacement of enzyme templates

As discussed above, an en masse replacement of {{enzyme links}}, {{enzyme references}}, {{GO code links}}, and {{CAS registry}} templates with the single {{enzyme}} template would reduce redundancy and make for more consistent looking enzyme pages. I have put together a bot script to automate this replacement. An example of a test run of the bot on a single page may be found here. Does anyone object to making these replacements? Also, any suggestions for improving the {{enzyme}} template or the way the bot is updating these pages would be appreciated. My plan is to run a couple of small test runs, register the bot, and if there are no strong objections, proceed with updating the ~3000 enzyme pages which transclude these templates. Cheers. Boghog2 (talk) 21:53, 30 July 2009 (UTC)

No objection from me. In fact, 100% support... Cheers, AndrewGNF (talk) 23:18, 30 July 2009 (UTC)
Agreed. Nice work. – ClockworkSoul 01:58, 31 July 2009 (UTC)
Thanks for your support! A script was run by BogBot on the 3055 pages that transcluded the {{enzyme links}}, {{enzyme references}}, {{GO code links}}, and/or {{CAS registry}} templates. These four templates have now all been merged into the single {{enzyme}} template on all 3055 pages. Cheers. Boghog2 (talk) 20:22, 9 August 2009 (UTC)
Well done. Thank you. --Arcadian (talk) 02:08, 10 August 2009 (UTC)
Excellent work! I suggest either proposing the other links for deletion (since they will no longer be used) or perhaps redirecting them to the main enzyme template for completeness. I would do it myself but I wanted to check in case there was a reason the redundant templates were left as they are. Cheers!Calaka (talk) 08:45, 10 August 2009 (UTC)
I think we need to keep the older templates in place to ensure that if previous version of articles that transclude these templates are viewed, they are still readable. I have however added the following message to the four older templates: "The use of this template is deprecated. Please consider using the {{enzyme}} template instead." I hope this is acceptable to everyone. Cheers. Boghog2 (talk) 15:45, 10 August 2009 (UTC)

FAR Sequence alignment

I have nominated Sequence alignment for a featured article review here. Please join the discussion on whether this article meets featured article criteria. Articles are typically reviewed for two weeks. If substantial concerns are not addressed during the review period, the article will be moved to the Featured Article Removal Candidates list for a further period, where editors may declare "Keep" or "Remove" the article's featured status. The instructions for the review process are here. —Mattisse (Talk) 01:02, 2 August 2009 (UTC)

Merge proposal: Voltage sensitive dye and Potentiometric dyes

Seems to be the same thing to me. I feel like someone from this project ought to do the merge however. Headbomb {ταλκκοντριβς – WP Physics} 18:30, 13 August 2009 (UTC)

GA Sweeps: Mitosis

Mitosis has been nominated for a good article reassessment. Please leave your comments and help us to return the article to good article quality. If concerns are not addressed during the review period, the good article status will be removed from the article. Reviewers' concerns are here. Nikki311 23:22, 16 August 2009 (UTC)

Amino acid GAR notice

Amino acid has been nominated for a good article reassessment. Please leave your comments and help us to return the article to good article quality. If concerns are not addressed during the review period, the good article status will be removed from the article. Reviewers' concerns are here.--TonyTheTiger (t/c/bio/WP:CHICAGO/WP:LOTM) 21:52, 18 August 2009 (UTC)

Proposal to link to external IUPHAR database

A request for comment has been made at the above link. Your input is welcome. Boghog2 (talk) 20:28, 19 August 2009 (UTC)

WP:JOURNALS need help.

I've noticed that most of the most popular missing journals are biology, and MCB related. Help would be appreciated to turn that see of red into a sea of blue. Most of these seem to be abbreviations that should be redirected to the main journal. Thanks. I've built a biology and MCB related list for the Biology Project and this one (see this), which is probably handier than going through the journal dump manually. Headbomb {ταλκκοντριβς – WP Physics} 05:04, 18 August 2009 (UTC)

See also Wikipedia:WikiProject Academic Journals/Writing guide. Headbomb {ταλκκοντριβς – WP Physics} 20:19, 21 August 2009 (UTC)

Phosphodiester bond

The article Directionality (molecular biology) is written not so clearly. Let me bring out a few points.

  1. The lead says

    The relative positions of structures along a strand of nucleic acid, including genes and various protein binding sites, are usually noted as being either upstream (towards the 5' end) or downstream (towards the 3' end).

    Since this is in the lead, I would expect this statement to be explained later on. That doesn't happen. Apart from that, I find it hard to understand what this sentence means. It seems ambiguous to me.
  2. We have here
  • 3' hydroxyl group
  • 3'-hydroxyl
  • 3'-OH group (in DNA polymerase)
  • 5'-phosphate group
  • 5'-phosphate
  • 5' phosphate
  • 5'-flanking region
  • 5' flanking region

In other words, no defined style as to the use of the hyphen and the word "group". I decided to write about it here because 1. the discussion page of Directionality (molecular biology) is empty and is likely to be poorly visited 2. this matter is likely to demand a general solution that would be applied over all articles of this WikiProject. Debresser (talk) 13:06, 4 September 2009 (UTC)

Boghog2 has added hyphens now where they were missing before. Debresser (talk) 15:01, 4 September 2009 (UTC)

Other problematic articles

  • Please also see Replication fork which I have partly rewritten for clarity. See the talk page there for my explanation of the necessity behind that rewrite, and the problem I have not been able to address. Debresser (talk) 14:28, 4 September 2009 (UTC)

Telomere

Telomere is rated mid-importance and B-class by your WikiProject, and I have reason to believe could benefit from being on the watchlist of a greater number of editors with some knowledge of the topic, if anyone has watchlist-space and time to spare. Regards, Qwfp (talk) 11:27, 5 September 2009 (UTC)

Asteroid body

I created an article about the asteroid body, a little curiosity that is seen in granulomas. At one time is was thought to be related to the centriole. Any insights/tweaking/merciless edits from a cellular biology enthusiast would be valued. Nephron  T|C 13:20, 7 September 2009 (UTC)

invitation to contribute GO annotations

All, I'm trying an experiment and I'd like to invite other MCB folks to participate. The gist of the experiment is this... GO annotations for human genes are currently assigned by a consortium of organizations, mostly by professional curators. As great a job as they do, it's difficult/impossible for them to keep up with the rate of biomedical publishing. The question: can the MCB community help the process by proposing candidate GO annotations, which would then be forwarded on to a curator for official review? If we can get enough activity here, it would be interesting to try to get MCB recognized as an official part of the Human GOA consortium...

I've started a table of candidate annotations at Portal:Gene Wiki/Annotations. Specifically, I'm interested in collecting candidate GO annotations that can be attributed to specific genes, specific diffs, and specific PubMed references. If anyone would like to contribute, feel free... Cheers, AndrewGNF (talk) 17:28, 14 September 2009 (UTC)

Wikipedia:Articles_for_deletion/Phage_monographs

Comments, please. NVO (talk) 07:01, 16 September 2009 (UTC)

Proposal for Gene Expression Atlas Box

We (User:ostolop and User:Mus4musculus) propose to add to the Protein Box Bot the generation of a Gene Expression Atlas box. As a test example, see ABCB1. The Atlas box is coming from the Template:ATLAS template and will include the meta-analytical expression summary heatmap for the given gene. We have such summaries for large numbers of genes in nine different organisms, and would eventually be able to generate graphics for the box as well. Any comments? Thanks! -- ostolop 11:01, 10 September 2009 (UTC)

The Gene Expression Atlas data is interesting and useful. However I believe this information is some what specialized and too detailed to be included on each an every Gene Wiki page. As an alternative, the EBI Gene Expression Atlas link could be included in the external ID section of the {{GNF Protein box}}. Cheers. Boghog (talk) 16:34, 10 September 2009 (UTC)
The current protein box displays, under RNA Expression Pattern, the results of one experiment (GNF SymAtlas), done on one technological platform (Affymetrix U133A). The Gene Expression Atlas provides data on RNA Expression Patterns from over a thousand experiments, done on dozens of different platforms - so, we propose an extended, more general view on gene expression patterns, composed from data from multiple independent experimental sources, as opposed to the specialized single-point-of-view information that is available now. We hope this would be a useful addition, more encompassing and not detailed... We could, for example, show tissue-level expression data or disease-level expression data to complement the GNF data, if that's viewed as informative. What do you think? ostolop 18:14, 11 September 2009 (UTC)
I think one thing we have to keep in mind is that it is more important to be clear than it is to be exhaustive. One reason I think the "Gene Atlas" barcharts are useful is exactly because it only displays one experiment, since that one experiment answers a reasonably basic question of "Where is this gene expressed in the human body?" Other less-universal data sets are hidden behind the link to More reference expression data. Perhaps one alternative to consider would be something like this: "More reference expression data (BioGPS, ATLAS)"? (Full disclosure: I have strong sentimental ties to the Gene Atlas data, which I think most here are aware of, but I don't think that is influencing my comments here...) Cheers, AndrewGNF (talk) 22:27, 11 September 2009 (UTC)
Seconding Andrew, I think information in info box templates which are displayed on many articles should be kept simple. According to WP:IBX, info boxes are meant to "present certain summary or overview information about the subject". Human tissue distribution is a basic starting point which many readers will be interested in. Information about gene expression in a certain cell line in a specific disease state or in response to drug treatment is very difficult to describe in a clear and concise way. As a compromise, this detailed information could included but the display is made collapsable similar to the way Gene Ontology data is presently in the GNF protein boxes. Boghog (talk) 07:08, 12 September 2009 (UTC)
Yes, what is a "Factor" and what is a "Factor value"? This template is a bit opaque. Tim Vickers (talk) 16:40, 10 September 2009 (UTC)
Factor - experimental factor: a test variable, such as "tissue", or "disease" or "radiation dose" or "developmental stage", Factor Value - values taken by the test variable, such as "kidney" or "lung", or "breast cancer" or "leukemia", etc. We use the Factor/Factor Value convention because we haven't got a better one - suggestions welcome! ostolop 18:14, 11 September 2009 (UTC)
I have to say that the interpretation still isn't entirely clear to me. Let's take the first line of {{ATLAS}} in ABCB1. It says that "factor value" = "Normal", "factor" = "Disease state", and "Up/Down" = "10/3". I understand that ABCB1 is upregulated in 10 conditions and downregulated in 3, but what is the comparison? I guess you're comparing different groups of "Disease state", one of which is "Normal", from this view, I'm not able to know what "Normal" samples are being compared to? Apologies if I'm being slow here... Cheers, AndrewGNF (talk) 22:18, 11 September 2009 (UTC)
We've been thinking about your comments and you made two important points - that clarity is above exhaustiveness and that basic knowledge about tissue-expression distribution is important. With that in mind we'd like to take a bit more time to get back to you with an alternative proposal that would present a clear view on tissue expression in the Gene Expression Atlas, we have what we think is a good idea but it'll take us a little more time. Cheers, ostolop (talk) 13:54, 16 September 2009 (UTC)
In response to valuable feedback, new version of template generated and applied to BRCA1 gene page. ABCB1 kept without changes for now, to keep reference for discussion. Human tissues are taken as least controversial experimental factor. Organism parts are outlined on the sketch of human body (derived from http://en.wikipedia.org/wiki/File:Human_body_features.svg), and numbers of experiments with non-trivial expression are displayed accordingly to legend. It is proposed to embed ATLAS template into GNF Protein Box, instead of editing each gene page. Please let me know your thoughts. Mus4musculus (talk) 16:41, 18 September 2009 (UTC)
I like the visualization of the human body (and presumably the tissues highlighted would change based on the specific gene?), but I still don't quite understand the metrics. See my comment above (regarding up/down-regulated relative to what?). As another example of my confusion, I see the kidney has one up-regulated study on the BRCA1 page. But then I click the data in ATLAS link and see there that kidney has two up-regulated studies. Why the difference? Anyway, my overarching comment is that it is a bit unclear to me how users should interpret the infobox and data. Cheers, AndrewGNF (talk) 18:24, 18 September 2009 (UTC)
You are right, images for all genes will be generated automatically with different set of features highlighted. As for data discrepancy, you probably looked up wrong gene, BRCA1 in kidney featured in 1 experiment: http://www.ebi.ac.uk/gxa/gene?gid=ENSG00000012048. Anyways, boxes to be re-generated as Atlas database grows, so number of experiments will change over time. About metrics - numbers in boxes are numbers of experiments where the gene is found over/under expressed, it is not a "number of conditions" as you said above (maybe that's the root of confusion?). Numbers tend to grow, they are not static. We do not treat numbers of experiments as a property of a gene, rather as an indication of content availability.
To answer your question "up/down-regulated relative to what." That varies somewhat from experiment to experiment, but in most cases it's safe to say - relative to the background made up by mean expression over multiple other tissues. For experiments like the GNF data set, over-expression in any one tissue is relative to the baseline level over some 60 tissues, and in certain other experiments the comparison might be relative to a reference tissue pool. In general concordance of activity over multiple studies indicates a more reliable finding. Thanks, ostolop (talk) 20:50, 18 September 2009 (UTC)
Okay, thanks for the additional clarification (and for catching my mistake with the wrong gene above). I think I'm starting to wrap my head around this now. One suggestion and one comment. First, I suggest that you might link the up/down numbers in the table directly to the specific experiment(s) that are up/down regulated. I think most naive users would look at "1/0", for example, and not know what to do with it. You'd be hoping that they'd scroll down to the bottom, and then be motivated enough to find their tissue of interest again on the gxa site. Better if they get the instant feedback of clicking on the number directly to get more info. My second comment is regarding your comment that "general concordance of activity over multiple studies indicates a more reliable finding". Since the comparison group changes for each experiment, I personally think it's tough to gauge how the numbers should be interpreted. Anyway, I'm interested to hear how others see this... Cheers, AndrewGNF (talk) 02:39, 19 September 2009 (UTC)
The human body visualisation is cool! I found the 'Uterine Cervix' label on a male figure a bit of a surprise. The numbers below are difficult to interpret at a quick glance. The classification seems very binary. Isn't there a large class of genes with an indeterminate expression level -- ie. neither up nor down? Colored/heatmap human figures based upon a p-value would be ideal wouldn't it? It might be too difficult to implement however (and be frightfully gaudy).--Paul (talk) 10:44, 19 September 2009 (UTC)
I have a suggestion. I think the expression data should be displayed in a 2D array where rows correspond to different tissues and columns would correspond to three different conditions (normal, diseased, compound treated). The normal column would indicate whether that gene is expressed or not expressed (or perhaps a finer gradation: none, low, medium, high) in a particular tissue. The second and third columns would indicate up or down regulated relative to the corresponding normal untreated tissue in the same row in column 1. (I also would propose that any data from an immortalized cell line would be treated as a disease state and therefore included in column 2.) The data in this format would convey useful and immediately understandable information. The data as it is presently displayed in BRCA1 page completely lacks context and therefore is impossible to interpret. Cheers. Boghog (talk) 18:10, 19 September 2009 (UTC)
On a somewhat related issue, both the GNF SymAtlas and Gene Expression Atlas contain mRNA expression data. For balance, it would also be desirable to provide links to protein expression data since the correlation between mRNA and protein expression is often not good and it is changes in protein expression rather than mRNA which normally results in a change in cell phenotype. One example data set may be found at the Human Protein Atlas (example: HPR:BRCA1). Boghog (talk) 06:39, 20 September 2009 (UTC)
It would have been great to add at least a link to the Human Protein Atlas if not a box (I felt like giving bot-coding a try when I first saw the suggestion). Problem for automated addition is, you seem to need the antibody ID for links and there doesn't seem to be system for getting from any gene ID/symbol; and the site doesn't allow database download. Narayanese (talk) 08:20, 20 September 2009 (UTC)
According to the Human Protein Atlas search FAQ: "In order to list all genes and antibodies, empty the query field and press the search button." Then on the upper right hand side, click on "Show search results: all". This will produce a table of all the proteins and antibodies in the database. The ensembl_gene_id is not directly visible in the table, however the antibody link is imbedded in the html source. For example: <a class="anti_link" href="tissue_profile.php?antibody_id=16673&g_no=ENSG00000121410">. So it is a bit messy, but we should be able to extract the necessary links from the html source. Cheers. Boghog (talk) 12:08, 20 September 2009 (UTC)
Cool. I'm on it. Narayanese (talk) 17:24, 20 September 2009 (UTC)
I'm not fond of the box. Neither number of experiments or up/down how much to to with the biology of the gene. Especially when it's based on p values - picks up many indirect and irrelevant effects (which might be why there are so many conditions with both up and down for well-studied genes). I have a feeling that showing fold change like Andrew's project does has so much better chance of showing something meaningful. Plus the box is uniterpretable without reading how the numbers were made (there's a bit on the EBI site, didn't seem to be a link to a publication though). Turning it into a collapsed box might be a good idea, it's hard to fit into a page in it's current form. Hope I didn't get too rambling, it's late here. Narayanese (talk) 22:58, 19 September 2009 (UTC)

changes to protein boxes

Chris Cunningham made many proposed changes to {{GNF Protein box}}, both to reduce the template size and to improve/standardize the visual appearance. The new version is at {{GNF Protein box/sandbox}}. I think it looks great. The before and after can be seen at Template:GNF_Protein_box/testcases. Any objection to these changes being promoted to the live version? Unless anyone objects, I'll put the edit request up tomorrow... Cheers, AndrewGNF (talk) 15:57, 22 September 2009 (UTC)

Looks great, I agree with the change. --Cyclopia (talk) 16:16, 22 September 2009 (UTC)
I like the smaller font. I don't get what "subject" means. I would spell Pubmed "PubMed" and Refeq "RefSeq". The current position format can't be copy/pasted into a genome browser, I think it would be better with e.g. chr5:156,540,432-156,614,687. But go ahead and put the version up live. Narayanese (talk) 16:21, 22 September 2009 (UTC)
Looking at ITK and p53, is the mouse gene location really right in the box? Narayanese (talk) 16:39, 22 September 2009 (UTC)
Thanks all... I agree, "Subject" is an imprecise header. What about changing this to "Organism"? For PubMed and RefSeq, I agree too and made the change. The mouse gene location was indeed incorrect due to a missing parameter, which I've fixed. (In parallel, Boghog is fixing the rest of these in the main namespace, since these are also incorrect...) Cheers, AndrewGNF (talk) 16:55, 22 September 2009 (UTC)
Looks good. I agree "organism" is preferable to "subject". Or how about "species" (one character shorter)? (or "beast" ;-) Boghog (talk) 19:08, 22 September 2009 (UTC)
Would it be worthwhile for the protein structure images to have a transparent background? Emw2012 (talk) 20:30, 22 September 2009 (UTC)
I would love it if we could, but right now we download those images directly from PDBe (for example, http://www.ebi.ac.uk/pdbe-srv/view/images/entry/1k09600.png from http://www.ebi.ac.uk/pdbe-srv/view/entry/1k09/summary). It's a good suggestion, but one I think we should deal with separately from this set of formatting changes... Sound reasonable? Cheers, AndrewGNF (talk) 21:19, 22 September 2009 (UTC)
Agreed. Emw2012 (talk) 18:16, 23 September 2009 (UTC)
FYI, this change has been made. Cheers, AndrewGNF (talk) 18:48, 23 September 2009 (UTC)
While I do like the new format, I just noticed one difference which in my opinion make the boxes slightly harder to read. In the old version, under the "Identifiers" and "Orthologs" section, the backgound was grey with thin white lines separating the rows. In the new version, the entire background is white which makes it slightly harder to distinguish between the subsections (Symbols vs External IDs vs EC number and Entrez vs Ensembl vs ... ). Hence I would appreciate if the grey backgound could be reintroduced at some point in the future. Sorry for noticing this sooner. Cheers. Boghog (talk) 21:24, 23 September 2009 (UTC)
I just made this change to {{GNF Protein box/sandbox}}. Do the examples at Template:GNF_Protein_box/testcases look okay now? Cheers, AndrewGNF (talk) 21:06, 24 September 2009 (UTC)
Yes, perfect! This formatting change is not a major issue, but in my opinion, it makes reading the data in the boxes easier. Thanks! Boghog (talk) 21:18, 24 September 2009 (UTC)
Sounds good... If there are no other requests for changes by tomorrow, I will request that this change be made to the template... Cheers, AndrewGNF (talk) 21:55, 24 September 2009 (UTC)
One additional minor request. The {{IUPHAR2}} template is transcluded into the {{GNF Protein box}} while the {{IUPHAR}} template is transcluded into the {{Infobox protein}}. In order to simplify the maintenance of the IUPHAR templates, I propose that both protein templates transclude the same IUPHAR template. Hence I have made this edit. Is this OK? Boghog (talk) 18:23, 25 September 2009 (UTC)
Looks good to me. Also, I was waiting until BogBot's edits are done before requesting that the sandbox be promoted, so that we can make this change at the same time. Cheers, AndrewGNF (talk) 20:00, 25 September 2009 (UTC)
Thanks. This latest small change makes it easier to describe how to maintain IUPHAR links. No rush on the update. This will allow others more time to comment. Boghog (talk) 20:04, 25 September 2009 (UTC)
The changes described above have been made here. Cheers, AndrewGNF (talk) 19:05, 28 September 2009 (UTC)

Orthology Database

(Moved from Portal:Gene_Wiki/Discussion#Orthology_Database.)

I am an author of the German wikipedia and also edit sometimes in the English wikipedia, mainly on biochemistry articles. I have been active on some gene articles and I noticed that the GNF Protein box and the GNF Ortholog box templates have a lot of useful links to other databases but these mainly cover single genes or gene products (like Entrez, Ensembl and Uniprot) but a link to a phylogenetic database is not present. So I felt that there would be a lot of added value if there were a direct link to a phylogenetic database that lists orthologs of a specific gene. This would allow the exploration of its corresponding genes in hundreds of complete genomes. There are already links from Uniprot to phylogenetic databases but you have to scroll all the way down to find them.

I am currently working with a group at ETH that created the OMA-database (http://www.omabrowser.org). It is one of the biggest orthology databases and many other website such as Uniprot and Ensembl link to OMA. Since I know this project best I would suggest to integrate this website into the GNF Protein box but there are also other projects which might be more suited for Wikipedia. On the technical side, the change in the infobox would only consist of a small adjustment since the database could be called directly with the uniprot entry ID (e.g. http://www.omabrowser.com/cgi-bin/gateway.pl?f=DisplayEntry&p1=PROCA02187 in the case of OMA). Did you discuss such an idea already? What do you think? Greetings --hroest 12:07, 9 September 2009 (UTC)

While the name is somewhat misleading, the HomoloGene link in the external IDs section of {{GNF Protein box}} does list orthologs of the human gene. In your example above, PROCA02187 is the 5-HT1A receptor and the HomoloGene link in that article points here. Even though the species included in the two lists are not identical, there is significant overlap. Is the HomoloGene link sufficient? Are there other databases that might be better? Cheers. Boghog (talk) 12:37, 9 September 2009 (UTC)
I too had the same question about OMA vs Homologene. On a separate note though, I did register OMA as a plugin in our gene annotation portal called BioGPS. Check out the help page to see how BioGPS works... Cheers, AndrewGNF (talk) 19:13, 9 September 2009 (UTC)
Hi, the overlap here is quite large because this protein is only present in higher eukaryotes but another example might look different if there are also prokaryotes in the group. For other databases see e.g. http://www.uniprot.org/uniprot/P08908. If you scroll all the way down you find Phylogenomic databases, unfortunately the link to HoverGene does not seem to work. To compare Homologene and OMA use these two links. There are also other databases such as EggNog (entry would look like this) or RoundUp (which could not find the sample gene I have used here but another example looks like [10] this).
The group that published OMA also wrote a comparative paper. They claim to be the biggest orthology database with currently 830 species. Homologene on the other hand has only eukaryotic species, so basically they have 20 species. This might be another point to consider. In their paper the group names several good orthology databases which we might consider here [...]the ranking of the best performing projects (OMA, RoundUp, Homologene, Inparanoid). Again, Inparanoid is limited to eukaryotic species. Greetings --hroest 11:29, 10 September 2009 (UTC)
Thanks for the explanation and additional details. I have a few thoughts. First, the GNF Protein box definitely has a human gene bias (to satisfy Wikipedia's notability criterion). Not sure how relevant differences in orthology assignments to prokaryotes are to WP users (thought there appear to be higher level differences as well in the example above). Second, if there were consensus, we could have a separate "Orthology" section in the GNF Protein box to contain multiple links. Third, to this non-specialist and at first glance, OMA is much less friendly than Homologene and eggNOG since it doesn't display the organism. Users either have to know the cryptic organism code or use the mouseovers. My two cents... Cheers, AndrewGNF (talk) 18:01, 10 September 2009 (UTC)
Well I do not believe that differences in orthology assignments in prokaryotes are relevant for a lot of users but I believe that linking to a database that does NOT have prokaryotes gives a wrong impression to the average wp user. Sometimes it would be very interesting to see that a certain gene has orthologs in prokaryotes and the other thing is that if a database does not list any orthologs then an average user might assume that there aren't any and he or she might not be aware that in Homologene only eukaryotes are listed. I do not believe that genes of prokaryotes are less noteable (but this is my personal opinion) and it would be nice to have a box that could be used for all genes and not only eukaryotic ones. Second, this might be a good idea but there is already some information about orthology in mice in the box. But I agree that it would be nice to have more information and more links. It would also be helpful have a field like "conservation" which would contain values such as "Mammals only", "Primates only" or "whole tree of life" which would inform the user, where the gene he/she is looking at is present in the tree of life. But I believe that evolution is not that simple thus making this idea not very feasible. Third, this is a point to consider especially since WP users are often nonspecialists. But we should also consider the opinion of the scientific community and maybe have a compromise solution. Greetings --hroest 19:59, 12 September 2009 (UTC)
any other opinions? --hroest 10:48, 30 September 2009 (UTC)

Proposal to change lead sentence of Gene Wiki articles

A request for comment has been made at the above link. Your input is welcome. Boghog (talk) 20:54, 1 October 2009 (UTC)

Vitamin GAR notice

Vitamin has been nominated for a good article reassessment. Please leave your comments and help us to return the article to good article quality. If concerns are not addressed during the review period, the good article status will be removed from the article. Reviewers' concerns are here.--TonyTheTiger (t/c/bio/WP:CHICAGO/WP:LOTM) 02:37, 2 October 2009 (UTC)

Telomeres, Telomerase and Nobel Prizes

Hi folks. Elizabeth Blackburn, Carol Greider, and Jack Szostak have won the 2009 Nobel Prize in Physiology or Medicine for the discovery of how chromosomes are protected by telomeres and the enzyme telomerase. Therefore we should probably take a good look at the Telomere, Telomerase, Telomerase RNA component and the Vertebrate telomerase RNA and other associated articles. The latter two should almost certainly be merged. --Paul (talk) 14:09, 5 October 2009 (UTC)

Proposed template merger

A merger of the Template:Kinins navigation footer into the Template:Autacoids navigation footer has been proposed. Please visit the discussion of this merger if you would like to register an opinion on this proposal. --RL0919 (talk) 23:49, 9 October 2009 (UTC)

AfD: Illumina Methylation Assay

An expert opinion on notability would be useful at Wikipedia:Articles_for_deletion/Illumina_Methylation_Assay -- Jheald (talk) 15:24, 12 October 2009 (UTC)

Lower eukaryotes

Hello all. When reading Wikipedia articles or articles found in PubMed I often come across the term 'lower eukaryotes'. In my opinion, it is a very confusing term and therefore I'd like to propose two possible things: translate 'lower eukaryotes' in Wikipedia articles to the organisms / tax intended, or create an article that explains what it is scientists mean when they (or we ;-)) refer to an organisms being a 'lower eukaryote'.

How do you feel about this subject and my suggested solutions? -- WKoets (talk) 13:26, 15 October 2009 (UTC)

I would write about it (possibly in a separate section) in the eukaryote article and then link the word to that section of the eukaryote article so if readers don't understand the term, they can quickly find out what it means. Tyrol5 [Talk] 20:33, 15 October 2009 (UTC)
You could mention it in that article, but as the term is quite meaningless in biology, I don't think it deserves a whole section. In common usage I think it means "eukaryotic microorganisms", but its precise meaning probably depends on the prejudices of the author concerned! :) Tim Vickers (talk) 20:40, 15 October 2009 (UTC)

Expanded genetic code

I expanded the stub page about Expanded genetic code and I think it is a very interesting topic and is definitely worth a "did you know..." spot in my opinion. However, I am the sole editor of it, so I wanted to know if someone concurs that it is interesting. say "did you known that the genetic code of cells can be reprogramed to accept non-natural amino acids, which may greatly benefit the fields biochemistry, medicine and biotechnology". --Squidonius (talk) 13:40, 16 October 2009 (UTC)

Not withstanding the above question, I was reading the MCB Portal, both the Did you know section and the In the News section are very out of date, certainly there is alot more going on in MCB. By all means, if you want to add stuff to update the portal, please do so, some currency is better than no currency at all.PB666 yap 01:23, 17 October 2009 (UTC)
I took the liberty of adding three did you knows in the portal as those there were not even remotely interesting, albeit more academic. (I did not add one about Craig Venter and synthetic biology as some people disagree on how awesome he is). --Squidonius (talk) 12:25, 19 October 2009 (UTC)
I nominated the did you know... that several groups have manage to add non-natural bases to DNA, while others have added non-natural amino acids into the genetic code? It did not get much attention, despite being phrased like a new scientist cover (which it did actually), so I am not sure that will do anything.
regarding Pdeitiker's comment, what is the difference between the MCB portal and the wikiproject? on the side panel I made to organise gene expression pages (link) the link is to the wikiproject... --Squidonius (talk) 10:00, 20 October 2009 (UTC)

Antibiotic resistance-role of animals

The antibiotic resistance#Role of animals section is a bit of a disaster. I think it should be completely deleted, save for a couple of sentences that could be put elsewhere in the article. I'm willing to do this myself, but want some input from others. Thanks! Pdcook (talk) 02:46, 17 October 2009 (UTC)

Category cleanup

I was reading Passaging just now, and found that the article is in Category:Molecular and Cellular Biology Unassessed articles. Two other articles are as well. This category seems to pre-date (slightly) the current convention of putting such categories on the talk page. The talk pages of those 3 articles are indeed in Category:Unassessed MCB articles, so I think we can safely remove the category that's on the the articles themselves, and delete the old category. Appreciate if someone could take care of this, or alternately confirm that I'm on the right track here and I'll do it myself. Thanks. Maralia (talk) 02:14, 21 October 2009 (UTC)

All three articles appear arguably to be within the scope of the MCB project. I went ahead and added ratings to these three articles and removed the now obsolete category templates on these three pages. Cheers. Boghog (talk) 17:55, 21 October 2009 (UTC)

Portal:Molecular and Cellular Biology

The portal of Molecular and Cellular Biology, is quite abdandoned.

  • is there any recent (1 year) news about MCB you deem worthy? please add: Portal:Molecular and Cellular Biology/Molecular and Cellular Biology news
  • Molecular biology is a science that is budding out from theoretical to applied with lots yada-yada on new scientist, so that brown tells me "we like retro 50s furniture", what colour would be better? (a fluorescence microscopy theme, maybe?) --Squidonius (talk) 10:31, 21 October 2009 (UTC)
I still check in here sometimes, but probably the color choice is not the most important issue here. Greetings --hroest 11:56, 21 October 2009 (UTC)

What is TATA BOX? Define it.

Insert formula here

Strange sutuation at the Dutch page for Reelin

Solejheyen very kindly decided to translate the Reelin into Dutch, but some folks there (at the talk page) want to delete all the references\footnotes, for some ambiguous reason. --CopperKettle 07:06, 7 November 2009 (UTC)

It seems our Dutch friends are more "laid-back" with regard to referencing non-controversial facts. Perhaps we could learn something from them? It seems to me that there is an increasing tendency on the English Wikipedia to use a reference for every statement—particularly in science articles, even though it does not say this here. But I am not suggesting we go down this nihilist path. I cannot see how and why we should want to influence our Dutch colleagues—it's their encyclopedia, not ours. Graham Colm Talk 08:53, 8 November 2009 (UTC)
A drive-by note: The reason some users intially wanted to strike the references was that Solejheyen copied them directly from the English source without checking them himself. They argue that you need to have actually verified the facts yourself in the sources when you write an article, or not cite these sources to support your statements. This issue gets confounded, though, with the difference between Dutch and English in the number of references preferred in articles. Ucucha 21:16, 10 November 2009 (UTC)

Riboswitches

I found out about riboswitches today, I'm pretty sure they should be mentioned in regulation of gene expression but I'm not quite sure where to place the info. Could someone with more expertise sort it out? Thanks Smartse (talk) 21:36, 9 November 2009 (UTC)

Another bullet point in the Posttranscriptional regulation should do the trick. --Paul (talk) 22:53, 9 November 2009 (UTC)
That section says "These processes occur in eukaryotes but not in prokaryotes" - riboswitches are (with one current exception) the opposite. Also they aren't a modification of the mRNA just it folding in a particular way so that it can bind a substrate. Does the Translational regulation seem like a better place for it to be? Smartse (talk) 19:38, 10 November 2009 (UTC)
I think that section is not terribly accurate or well written. I don't see how the things mentioned under translational regulation are not forms of posttranscriptional regulation. How can there be only 3 types of posttranscriptional regulation? The section has little in common with the full article on Post-transcriptional regulation and does not cite a single reference. Is it time to tear it down and start again? --Paul (talk) 22:02, 10 November 2009 (UTC)
Time ago, the core set of concepts associated with expression were really terrible so I gave them a bit of a clean (and gave up as not fun and nobody cares). I tried to get some interest and it has been Collaboration of the Month for the past year. The thing is, the most qualified people want to improve their pet projects and not high school/beginner UG level articles... so they end up abandoned. So please re-write what ever you feel like. Secondarily, the first paragraph is correct (sequence specific modulation) but the bullet points are talking about expression: mechanisms of expression and mechanisms of regulation/differential regulation are often confused in these articles... --Squidonius (talk) 10:16, 11 November 2009 (UTC)
Good point, translational regulation is by definition Post-transcriptional regulation. The separate article on Translational regulation is crap too, I think it should probably be redirected to Post-transcriptional regulation. There's no mention of RNAi in the section either. I'm a bit busy at the moment so if anyone can sort it all out please do. Smartse (talk) 14:08, 11 November 2009 (UTC)
I just noticed that Protein biosynthesis should be merged with gene expression... --Squidonius (talk) 17:36, 11 November 2009 (UTC)
There's Translation (genetics) as well, which seems even more redundant. Tim Vickers (talk) 17:45, 11 November 2009 (UTC)

Synthase vs synthetase

I've noticed (what I consider to be) some inconsistencies in Wikipedia regarding the utilization of synthase versus synthetase. My understanding is that if an enzyme produces molecule X, it can be called X synthase. However if that enzyme catalyzes a concomitant hydrolysis of ATP, then the enzyme would be called X synthetase. Is that right or outdated? Thanks, Pdcook (talk) 02:06, 16 November 2009 (UTC)

That is the correct distinction, with synthetases breaking a diphosphate bond in a nucleoside triphosphate. However, this is no longer the recommended nomenclature. The systematic names of all these enzymes are now ligases. For example, EC 6.3.1.2 glutamine synthetase has the official name of glutamate-ammonia ligase. These are common names though and still in wide use. Tim Vickers (talk) 19:53, 16 November 2009 (UTC)

Hormones?

NGF · BDNF · NT-3 are included in the Template:Hormones, but are they really? If yes, some mention of it should be on their respective pages. --CopperKettle 12:45, 16 November 2009 (UTC)

Well, they for sure fall somehow into the broad definition of hormone, as it is in the article: ...a chemical released by one or more cells that affects cells in other parts of the organism. Only a small amount of hormone is required to alter cell metabolism. It is essentially a chemical messenger that transports a signal from one cell to another. -the problem with this definition is that basically every free-floating cell-receptor ligand is an hormone. But I am no expert on this precise subject. --Cyclopiatalk 12:49, 16 November 2009 (UTC)
Well with the discovery of diffuse activation in the CNS, every neurotransmitter can also be a hormone. (0: --CopperKettle 13:00, 16 November 2009 (UTC)
Agree. That's a problem with the hormone definition, I think. --Cyclopiatalk 13:01, 16 November 2009 (UTC)
I think the difference is that hormones are released from one tissue and act on another, while growth factors and cytokines tend to act within a tissue over short distances. However, that's my personal definition! Tim Vickers (talk) 18:26, 16 November 2009 (UTC)
I've read that during inflammation or stress cytokines go to hypothalamus to hike the CRF, which in turn hikes up the ACTH, which in turn revvs up the HPA axis. Not sure about the distance; only glanced yet at this review. --CopperKettle 19:25, 16 November 2009 (UTC)
But the question is whether NGF · BDNF · NT-3 are mentioned somewhere as hormones. I've translated the template into Russian and somebody might just ask me there - why these three are included. (0: --CopperKettle 19:27, 16 November 2009 (UTC)
Probably not - Hancock, John T. (1997). Cell signalling. New York: Longman. ISBN 0-582-31267-1.  states that the definition is "somewhat vague" and that the distinctions between hormones, cytokines and growth factors are loose, but that a hormone is a small molecule "released by the cells of one tissue and carried to a new site of action, such as a different tissue, where they provoke a specific response." The book says that cytokines and growth factors tend to have local effects, so are not classed as hormones. Tim Vickers (talk) 19:45, 16 November 2009 (UTC)
  • Then we should probably strike them out of the "hormones" template. I've notified Arcadian, he is the author of many templates. --CopperKettle 19:54, 16 November 2009 (UTC)
  • Agree. Some quick Gscholar search shows that NGF, for example, is at best called a "hormone-like protein" but never a hormone, apparently. --Cyclopiatalk 20:45, 16 November 2009 (UTC)
I agree with the proposal to remove them. (They were added by User:Gacggt, in this edit.) --Arcadian (talk) 02:38, 17 November 2009 (UTC)
Done. Thank you for your opinions. Best regards, --CopperKettle 11:44, 18 November 2009 (UTC)

Uncategorised category

Hi WikiProject Molecular and Cellular Biology. I've noticed that Category:CAMs (which I have proposed for renaming to "Category:Cell adhesion molecules" - feel free to add any views you may have on the topic here) is currently uncategorised. I thought somebody here might know the correct category/ies in which to include it. Thanks. DH85868993 (talk) 22:44, 26 November 2009 (UTC)

A category has now been added. Thanks. DH85868993 (talk) 01:05, 28 November 2009 (UTC)

DNA replication image

i created the image File:DNA replication en.svg and since i made it there has been a issue with the order in wich the 3' and 5' apear on it. i have been told them to invert them (i did) and then to invert them again ( went back as they were) as no matter in wich way i do them someone comes and says is the wrong order to the point in wich i myself no longer know wich would be the correct way of placing them. i tryed looking for some definitive reference in the net but i havent found any so i wonder if you could help me? i need to know if it is right as it is or i should revert them. thank you-LadyofHats (talk) 17:00, 4 December 2009 (UTC)

It looks right to me as is. Maybe people are getting confused and not following the strands around the helix very well. You could color each strand (sense, antisense) different colors (just not red and green!) PDCook (talk) 17:11, 4 December 2009 (UTC)
Looks lovely! --Paul (talk) 20:29, 4 December 2009 (UTC)
Seems OK to me as well. I suppose the diagram isn't as clear as it could be that the two polymerases move in opposite directions in the diagram, with each one moving in the 3' to 5' direction on opposite strands. Would probably be better to show Pol alpha actually synthesising DNA rather than just sitting to the side. Tim Vickers (talk) 20:39, 4 December 2009 (UTC)
I agree with PDCook -- it looks correct, but people are most likely getting confused with the twists, and colour coding the different strands may help. And Tim's comment about making the directions of synthesis a little clearer is valid too -- perhaps adding some extra/different arrows? Great diagram though!! ~ Ciar ~ (Talk) 00:42, 5 December 2009 (UTC)
I should have mentioned that I do think the figure looks great. Much better than the ones from my text books from college! PDCook (talk) 01:57, 5 December 2009 (UTC)

Allopregnonolone

According to KEGG the enzyme is EC 1.1.1.278, which is 3beta-hydroxy-5alpha-steroid dehydrogenase. Tim Vickers (talk) 17:57, 10 December 2009 (UTC)
Thank you, Tim! --CopperKettle 18:07, 10 December 2009 (UTC)

FAR Anabolic steroid

I have nominated Anabolic steroid for a featured article review here. Please join the discussion on whether this article meets featured article criteria. Articles are typically reviewed for two weeks. If substantial concerns are not addressed during the review period, the article will be moved to the Featured Article Removal Candidates list for a further period, where editors may declare "Keep" or "Remove" the article's featured status. The instructions for the review process are here. Doc James (talk · contribs · email) 11:37, 11 December 2009 (UTC)

pregnenolone sulfate

Does it deserve to be described in a separate article or should it be only mentioned in a subdivision of pregnenolone article? Cheers, --CopperKettle 06:26, 13 December 2009 (UTC)

Mass update of PDB images

Based on a discussion at GeneWiki, I've written a small program to do some automated polishing of PDB images first uploaded by ProteinBoxBot. A list of test case images is available at User:Emw/PDB Sandbox -- here, for comparison, original images uploaded by ProteinBoxBot are set alongside images produced by the new method. Before going on to apply these changes to the roughly 2800 PDB images contained in PBB templates, I'd like to gather feedback and suggestions from the WP:MCB community. Thanks in advance for any input. Emw (talk) 22:27, 24 November 2009 (UTC)

They are better in full size, but definitely more fuzzy (and therefore worse) when rescaled. --Cyclopiatalk 23:04, 24 November 2009 (UTC)
I don't quite understand. Are you saying that the protein structure images are fuzzier (less resolution?) when they're scaled down to fit in the template? Could you give an example? Emw (talk) 04:43, 25 November 2009 (UTC)
I don't know how to quantify, but it's not a resolution problem. Your new images are much better in general, but do not look nice when rescaled to fit in the template. To me the new ones look fuzzy, while the lo-res old ones seem definitely more crisp when rescaled in the template -I guess it's an aliasing problem, but I don't know how to solve it. --Cyclopiatalk 14:44, 25 November 2009 (UTC)
Left hand image is rather lower quality and taken from a lower resolution image. It includes JPEG compression artifacts. :-/ Any "sharpness" you might perceive is illusionary. Possibly due to those artifacts? --Kim Bruning (talk) 20:55, 25 November 2009 (UTC)
It is utterly irrelevant if it is illusionary -I mean, it is obvious that it is "illusionary" because the left images is of objectively much lower quality. But when rescaled, the higher quality image looks worse. That's all it matters, even if it is just an artefact. It is counterintuitive but it is not as strange as it may seem -it depends on the rescaling, aliasing effects, etc. A way should be found to make the new image look good even when rescaled. I checked on different LCD screens of different resolution and I still see the same effect. --Cyclopiatalk 21:29, 25 November 2009 (UTC)
I also tried now with both Firefox and Konqueror, to see if it's a browser-specific effect, but it seems not. --Cyclopiatalk 21:32, 25 November 2009 (UTC)
I wasn't able to pick out the more pronounced pixelation typical of aliasing issues in the down-sized new images. But I may just be insensitive to it. (FWIW, I've viewed it in several browsers on Windows Vista. Could this be an OS-specific issue?) To get a better idea of the situation I zoomed in on the old and new images in the templates using the Image Zoom extension for Firefox. With both images zoomed to 200%, the old image at left is noticeably more pixelated than the new image at right. Emw (talk) 22:06, 25 November 2009 (UTC)
I'm quite puzzeled by this. The right hand image has a higher resolution and *should* downsample more cleanly. If it's not an illusion, it might be interesting to ask a developer to take a more detailed look (perhaps a different downsampeling method is used for the two images? I can't imagine why though, unless it has to do with timing.)
At any rate, I think the higher resolution image should be retained (as well), even if the thumbnail appears more "fuzzy". --Kim Bruning (talk) 00:32, 26 November 2009 (UTC)

────────────────────────────────────────────────────────────────────────────────────────────────────I am sorry of not having made myself clear. The effect I see is the opposite of pixelated. The correct word I wanted to say (I am not a native English speaker) is blurry. In my view the new image, when resized, looks subtly but noticeably blurry, noticeably enough that it is quite annoying for the eyes to look at it. I fully agree that the high resolution image should be retained, but I'd like to have a way to retain it or to process it so that the resized image looks better. --Cyclopiatalk 13:17, 26 November 2009 (UTC)

In order to produce crisp ray-traced images with a light background in PyMol, add the following to your script:
  • set cartoon_transparency = 0.0
  • set depth_cue = 0
  • set ray_trace_fog = 0
I think this will make the PyMol generated image look sharper even when reduced in size. In any case, fuzzy or not, I think the new png PyMol images (right hand side) look better at any size compared to the older jpg (left hand side) images. Cheers. Boghog (talk) 21:47, 26 November 2009 (UTC)
Thanks for the suggestion. I've added fogless versions of the new images for 1xu7, 1lui and 2a07. Which is preferable -- the foggy or fogless version? Emw (talk) 00:23, 27 November 2009 (UTC)
These are much better than the JPEGs, excellent work. In my system, both foggy and fogless look equally awesome at thumbnail size, but I believe "fogless" is preferable, as it does produce a crisper image and a smaller file size (that's how I always produce my PyMol images, anyway). Fvasconcellos (t·c) 00:31, 27 November 2009 (UTC)
To me they look practically identical. They both still look definitely blurry to me at thumbnail size. Again, they are for sure much better than the JPEGs, I don't dispute that, but it is disappointing that the thumbnail can't be crisp. However for some reason it seems it is just me, so let's be it. --Cyclopiatalk 00:54, 27 November 2009 (UTC)
I briefly discussed the blurriness problem with User:Brion last night at #mediawiki. He mentioned that some sharpening is applied to JPGs -- usually photographic images -- but wasn't sure what is done to PNGs. Perhaps that's the culprit, but as Cyclopedia notes others apparently aren't seeing any problematic blurriness (and it is independent of whether the image is foggy or fogless).
It seems there's consensus to move forward with the mass update using a fogless rendering. Are there any other feature requests? Emw (talk) 01:46, 27 November 2009 (UTC)
Come to think of it, I think the rendering of DNA in File:C-Myc-DNA_complex.png is better than the way it's shown in the test images (e.g. File:Protein_FOXP2_PDB_2a07.png). I've added a new test case for DNA rendering here -- any thoughts? Emw (talk) 17:39, 27 November 2009 (UTC)
I agree that the default brown color for DNA backbones looks better than the magenta that I suggested. Thanks for posting the examples. Boghog (talk) 19:02, 27 November 2009 (UTC)
Agree too, even if I would use a brown palette for the bases too, to avoid confusion and cluttering (having different brown hues for different bases would be great, but maybe too much of a hassle). --Cyclopiatalk 19:06, 27 November 2009 (UTC)

──────────────────────────────────────────────────────────────────────────────────────────────────── I've created a bot (dubbed PDBbot) and it's ready to upload images for the ~2700 proteins listed here. Its six most recent uploads are representative of how the remaining images should look once the bot gets approved at Commons. If anyone has suggestions (e.g. for a better summary description, better categories, image quality, etc.), then I would appreciate the feedback. Emw (talk) 15:13, 15 December 2009 (UTC)

Merge?

Seem to be the same enzyme:

But I could be mistaken. --CopperKettle 07:17, 13 December 2009 (UTC)

  • I think they are the same and ought to be merged. This is probably a case of a geneticist creating an article for the gene and an enzymologist creating an article for the enzyme. I've seen this happen a number of times.PDCook (talk) 15:25, 13 December 2009 (UTC)
  • In this particular case, I think these two articles could be merged since there appears to be only one protein in the human genome that possesses this particular enzymatic activity (i.e., same EC number) . However there are other cases where several proteins in the same genome may have the same enzmatic activity in which case it would be useful to retain the enzyme page (in addition to the individual gene/protein specific pages) to represent the family of proteins. Cheers. Boghog (talk) 07:28, 15 December 2009 (UTC)

Suggested Links in Gene Wiki

How about including links to our GeneCards site in Gene Wiki? ( http://www.genecards.org, see also http://biogps.blogspot.com/2009/09/gene-wiki-google-update.html)

What do you all think? We could offer the developer resources to do this...

Marilyn Safran marilyn.safran@weizmann.ac.il Safranmar (talk) 11:38, 2 November 2009 (UTC)

Tentative support. GeneCards does seem to contain unique and useful information. In addition, the fact that GeneCards provides a link to the corresponding Gene Wiki article is definitely a plus. However I do have several reservations. The first is that commercial entities require a license to access GeneCards whereas there is no such requirement to access Wikipedia. Second, there are links from GeneCards to commerical sites which presumably generates some revenue for GeneCards. On the technical side, it should be very straight forward to add a link from {{GNF Protein box}} to GeneCards (e.g., Estrogen receptor alpha[11] using the Hs_EntrezGene=2099 parameter value that is already included in the {{PBB/2099}} template). So I guess I would tentatively support adding such a link, but I would like to hear what other think first. Cheers. Boghog (talk) 20:01, 2 November 2009 (UTC)
Support, though Boghog's point about the licensing terms is a good one. Officially, commercial entities do require a paid license, but I think this is a "soft" requirement meaning all users will be able to get to the site. Presumably it's only after the fact that GeneCards tries to get subscriptions from heavy users. I don't know of another site that uses a similar model that we can use for precedent/guidance. In any case, I fully support on the scientific merits... Cheers, AndrewGNF (talk) 22:13, 2 November 2009 (UTC)
Comment: I have implemented a link to GeneCards in the {{GNF_Protein_box/sandbox}} and the result can be seen here (look in the External IDs section). How does this look? Boghog (talk) 16:44, 3 November 2009 (UTC)
Comment: Looks great. Thanks for your effort. I think this would be useful to many if added to all of the Gene Wiki pages. Comments from anyone else? Safranmar (talk) 08:10, 8 November 2009 (UTC)
Comment: What would be the next step in making this live? Thanks. Safranmar (talk) 07:43, 24 November 2009 (UTC)
I was waiting a bit to see if others had an opinion. Since the consensus above is favorable and sufficient time has past to allow comment, I think we can go ahead and implement the proposal. AndrewGNF, would you like to put in the reguest to have an adminstrator implement these changes or would you prefer that I do it? (in a somewhat related issue, I would also like to make the display of avaiable PDB structures collapsable since ocassionally these lists can get quite long, but I cannot seem to get this to work). Cheers. Boghog (talk) 12:06, 24 November 2009 (UTC)
Yes check.svg Done Per this request by AndrewGNF, David D. has updated the production version of the {{GNF_Protein_box}} template in this edit to now includes a link to the GeneCards database. Cheers. Boghog (talk) 11:35, 23 December 2009 (UTC)

Translation project

User:Proteins and I are in contact with a technology company that wishes to use some software it has developed that is a kind of graphic interface for translators to increase the amount of health-related information in developing-world language Wikipedias. Since this is quite a large company, this project might eventually cover many languages, but we are thinking about starting off small at around five (eg transferring content from the English to the Swahili Wikipedia is one leading option). The real work will be in developing a community of translators and bilingual experts in each destination language, and the company is willing to help with this as well, but at our end we will need to provide a list of articles on "essential health information", internationalize these as much as possible, and polish them a bit. This proposal is still in its initial stage, but could people who would be interested in participating sign up here. Thank you Tim Vickers (talk) 17:05, 22 December 2009 (UTC)

Userbox

I have created a userbox for this project. What do you all think of it? --NerdyScienceDude :) (click here to talk to me) 21:42, 21 December 2009 (UTC)

Nucleus ER.png This user is a member of WikiProject Molecular and Cellular Biology.
Look good. Thank you. Tim Vickers (talk) 00:12, 22 December 2009 (UTC)
We already have a a user box template, but the more the merrier I say! – ClockworkSoul 16:43, 4 January 2010 (UTC)

Placental alkaline phospatate - page move

I've proposed a page move from ALPP to PLAP - see the ALPP talk page. I've created some redirects for PLAP and placental alkaline phosphatase to the ALPP article, and I thought to suggest the move because that's the terminology we use in pathology. I don't know if I'm just being a presumptuous medico, but thought maybe molecular and biochem folk may be using the same term? Mattopaedia Have a yarn 01:03, 27 December 2009 (UTC)

Beta clamp

Greetings, the new file Beta clamp is ready for scrutiny. I hope the presentation style warrants it being made an article. Please note that only earlier today did I find and read the article 'DNA clamp' 2006. Many Thanks .Betaclamp (talk) 00:10, 13 January 2010 (UTC)

Oops! I think the moral of this story, Betaclamp, is to always thoroughly check Wikipedia's existing coverage before taking the time to write a new article. DNA clamp already covers this topic in more detail and in a more focused way than Beta clamp.
I'm not sure there's much that can be salvaged from Beta clamp. Much of the information there is background that is more properly included in the articles wikilinked in the introduction to DNA clamp. I don't find the auto analogy helpful, as it assumes the reader is quite knowledgable about automobile mechanics, and the equivalences drawn in the analogy (eg fuel to information) are not (to me) intuitive.
What this article does achieve is to expose a hole in DNA clamp: it never mentions the term "Beta clamp". Based on http://dx.doi.org/10.1074/jbc.M100592200, I see that "Beta clamp" (or "Beta sliding clamp") is synonymous with "DNA clamp" for prokaryotes; does anyone know if "Beta clamp" has a meaning in eukaryotes? I suggest DNA clamp be updated to explain the term "Beta clamp", and then Beta clamp be redirected to DNA clamp. Adrian J. Hunter(talkcontribs) 04:36, 13 January 2010 (UTC)

WP 1.0 bot announcement

This message is being sent to each WikiProject that participates in the WP 1.0 assessment system. On Saturday, January 23, 2010, the WP 1.0 bot will be upgraded. Your project does not need to take any action, but the appearance of your project's summary table will change. The upgrade will make many new, optional features available to all WikiProjects. Additional information is available at the WP 1.0 project homepage. — Carl (CBM · talk) 03:33, 22 January 2010 (UTC)

Addition of links to National Institutes of Health GeneReviews

Addition of links to National Institutes of Health GeneReviews. AN/I discussion of relevance to this project. Tim Vickers (talk) 20:13, 25 January 2010 (UTC)

Morpholino GA Sweeps: On Hold

I have reviewed Morpholino for GA Sweeps to determine if it still qualifies as a Good Article. In reviewing the article I have found several issues, which I have detailed here. Since the article falls under the scope of this project, I figured you would be interested in contributing to further improve the article and help it maintain its GA status. Please comment there to help resolve the raised issues. If you have any questions, let me know on my talk page and I'll get back to you as soon as I can. --Happy editing! Nehrams2020 (talkcontrib) 03:55, 7 February 2010 (UTC)

Update of PDB images complete

I've finished updating over 2500 protein structure images in Gene Wiki templates, as outlined here and here. If there are any concerns, please let me know. Emw (talk) 17:33, 10 February 2010 (UTC)

Beautiful, well done. A step up from the current images from EBI for sure... Has anyone at wikicommons complained that the images are all uploaded to a single category? I seem to recall that we hit this criticism when we were doing our uploads, and someone had the good suggestion of categorizing by SCOP. Anyway, not sure if it's worth the effort, but I do think it would be another potential improvement. But anyway, nice job... Cheers, AndrewGNF (talk) 21:43, 10 February 2010 (UTC)
Yes, someone made that very complaint at the PDBbot's BRFA at Commons. As I mentioned there, I think it would take less work to add a SCOP category for each image if source code by Donabel_SDSU were ported for use by PDBbot.
I was also thinking that it may be worthwhile to replace the static image in the Gene Wiki with a spinning animation of the protein structure, similar to the animated .gif in the lead of DNA. I think building such animations can automated, e.g. with PyMOL's movie commands. To minimize reader distraction, the movie files produced by PyMOL could perhaps be automatically converted to Ogg Theora videos, which would allow the animations to be paused. Emw (talk) 23:07, 10 February 2010 (UTC)
Yeah, I'm much less enthusiastic about the animations. A bunch of interested users prototyped a few ideas a while back (the discussion must be in the archives here somewhere). But I think the consensus then was that they were a) distracting, b) resource-intensive on the client's browser, and c) of lower visual quality than the static images. In retrospect, I strongly agree with the eventual decision to stay with the static images (and especially so now that we have your higher quality static images)... Cheers, AndrewGNF (talk) 18:00, 11 February 2010 (UTC)
Nice job! A big improvement and very much appreciated. For reference, the previous discussion about animated pdb images may be found here. Boghog (talk) 19:30, 11 February 2010 (UTC)
Thanks for the pointer to that discussion. In that thread there seemed to be some enthusiasm for an animation within a 'show/hide' template. There weren't any examples provided, so I made a rough prototype at User:Emw/PDB_Sandbox/Animation. There are a few elements that could likely use polishing (e.g., minimizing or doing away with the 'v d e' links). As it is, though, the animation seems easily ignorable and allows the client to decide whether to use a resource-intensive feature of the page. With regard to visual quality, I think higher-resolution videos (i.e., with ray-traced frames) would be possible. Emw (talk) 06:26, 12 February 2010 (UTC)
Thanks for experimenting with this. I think making the animation collapsible is a good idea. However if we do go down this route, I think it would be perferable to use JMOL (for an example, see Proteopedia) which makes the display fully interactive. While jmol has been ported to MediaWiki, it hasn't yet been activated in Wikipedia (see Wikipedia_talk:Using_Jmol_to_display_molecular_models). So far this effort has been driven by WP:CHEMISTRY, but perhaps if WP:MCB adds moral support, Jmol might get activated sooner. Boghog (talk) 14:27, 12 February 2010 (UTC)

GA reassessment of Yeast

I have conducted a reassessment of the above article as part of the GA Sweeps process. I have found some concerns which you can see at Talk:Yeast/GA1. I have placed the article on hold whilst these are fixed. Thanks. Jezhotwells (talk) 17:05, 14 February 2010 (UTC)

GA reassessment of Vitamin C

I have conducted a reassessment of the above article as part of the GA Sweeps process. You are being notified as this project's banner is on the talk page. I have found some concerns which you can see at Talk:Vitamin C/GA1. I have placed the article on hold whilst these are fixed. Thanks. Jezhotwells (talk) 23:08, 19 February 2010 (UTC)

Looking for input on peer review

I just opened a second peer review for the article on homologous recombination, and if possible would like to get some feedback from the MCB community so the article will be ready for FAC. Thanks in advance for any input. Emw (talk) 02:40, 20 February 2010 (UTC)

GA reassessment of Genetic code

I have conducted a reassessment of the above article as part of the GA Sweeps process. You are being notified as you have made a number of contributions to the article. I have found a number of concerns which you can see at Talk:Genetic code/GA1. I have de-listed the article as the referencing is so poor. However, if improvements are made bringing the article up to standards, the article may be nominated at WP:GAN. If you feel this decision has been made in error, you may seek remediation at WP:GAR. Thanks. Jezhotwells (talk) 21:59, 26 February 2010 (UTC)

GA reassessment of Heparin

I have conducted a reassessment of the above article as part of the GA Sweeps process. You are being notified as this project' banner is on the article talk page. I have found some serious concerns which you can see at Talk:Heparin/GA1. It appears that large parts of the article are copyright violations. I have placed the article on hold whilst these are fixed. Thanks. Jezhotwells (talk) 20:18, 27 February 2010 (UTC)

GA reassessment of Stem cell

I have conducted a reassessment of the above article as part of the GA Sweeps process. You are being notified as this project's banner is on the article talk page. I have found some serious concerns which you can see at Talk:Stem cell/GA1. The artcile appears to contain many copyright violations. There are other concerns to be addressed. I have placed the article on hold whilst these are addressed. Thanks. Jezhotwells (talk) 21:13, 27 February 2010 (UTC) Jezhotwells (talk) 20:53, 28 February 2010 (UTC)

GA reassessment of Multiple sequence alignment

I have conducted a reassessment of the above article as part of the GA Sweeps process. You are being notified as this project's banner is on the article talk page. I have found some concerns which you can see at Talk:Multiple sequence alignment/GA1. I have placed the article on hold whilst these are fixed. Thanks. Jezhotwells (talk) 19:36, 28 February 2010 (UTC)

GA reassessment of Photosynthetic reaction centre

I have conducted a reassessment of the above article as part of the GA Sweeps process. You are being notified as this project's banner is on the article talk page. I have found some concerns which you can see at Talk:Photosynthetic reaction centre/GA1. I have placed the article on hold whilst these are fixed. Thanks. Jezhotwells (talk) 20:53, 28 February 2010 (UTC)

GA reassessment of Prion

I have conducted a reassessment of the above article as part of the GA Sweeps process. You are being notified as this project's banner is on the article talk page. I have found some concerns which you can see at Talk:Prion/GA1. I have placed the article on hold whilst these are fixed. Thanks. Jezhotwells (talk) 21:35, 28 February 2010 (UTC)

Reactivate the collaboration of the month

I realized that the MCB Collaboration of the Month is no longer active (probably for a long time). Since I think that these kind of collaborations are very helpful for articles, I am wondering what it would need to reactivate this. I could give a hand in organizing this; but I don't know whether it is desired and how the process is running in detail. It may also be that this has already been discussed many times and the final conclusion was to stop this. What do you think? If desired, I would be glad to get some infos on the workflow. Thanks in advance, --Firefly's luciferase (talk) 04:35, 24 February 2010 (UTC)

I hope someone proves me wrong, but unfortunately there does not appear to be enough remaining active editors to make restarting this worth while. One problem is the very broad scope of MCB which makes it difficult to attract a critical mass of editors to work on any one specific topic. Another problem which is not unique to MCB but is affecting the entire Wikipedia project as a whole is that established editors have been departing the project faster than new ones have been joining.
That being said, in my opinion, there are a couple of high priority articles that should be improved. The first is testosterone which was suggested suggested by Tim Vickers. This article is the 2134th most viewed article on Wikipedia and is C class. In addition, articles like action potential and genetic code are currently undergoing featured or good article reviews respectively and if not improved will be delisted. My preferences would be to first work on the articles currently being reviewed and then concentrate on improving high impact but incomplete articles like testosterone. I would be interested in hearing what other members of this project think. If there is enough interest, I am all for restarting the MCB Collaboration of the Month. Cheers. Boghog (talk) 17:25, 27 February 2010 (UTC)
Thank you for your interest in restarting the COTM. I completely agree, that the reading frequency of an article is an argument for the selection of articles. As you can see, I jumped ahead and nominated Genetic code as the COTM of March; this project is thus officially active again. :-) I deliberately did not pick one of the older articles since there were no recently added supports. Furthermore, genetic code is going through reassessment. We could actually aim to go for FA. Thank you already for your contributions. We may also already plan for April. --Firefly's luciferase (talk) 08:17, 1 March 2010 (UTC)
Great job, I hope we can get some activity here again. Greetings --hroest 09:41, 3 March 2010 (UTC)

(Unintend) I also agree that it would be wise to take article viewership into account when coordinating work. The tool here ranks MCB articles by page views, and also shows each article's quality and importance ratings. Below is a list of the first 10 MCB articles as ranked by page views in February that are of C-class quality or below and either 'High' or 'Top' importance:

19. Testosterone, C class, high importance
21. Meiosis, C class, top importance
28. Cell membrane, C class, top importance
32. White blood cell, Start class, top importance
34. Endocrine system, Start class, high importance
43. Osmosis, Start class, top importance
46. Genetic engineering, Start class, high importance
53. Sperm, Start class, top importance
79. Fat, Start class, top importance
82. Lactic acid, Start class, high importance

These articles seem like excellent candidates for COTM. However, as Boghog notes, articles listed in the recent deluge of reassessments are probably of more immediate concern. Emw (talk) 10:58, 3 March 2010 (UTC)

I am really pleased to hear that it is back! Although I am saddened to hear lots of people left. Additionally it kind of gives a sense of community: I have no idea what anyone else does and viceversa. I am one of the departees, or in my case fadees/transferee (due to war with deletionists about protocols and possible banners to avoid deltion in the first place).
What if we also introduced editor of the month? Either my seeing number of edits etc or say I adopt a pet project and work on it, I could nominate it (it'd feel more worthwhile and less people would leave, maybe).--Squidonius (talk) 06:43, 24 March 2010 (UTC)

Bimolecular fluorescence complementation

A couple of new users expanded this article quite a bit for a college assignment. I think it looks pretty good, but someone familiar with the technique might want to check the article out. PDCook (talk) 13:33, 4 March 2010 (UTC)

Separate gene from protein?

I suggest we do not write separate articles for proteins and their genes, at least not when there is a 1-1 correspondence and there is not too much text. I came across this phenomenon in the case of Cystic fibrosis transmembrane conductance regulator, the protein, and CFTR (gene). In this case most of the info about the gene is also in the article about the protein. Are there any other views on this? --Ettrig (talk) 15:40, 12 March 2010 (UTC)

I agree that this sort of thing is an issue (content forking for one), but I don't know how to remedy it. As an enzymologist I think that the gene articles should be merged into the protein articles. My bet is a geneticist might think just the opposite. I don't know if others think this is an issue at all, but I find it a bit untidy, and wonder if a good brainstorming discussion is in order. PDCook (talk) 16:28, 12 March 2010 (UTC)
In the vast majority of cases, I think there should be a single unified article about the gene and the protein encoded by that gene. In the case of the two CFTR articles, there was a lot of overlap in both content and citations. In particular, the gene article mentioned the function of the protein while the protein article contained considerable details ({{PBB/1080}}) about the gene. Information about both, especially since they are so interrelated, can happily coexist in the same article. In the spirit of WP:BOLD, I have gone ahead and merged these two articles. Cheers. Boghog (talk) 19:04, 12 March 2010 (UTC)
OK, OK. Inspired by the first response, I took this question to Wikipedia:WikiProject Genetics a response there referred to talk:Huntingtin, where quite a few editors agreed on combining the articles. --Ettrig (talk) 08:23, 13 March 2010 (UTC)
I feel the same way, there is no need to duplicate information. In most cases there is a 1:1 relationship and there will be hardly any cases where splice variants are noteable enough to get their own article. That might change though ;-). Greetings --hroest 11:52, 27 March 2010 (UTC)

Cell research

Someone created this article, and it reads more like a school essay. It's completely unreferenced, and there is a proposal to merge it into cell (biology), but I'm not so sure there is anything worth merging. Someone else may want to look at it. PDCook (talk) 18:50, 31 March 2010 (UTC)

I'm inclined to agree... there's nothing there that wouldn't be more appropriate in (or is already in) the cell (biology) article. – ClockworkSoul 18:58, 31 March 2010 (UTC)
Perhaps a redirect would suffice, as I suppose the title is a plausible search term. Or should it just be deleted all together? PDCook (talk) 19:08, 31 March 2010 (UTC)
"Cell research" seems like something that somebody might actually search for, so I'm all for the redirect. – ClockworkSoul 19:31, 31 March 2010 (UTC)
Perhaps redirect to Cell biology instead, it's more research. Narayanese (talk) 21:25, 31 March 2010 (UTC)
The author has removed the merge proposal but I reinstated it. This article should not continue as is, I don't think. It is not a quality to continue as a standalone article. Xtzou (talk) 13:37, 1 April 2010 (UTC)
(ec) Well, I think the article is mis-named, as it's more about the early history of cell research. So I personally think it should be redirected to Cell_(biology)#History. If there are no objections, I'm going to redirect it, as the original page author keeps making poor edits and has removed maintenance templates. I'm not sure there is anything worth merging, but the page history will be intact, and if someone wants to expand the Cell_(biology)#History section, they can pull material from there if they want it. PDCook (talk) 13:40, 1 April 2010 (UTC)
Although the issue here is that cell research is a valid search term, so where should it point? If others can think of a better target, let me know. PDCook (talk) 13:51, 1 April 2010 (UTC)

I went ahead and redirected the page to Cell (biology) as the original merge proposal suggested. If someone thinks the article should point elsewhere, feel free to change it. PDCook (talk) 14:15, 1 April 2010 (UTC)

Pfam boxes question

I have noticed that for some pfam boxes I would like to add multiple links to the same database. For example the C2 domain Pfam box should link to both Pfam entry PF00168, but also to PF00792. Can anyone either let me know how to do this (I've tried the obvious things I think). Or would it be possible to change the Pfam box definition to allow this? Alexbateman (talk) 12:32, 30 March 2010 (UTC)

Interesting question. In this particular case, PF00792 has corresponding entries in InterPro (IPR002420), SMART (PI3K_C2), and PROSITE (PDOC50004), as well as a non-overlapping set of PDB structures. Hence I think the best option is to add a second Pfam box as I did here. A better solution might be to allow adding additional columns in the {{Pfam_box}} template as well as {{Infobox protein}} and {{Infobox enzyme}} templates. However technically I am not the best person to implement such changes. Boghog (talk) 17:15, 30 March 2010 (UTC)
Thanks Boghog, I didn't think of doing that. Another point I note for the link to Pfam. Sometimes it may be better to link to a Pfam clan (e.g. CL0001) than to a Pfam family (e.g. PF00001). The current box doesn't allow for that, or at least the link would be wrong. If anyone who maintains the box can have a think about that I'd appreciate it. Alexbateman (talk) 07:09, 31 March 2010 (UTC)
Alex, so would clan be the highest level of organization that you'd want to link to (or are there others)? And in the case where the most natural link is to a clan, would you want to see that in addition to or instead of multiple links to PFAM entries? If in addition to, what's the largest number of PFAM entries per clan? Just trying to think of the possibilities here... Cheers, AndrewGNF (talk) 16:14, 31 March 2010 (UTC)
Yes clan is the highest level we would want to link to. The link looks like this: http://pfam.sanger.ac.uk/clan/CL0001 I was thinking about using this instead of a link to a Pfam family. But I guess one could consider having a Pfamclan link in the box and link to both the family and the clan. Thats an interesting idea and would be simpler to implement than having two sorts of identifiers for a Pfam link in the family box. A small number of clans contain over 100 Pfam families, so I don't think we would want to link to every family in a clan from a wikipedia page. Alexbateman (talk) 10:06, 1 April 2010 (UTC)

{{Infobox protein family clan | Symbol = EGF | Name = EGF superfamily | image = | width = | caption = | Pfam_clan = CL0001 | InterPro = | SMART = | PROSITE = | SCOP = | TCDB = | OPM family = | OPM protein = | Clan_members = DSL, EGF, EGF_2, EGF_alliinase, EGF_CA, FOLN, Laminin_B, Laminin_EGF, Tme5_EGF_like }}

C2 domain
Identifiers
Symbol C2
Pfam PF00168
Pfam clan CL0001
InterPro IPR000008
SMART C2
PROSITE PDOC00380
SCOP 1qas
SUPERFAMILY 1qas
I have created a new template called {{Infobox Pfam clan}} and have added an additional parameter called Pfam_clan to the {{Pfam_box}} template. Examples are shown to the right. As you have already suggested above, I don't think the first solution is very practical whereas the second does make sense. Cheers. Boghog (talk) 12:12, 1 April 2010 (UTC)
The new template looks great! So just to clarify though, on C2 domain, you guys would propose to have what combination of {{Infobox Pfam clan}} and {{Pfam_box}}? Still two Pfam boxes for PF00168 and PF00792, or replacing them with the Pfam clan box for CL0154, or having all three infoboxes? Not exactly clear to me which is best... Cheers, AndrewGNF (talk) 16:53, 1 April 2010 (UTC)


That does look great. Thanks Boghog. I suspect the box usage should be determined by the scope of the article. For example, the AAA proteins article seems to be discussing the clan rather than the family. In this case {{Infobox Pfam clan}} would be more appropriate.--Paul (talk) 20:36, 1 April 2010 (UTC)
OK that looks good, thanks! I am getting bit confused with all the different boxes though. I don't think we need to proliferate and have another box {{Infobox Pfam clan}}. Can we just edit the existing box {{Pfam_box}}? BTW I'm not sure the name Pfam box is really right. These boxes link to many different family databases than Pfam. I notice there is also a {{Infobox protein family}} that is used. It would be quite a bit of work to move all the Pfam info boxes to be {{Infobox protein family}} but perhaps that would be the most consistent thing to do and add the pfam clan link to that infobox. Alexbateman (talk) 08:50, 4 April 2010 (UTC)
Sorry for the confusion. {{Pfam box}} is a redirect to {{Infobox protein family}}, so there is really only one protein family infobox. For consistency, I have renamed {{Infobox Pfam clan}} to {{Infobox protein family clan}}. Finally I intended the {{Infobox protein family clan}} template to be more of a mock-up to see what it would-like and to assist in the discussion. I agree that we should avoid unnecessary proliferation of infoboxes. I think for most purposes, the {{Infobox protein family}} template that now contains a Pfam_clan parameter should be sufficient and the {{Infobox protein family clan}} template will rarely, if ever be needed. Cheers. Boghog (talk) 10:05, 4 April 2010 (UTC)
OK the confusion is just my lack of knowledge about how the boxes work :) I just added the clan link into the {{Pfam_box}} for the AAA proteins page as Paul suggested. That is really what I was looking for so thanks for your help with this talk! —Preceding unsigned comment added by Alexbateman (talkcontribs) 10:21, 4 April 2010 (UTC)
Yes, it's great. The box allows including any number of different databases (e.g. PANTHER or enzyme databases), some of which may or may not be used for each specific family. The real problem is to have someone to do this job. The best technical solution would be creating a bot for generating protein families from Pfam and Interpro, similar to ProteinBox bot.Biophys (talk) 15:05, 4 April 2010 (UTC)

Missing topics about metabolism

Can you have a look of the list of missing topics related to metabolism - Skysmith (talk) 13:21, 8 April 2010 (UTC)

weird essay, needs adoption

Teleost leptins is part of this project (I think), and desperately needs adoption/cleanup/merging/help. tedder (talk) 02:06, 10 April 2010 (UTC)

I have cleaned it up a bit. It certainly could use some more work, but I think it now is in relatively good shape. Cheers. Boghog (talk) 13:11, 10 April 2010 (UTC)

Suppressor-inducer T cells

I can't seem to find any references to support the Suppressor-inducer article. Does anyone know anything about this topic? If these cells do exist, the page also probably needs to be moved to include T cell in the title. Cmcnicoll (talk) 02:08, 12 April 2010 (UTC)

A quick search of PubMed came up with a large number of hits. I have included a few citations in the article as well as renamed it as you suggested to suppressor-inducer T cell. Boghog (talk) 05:48, 12 April 2010 (UTC)

Medicine and molecular cellular biology Wikiprojects announce collaboration with Google.org

Announcement of the first stages of a project to peer-review, improve and translate medical and biology articles so that material can be transferred from the English Wikipedia to other Wikipedias that are written in languages used in developing world. Tim Vickers (talk) 17:41, 16 April 2010 (UTC)

That's awesome, good stuff... Well done Tim! Cheers, AndrewGNF (talk) 20:00, 16 April 2010 (UTC)

growth media and a series of possibly stupid questions

I have found a set of pages which could do with a tidy up (except I am not a microbiologist and I just grown plasmids and protein), basically:
Growth media is used to grown microbial cultures and can be in the form of Broth or Agar plates, which are petri dishes with agar.
However this is what I found odd:

  • growth media and agar plates seem to be repeated (with the comment "omit agar for liquid broths") but growth media has a better organization
  • broth is about culinary soup
  • I though "petri dishes" in mammalian cell culture were called "plates" (flasks cannot always be used), say a 15cm plate? or is it a size thing? So apart agar and from makeshift usage (e.g. thumb-tack storage), is there any other use of a petri dish?
  • microbial culture has a stub section on cell culture ("cell culture" is only for multicellular Eukaryotes, right?).
  • thumb up to the author of {{Growth media}} --Squidonius (talk) 07:34, 22 April 2010 (UTC)

Massive reorganization of biomolecular structure articles

I've been perusing the articles on nucleic acid and protein structure recently, and I think that this set of articles could be improved by some reorganization. The theory behind this is that protein structure is fairly different than nucleic acid structure, but DNA structure and RNA structure are very similar, and the article organization should reflect this. Currently, the coverage of many of the articles is skewed towards one type of biomolecule or structure even though the title indicates a broader topic. Since there are pretty major changes, I thought it would be a good idea to discuss them here first.

I suggest the following article moves:

Primary structure -> Protein primary structure
Secondary structure -> Protein secondary structure
Tertiary structure -> Protein tertiary structure

All three of these articles are almost entirely about protein structure. The short bits about nucleic acid structure can be easily moved elsewhere.

DNA structure -> Nucleic acid secondary structure
RNA tertiary structure -> Nucleic acid tertiary structure

As it turns out, the DNA structure article is almost entirely about secondary structure. A moderate amount of rewriting will be required to explain the differences between DNA and RNA structure. A Nucleic acid primary structure article should be written, either from scratch or by moving text from another article.

RNA structure -> Biomolecular structure

This article will serve as a summary-style introduction pointing to all the other pages. The current RNA structure article has the right organization to form the core of this article. "Primary structure", "secondary structure," and "tertiary structure" should all redirect here.

One random question—is there such a thing as nucleic acid quaternary structure? Such a term doesn't seem to be in general use, but I want to make sure I'm not just unaware of it.

Antony-22 (talk) 03:29, 7 April 2010 (UTC)

The renaming you are proposing makes sense. My only reservation for making all these change are all the double redirects this will create. The nucleic acid quaternary structure question is an interesting one. I suspect that nucleic acid biopolymers are as or more likely to be associated with proteins rather than other nucleic acids. Hence a new section to the quaternary structure article probably should be added to address protein/nucleic acid complexes. Boghog (talk) 18:29, 7 April 2010 (UTC)
I intend to resolve the double redirects when I do the moves. I did a quick search on Google Scholar, and it looks like "DNA quaternary structure" is used in relation to the higher-level organization of DNA in a chromosome (e.g. doi:10.1002/bip.1977.360160308). I suppose this includes DNA-histone interactions as well. There might be enough material to make a short article; if anyone comes across any good references I'd much appreciate it. Antony-22 (talk) 19:03, 7 April 2010 (UTC)
One other question: what's a better wording for the titles: "Nucleic acid primary structure", or "Primary structure of nucleic acids"? Antony-22 (talk) 19:06, 7 April 2010 (UTC)
Good point about higher-level organization of DNA in chromosomes. I am not an expert on this subject, but from my understanding, an integral part of chromosomal organization are histone proteins. Hence any discussion of chromosomal quaternary structure would be incomplete without mentioning histones. Concerning proposed article names, I think "Nucleic acid primary structure" is preferable to "Primary structure of nucleic acids" per WP:TITLE. Boghog (talk) 19:41, 7 April 2010 (UTC)
The reorganisation all sounds reasonable. For consistency with the other titles I agree that "Nucleic acid primary structure" is better. For the quaternary the Spliceosome page has a nice image showing interactions between U4, U5 and U6. I guess "quaternary structure" between RNAs is generally called antisense since the interactions are primarily due to base pairing. Altho there are Triplexes and quadruplexes. --Paul (talk) 20:14, 7 April 2010 (UTC)

Done

Okay, 81 edits later, I've finished the reorganization. I've also moved Quaternary structure to Protein quaternary structure, and created Template:Biomolecular structure to link everything together. I have the following notes:

Any revisions to any of the articles that have been moved would be greatly appreciated. Antony-22 (talk) 21:26, 10 April 2010 (UTC)

Nice work Antony-22! Regarding the Nucleic acid design, the Vienna suite of programs has a tool RNAinverse which has been fairly widely used for generating sequences consistent with a defined structure:
  • Gruber AR, Lorenz R, Bernhart SH, Neuböck R, Hofacker IL (2008). "The Vienna RNA websuite.". Nucleic Acids Res 36 (Web Server issue): W70–4. PMID 18424795. 
The Protein design article makes no mention of Ancestral sequence reconstruction but I believe it and the nucleic acid design should. Eg. there has been quite a bit of work on reconstructing ancient genomes:
  • Chauve C, Tannier E (2008). "A methodological framework for the reconstruction of contiguous regions of ancestral genomes and its application to mammalian genomes.". PLoS Comput Biol 4 (11): e1000234. PMID 19043541. </ref>
  • Ma J, Ratan A, Raney BJ, Suh BB, Zhang L, Miller W, Haussler D (2008). "DUPCAR: reconstructing contiguous ancestral regions with duplications.". J Comput Biol 15 (8): 1007–27. PMID 18774902. 
  • Ma J, Zhang L, Suh BB, Raney BJ, Burhans RC, Kent WJ, Blanchette M, Haussler D, Miller W (2006). "Reconstructing contiguous regions of an ancestral genome.". Genome Res 16 (12): 1557–65. PMID 16983148. 
ASR has also been proposed for vaccine design:
  • Nickle DC, Jensen MA, Gottlieb GS, Shriner D, Learn GH, Rodrigo AG, Mullins JI (2003). "Consensus and ancestral state HIV vaccines.". Science 299 (5612): 1515–8; author reply 1515–8. PMID 12624248. 
  • Mullins JI, Nickle DC, Heath L, Rodrigo AG, Learn GH (2004). "Immunogen sequence: the fourth tier of AIDS vaccine design.". Expert Rev Vaccines 3 (4 Suppl): S151–9. PMID 15285713. 
And it's been used for boosting homology search methods:
  • Collins LJ, Poole AM, Penny D (2003). "Using ancestral sequences to uncover potential gene homologues.". Appl Bioinformatics 2 (3 Suppl): S85–95. PMID 15130821. 
All for now, keep up the good work! --Paul (talk) 08:49, 11 April 2010 (UTC)
For a Nucleic acid primary structure article, I propose moving DNA sequence to Nucleic acid sequence and redirecting Nucleic acid primary structure to that. Narayanese (talk) 15:47, 11 April 2010 (UTC)
Regarding the reorganization of the biomolecular structure sections: Certainly this was needed, and overall, the approach taken is very good. Last year, when I set out to find a topic for my class to work on, it was clear the entries were a disorganized collection of good intentions. I would like to make a few suggestions:
1) I would not lump RNA and DNA higher order structure (tertiary) together. The RNA tertiary structure section is already missing a lot of text and figures that I removed from my classes' efforts as they did not pass our quality control. In short, this is a section that will grow in size. DNA higher order structure is different and more limited compared to RNA. Also, structures formed by DNA often serve different purposes. I think if you make a single Nucleic Acid Tertiary structure section, you will find in a year that you are trying to divide it in two (or more!). You might as well start now by having a separate DNA and RNA section. Alternatively, you can have a Nucleic Acid Structure section that is relatively brief and describes differences between RNA and DNA tertiary structures, but then points to an RNA Tertiary Structure page and a DNA Tertiary Structure page
2) Quaternary structure is a not a very modern idea. While it is a term worth knowing, the difference between quaternary structures and tertiary structures are simply the presence of a linker. For example, a coiled coil can be a quaternary structure formed from two alpha-helices. It is also a a tertiary structure in helix bundle proteins. The details of the structure interactions are identical. Function, and energy is affected, but not structure.
3) The biomolecular world is bigger than just protein and nucleic acids. I would make entries that anticipate polysaccharides, lipids and small molecules. Instead of quaternary structure, you might imagine making entries that represent recognition of one biomolecule by another. All the other fun structure entries represent interactions among these different molecule types. Helicases are an example of protein:DNA interactions, riboswitches are examples of RNA:small molecule interactions etc etc. Quaternary structure then just becomes the special case of self:self recognition. MirankerAD (talk) 08:36, 12 April 2010 (UTC)
Paul: thanks for the refs! I'm not very familiar with ancestral sequence reconstruction, but feel free to add the material wherever you think it is appropriate. I'll definitely use the Vienna reference in Nucleic acid design, which should be appearing very soon.
Narayanese: Sounds like a good plan. I'm a bit torn since "Nucleic acid sequence" is more common especially in a less technical setting, but "primary structure" is consistent with the nomenclature of the other articles. I think your plan would work well, though.
MirankerAD: I figure that RNA and DNA tertiary structure articles can be split out as you describe once there's actually material on both. I too am not entirely clear on the difference between tertiary and quaternary structure for nucleic acids; I don't think the latter term is used frequently or particularly consistently. I figure that the Nucleic acid quaternary structure article would be a shorter article describing the different ways in which the term is used, and linking to other articles that describe them. I also think it could be great if Biomolecular structure could be further expanded to talk about the higher-level structure of other biomolecules; unfortunately I don't really know enough about non-nucleic acid structure to do it myself.
Antony-22 (talk) 20:52, 13 April 2010 (UTC)
I'd like to extend my earlier thoughts. It strikes me that there isn't so much of a distinction between DNA and RNA structure, as there is between double-helical and "globular" nucleic acid structures: an RNA double helix will have similar properties as a DNA duplex, and globular DNA structures like DNAzymes are similar to globular RNA structures. The thing is, biologial DNA's are almost always double helical, while biological RNA's are almost always globular, so it's easy to conflate the two. I've been trying to introduce this distinction as I've been editing the articles, but the implications for the article organziation still needs further thought. Antony-22 (talk) 02:58, 14 April 2010 (UTC)

Biomolecular structure, phase II

I've been doing some more thinking. My reading indicates that nucleic acid secondary structure strictly consists of a list of the base pairs; the structure of the double helix itself strictly speaking is tertiary structure, though it's intimately related with secondary structure. A lot of the material in Nucleic acid secondary structure is about double helix structure though. So I'm thinking about the following changes:

The expansions in the primary and secondary structure articles will mostly be summary-style grabs from other articles. Please feel free to suggest additional articles to include, and let me know what you think of the changes in general.

It's also worth mentioning, Nucleic acid design is up and was DYK a few days ago. Antony-22 (talk) 05:38, 24 April 2010 (UTC)

Default portal image

Currently, there are two different portal images, depending on how the portal template is called. Which one would people prefer? I'm not watching this page, so it would be great if you could comment at Template talk:Portal#Case duplicates. Thanks! Plastikspork ―Œ(talk) 17:35, 17 April 2010 (UTC)

{{Portal|Molecular and cellular biology}}
{{Portal|Molecular and Cellular Biology}}
The first is relevant graphic of a protein but way too detailed and therefore fuzzy at the displayed size. The second is a very clear but generic icon. Another issue is that the MCB portal encompasses both molecular and cellular aspects and it would be nearly impossible to capture both a small icon. Here is another suggestion, but unfortunately it is not much better:
{{Template:MCB portal}}
Unless someone can devise a clearer and relevant icon, my preference would be the generic icon. Boghog (talk) 20:13, 17 April 2010 (UTC)
One can't do too much in that size. This image is off {{Template:MolBioGeneExpl}} with darker colour for contrast and you can barely see it...
DNA small.svg

--Squidonius (talk) 11:52, 18 April 2010 (UTC)

A way to capture both molecular and cellular aspects in one image might be to use a depiction of the place of DNA in a cell nucleus, like this, which actually looks pretty decent at 40 px. I searched chromosome, dna, dna cell, and the first 400 results of cell on the commons but couldn't find anything similar to that. The closest was this which doesn't work as an icon. Adrian J. Hunter(talkcontribs) 14:07, 18 April 2010 (UTC)
Wow, I just realised what a bizarre page my off-wiki suggestion came from... DNA testing of dog poo to "motivate" owners to pick up after their dogs??? Anyone feel like updating DNA profiling? Adrian J. Hunter(talkcontribs) 14:18, 18 April 2010 (UTC)
Brilliant! Even if it was inspired by dog poo ;-) Now all we need is a public domain version. However I wouldn't know how to begin creating such a graphic. Any volunteers? Boghog (talk) 17:00, 18 April 2010 (UTC)


I tried my best for a quick stab at a 40px icon based on the image given and this is what I came up with (the black line around the DNA can be improved a small bit in the kinks, but not much)
MCB small icon test.png

. Which having more going on is less clear than the DNA above (which can still be tweaked a bit, low res vectors always look worse than custom made small raster) --Squidonius (talk) 05:39, 20 April 2010 (UTC)

Not bad! Here's how it looks in the template:
Portal icon MCB portal
Thanks. Boghog (talk) 05:46, 20 April 2010 (UTC)
I merged the two case-variations. If you would like to use File:MCB small icon test.png, just place an edit request at Template talk:Portal. Thanks! Plastikspork ―Œ(talk) 16:33, 1 May 2010 (UTC)

Microscopy illustration

Since microscopy is within your scope, I'm letting you know about this figure that I composed (from previously existing material) that might be useful for illustrating aspects of light and/or electron microscopy. If you need to make changes that will reduce the EV in the three butterfly-related articles where it's currently placed, please create a fork instead. Thank you.

Photographic and light microscopic images Inachis io top MichaD.jpg Inachis io top detail MichaD.jpg Microphoto-butterflywing.jpg
Zoomed-out view of an Inachis io. Closeup of the scales of the same specimen. High magnification of the coloured scales (probably a different species).
Electron microscopic images SEM image of a Peacock wing, slant view 1.JPG SEM image of a Peacock wing, slant view 2.JPG SEM image of a Peacock wing, slant view 3.JPG SEM image of a Peacock wing, slant view 4.JPG
A patch of wing Scales close up A single scale Microstructure of a scale
Magnification Approx. ×50 Approx. ×200 ×1000 ×5000


Papa Lima Whiskey (talk) 11:38, 1 May 2010 (UTC)

limits

what are the permissiable limits for pollutants and heavy metals in soil and water?--59.97.248.171 (talk) 14:00, 4 May 2010 (UTC)

There are lots of types of pollutants, lots of different countries and different types of water (drinking, bathing, waste etc) so the question is very vague. The best thing to do is just check the EU standards link, which the whole world copies (with the comical exception of the additive numbers which out of the EU are identical but are not called E numbers as E stands for europe). This question is out of place, please use the help desk. --Squidonius (talk) 14:31, 4 May 2010 (UTC)

Mitochondrion Cleanup

(copy of Wikipedia talk:WikiProject Microbiology#Mitochondrion Cleanup)

I am a reasonably experienced editor, but domain non-expert, interested in the Mitochondrion and related articles. I've been somewhat unsatisfied with the overall article structure for some time and I feel that it needs improving from an editorial rather than content perspective. For example the article has a number of daughter articles (eg. Outer mitochondrial membrane for the section Outer membrane) are based on a clone of content. However there seem to be three main problems:

  1. The cloned copy has only pulled across the text and not the corresponding references, leaving the daughter page unreferenced.
  2. Content has been added to the main article, but not the daughter so that the latter is different to the former rather than a superset.
  3. There are sometimes minor inconsistencies between the two versions.

I propose to clean up some of these, but given my non-expert status, I wanted to alert project members and get feedback before doing so. I will create a discussion and repeat this post on the Talk:Mitochondrion page. I'll leave it a week or so for comment before starting. -- TerryE (talk) 14:42, 4 May 2010 (UTC)

Rilonacept

Rilonacept is an engineered fusion protein. I'm wondering if it is also classified as a designed protein, i.e. one created by site-directed mutagenesis rather than directed evolution. Any idea? Lfh (talk) 20:26, 15 May 2010 (UTC)

This is a semantic question and hence there may be no universally agreed upon answer. The following is my interpretation. While Rilonacept in a broad sense is a designed protein, it was not designed from scratch nor was it made from calculated changes from a known structure. Rather it is a fusion protein composed of parts of two known proteins and combines properties of each of the two proteins into one molecule. Hence in the way that designed proteins are usually defined, Rilonacept is not a designed protein. Boghog (talk) 21:29, 15 May 2010 (UTC)
Boghog is right (and crystal clear, kudos). Parenthetically, it is also non-sythtetic (also a grey definition). I was wondering are all artificial proteins engineered protein? In vitro/directed evolution creates artificial/engineered proteins (I think at least), but do random shuffling experiments?
I think a nice glossary may be building up for Protein engineering... --Squidonius (talk) 00:45, 16 May 2010 (UTC)