Wikipedia talk:WikiProject Molecular Biology/Molecular and Cell Biology/Archive 3

I have recently been looking at the referral stats for a number of biological databases to find out how much traffic Wikipedia is generating for them. I contacted the nice people at the RCSB PDB and they tell me that 9% of referrals (not including direct traffic from bookmarks etc) come from Wikipedia. This is a cool statistic! Andreas at PDB tells me that on average visitors to PDB from Wikipedia stay for less time than others. But one final statistic that Andreas would like suggestions about is why, "in contrast to all other site trends we have fewer wikipedia referrals this year compared to last year. Perhaps something got changed in the presentation of links back to us, or wikipedia usage is dropping?". Does anyone have any insight into this? Thanks Alexbateman (talk) 13:23, 28 February 2011 (UTC)

In this edit, the PDB codes became hidden by default in the Gene Wiki template. Now you have to hit the "show" link next to "Available structures" to get the link to RCSB (see for example STK11). That's my best guess... Cheers, AndrewGNF (talk) 18:17, 28 February 2011 (UTC)

That is cool! I think Andrew hit the nail on the head. An analogous change to the {{Infobox protein family}} template was made in this edit. Additional {{PDB}} links that may have been included in-line or in the further reading sections are slowly being deleted since they are already contained in the Gene Wiki and Pfam infoboxes and therefore are redundant. While the number of referrals may be down, those that do find and follow the links are probably more determined and therefore may stay longer. Boghog (talk) 20:04, 28 February 2011 (UTC)

Thanks, that explains a lot. The hidden database IDs result in fewer clicks that go through to PDB... We have a number of widgets and tagging libraries which might serve as an inspiration of how lists of database cross-references could be displayed to the user in a more graphical way. http://www.rcsb.org/pdb/static.do?p=widgets/widgetShowcase.jsp I understand that wikipedia won't be dynamically loading any content from other sites, but I wonder if a better presentation might still be possible within mediawiki... Something else: Seems there is a systematic issue and there are several pages that contain a section labeled "Available PDB structures" but the links don't go to any of the PDB sites, but to PDBsum. I suggest renaming the section to "Links to PDBsum" and adding another section that redirects to the PDB. Examples: Leucine-rich_repeat, Ligand-gated_ion_channel Andreas (Andorsch (talk)) —Preceding undated comment added 22:41, 28 February 2011 (UTC).

For at least Leucine-rich_repeat, it apparently was a conscious decision to link to PDBsum because of the use of {{PDB3}}. If the editor had used {{PDB2}} (or if someone wanted to change the template to PDB2), then the links would go to RCSB... Cheers, AndrewGNF (talk) 00:36, 1 March 2011 (UTC)

There was some disagreement as to which external link was most appropriate (see Template_talk:PDB for the gory details). We left it to the individual contributor to decide which link to include (see for example Hsp90 for an article that contains pfam infoboxes that point to the rcsb). There is another template called {{Infobox enzyme}} that links to PDBSum since it is not clear at least to me how to format a link to the PDB that will produce a list of structures for a given EC number. Andreas, do you if it is possible to construct such a link (for example a link that would produce output equivalent to the advanced search query parameter: Enzyme Classification Search : EC=1.1.1.1)? Boghog (talk) 09:18, 1 March 2011 (UTC)

Thanks for the pointer to that thread. It seems a bit out of date and many things have changed since then. PDB is the primary database and my feeling is that outgoing links should point to it, rather than derived databases. If links go to a secondary site, they should be labeled with the correct database name. At the present you can link via EC numbers to RCSB PDB using this URL http://www.rcsb.org/pdb/search/smartSubquery.do?smartSearchSubtype=EnzymeClassificationQuery&Enzyme_Classification=1.1.1.1 (there prob. will be an alternative and simpler URL available as well soon). Such URLs are available for pretty much each of the advanced queries. Let me know if you have any other PDB related questions. Andreas (Andorsch (talk) 14:44, 1 March 2011 (UTC))

And thank you for the PDB EC link. I have updated the {{Infobox enzyme}} template so the link now points to the RCSB PDB. From the beginning I thought it was better to link to the RCSB PDB and with the recent improvements, I now even more strongly believe that. Again, thanks for your help. Cheers. Boghog (talk) 19:41, 1 March 2011 (UTC)

Awesome... What is needed to get the the text "Available PDB structures" changed to "Links to PDBsum" at {{PDB3}} (or update the link to point to PDB) ? I am happy if article authors have free choice to which external resource they want to link, however PDBsum is not related to PDB and as such the headline over the box should be precise. --Andreas (talk) 02:08, 2 March 2011 (UTC)

It is trivial to change the {{PDB3}} template to point to the RCSB PDB and create a new PDBSum template, but as can be seen from the previous discussion, there were disagreements. As you point out, there have been many enhancements to the RCSB PDB since then (perhaps the most important in the context of the {{Infobox enzyme}} template is that links to UniProt are now included and Pfam and InterPro domain assignments can now be displayed over the sequence graphic) so I think standardizing on RCSB PDB should now be less controversial. I will raise the issue again at the PDB template talk page. Boghog (talk) 07:26, 3 March 2011 (UTC)

Back to the original question by Alex, nothing has changed with links from wikipedia during this time, according to my knowledge. Perhaps the number of people who are using wikipedia decreased during this time, and this is an explanation. We now have several templates with links to different sources of PDB files, which is only convenient. As about links from Pfam template, I would trust the opinion of Alex. What he thinks? Which PDB link would be best from Pfam template? That could be PDB in US, PDBe in Europe (which is definitely better than PDB in US), or PDBsum. I do not have any personal interest here, except that PDBsum is the best for wikipedia users (we had quite a dispute with Boghog about this here).Hodja Nasreddin (talk) 03:00, 4 March 2011 (UTC)

Hodja, I see that you have been making strong statements in the past. Just to make sure your opinion is based on the current state of the RCSB PDB (see ^[1] as well as the releases over the last years) and not on a state it might have been several years ago... --Andreas (talk) 06:58, 4 March 2011 (UTC)

Andreas from the PDB, we are not in a business to increase PDB traffic, but there is a good way to do it: run ProteinBoxBot for every protein currently in PDB and create articles about them. This can be done by using Uniprot summaries about proteins (it has the same copyright conditions as wikipedia). Remember that number of different proteins in the PDB is several times smaller than number of PDB files. Exclude proteins from Structural Genomics projects as not notable. I am sure that PDB staff can easily do it. This is the way to do well for PDB, but still be in agreement with wikipedia policies. The issues abouta Pfam box and PDB3 templates are irrelevant. Thanks, Hodja Nasreddin (talk) 23:06, 4 March 2011 (UTC)

My intention is only to get the link corrected that is wrongly attributed as pointing to the PDB. We don't need wikipedia to increase our traffic. Besides this, we are suporters of open access and you can already find content from us on various pages, although not as systematic as you are suggesting. --Andreas (talk) 00:38, 5 March 2011 (UTC)

The thread is about PDB traffic through wikipedia. There is nothing obviously "wrong" in Pfam template. It tells "available PDB structures" (not PDB RSGB site) and directs user to PDB files through the PDBsum site. All these links (PDD, PDBe, PDBsum, etc) are good likns rather than "links to avoid". Hence this is more a matter of personal preference for an editor who creates/modififes a page. Hence we have a number of different templates. Hodja Nasreddin (talk) 01:10, 5 March 2011 (UTC)

Molecular and Cellular Biology WikiProject members, please, this is being discussed at:

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

Thank you. Pandelver (talk) 00:17, 12 March 2011 (UTC)

In wikipedia if bacteria cause a disease they are well documented, otherwise they are a red link. Escherichia coli has an extensive review of its pathogenic strains and a malformed Biotech section. I added a section on diversity and created a new page called (Escherichia coli (molecular biology), where I have written about the history of K-12 and B strains but have not mentioned molecular cloning, unfortunately I will not have any editing time in the near future, so if anyone wants to add a section please do! --Squidonius (talk) 13:47, 12 March 2011 (UTC)

Over at BRCA2, a mutation "999del5" is identified as truncating the protein. What does the "5" mean here? I know what "999delA" would mean, but I don't think I've seen a number used, and I can't find the answer. WhatamIdoing (talk) 20:32, 17 March 2011 (UTC)

Not 100% sure, but from Am. J.Hum. Genet. 60:1050-1058, 1997, table 2, it appears that 999del5 = 999delTCAAA, meaning starting at nucleotide position 999 of the BRCA2 gene, the five nucleotides "TCAAA" have been deleted producing a frameshift mutation. Boghog (talk) 21:33, 17 March 2011 (UTC)

It was my impression that frameshift shouldn't produce a truncated protein, which is what the article asserts. It should, in theory, produce an equally long protein, with a nonsensical amino acid sequence. (Shouldn't it?) WhatamIdoing (talk) 01:15, 18 March 2011 (UTC)

A frameshift mutation will result in the original stop codon not being read and depending on the sequence, will produce new stop codons that may appear before or after the original stop condon. In the case of the 999del5 mutation in BRCA2, a new stop condon appears before the old one resulting in a truncated protein. Boghog (talk) 06:36, 18 March 2011 (UTC)

Yep. Frameshifts usually result in protein truncation: 3 of the 64 possible nucleotide triplets are read as stop codons, so generally a stop codon will appear shortly downstream of a mutation that causes a frameshift. Adrian J. Hunter^{(talk•contribs)} 12:24, 18 March 2011 (UTC)

Thanks for the explanation. I appreciate it. WhatamIdoing (talk) 05:08, 19 March 2011 (UTC)

Why are em dashes used on List of EC numbers (EC 2) and many of the templates at the bottom of that page? Sources may use en dashes, but no-one uses an em dash within a word. These shouldn't even be redirects. I thought about moving the em-dash redirects to en dashes, but there are so many of them that I was worried I might gunk things up. Am I missing something? Also, aren't many of these ambiguous with the use of only hyphens? — kwami (talk) 22:50, 18 March 2011 (UTC)

I see that many of the links that used em dashes were redirects to page names without em dashes, so I went ahead and edited the links. It appears that the em dashes are part of the IUBMB accepted name (see EC 2.1.1.3 for example). I also tried to find to find an official IUBMB guidelines concerning the use of dashes, but I cannot find any. I am not certain what is the best course of action is. Rename the articles or eliminate the directs from the category pages. Given the number of enzyme pages, either course of action would be an enormous amount of work. Boghog (talk) 09:24, 19 March 2011 (UTC)

On second thought, it is clear that em dashes in enzyme names are used to separate the names of different reactants in the catalyzed reaction whereas hyphens are used within a chemical name. So to be correct, the enzyme pages should really be renamed to include an em dash if one is used in the IUBMB accepted name. However again would be an significant amount of work and it is probably best that a bot do this. If there is consensus for doing this, I might be willing to bring BogBot out of hibernation to complete this job. Boghog (talk) 09:40, 19 March 2011 (UTC)

I'll be damned! They really do use em dashes. I thought it was just an editor who couldn't tell the difference. Yes, they should be moved to the more precise punctuation. I can do that with AWB. But first, can we verify that that web site has it right? Surely they should say somewhere that's the convention. It really is bizarre to use em dashes rather than en dashes in the middle of names. — kwami (talk) 19:13, 19 March 2011 (UTC)

The link EC 2.1.1.3 is to the International Union of Biochemistry and Molecular Biology (NC-IUBMB), so it doesn't get any more official than this. Hence I certainly believe that the web site is correct. There are 3246 pages that transclude the {{Infobox enzyme}} template so that there are at least that many enzyme articles. Not sure how many have names with em dashes in them however. Probably a relatively small fraction, may be on the order of a few hundred. I think the reason that em dashes are used instead of en dashes is that enzyme names often contain many hyphens (and spaces) and an single en dash may not stand out enough. For the most part, links containing em dashes are redirects to names where the em dash has been replaced by a single hyphen. Boghog (talk) 21:08, 19 March 2011 (UTC)

Yes, I figured that might be the reason. But the number of articles is not convincing in itself: if a typographic mistake were made, it could easily be site-wide. (I've done that myself, typesetting dozens of articles with AWB only to realize that I'd been using a wrong symbol.) I don't have any reason to think that's the case, but it would be nice to verify this verbally. — kwami (talk) 22:13, 19 March 2011 (UTC)

I now have some hard numbers. Based on enzyme.dat (Bairoch A (1993). "The ENZYME data bank". Nucleic Acids Res. 21 (13): 3155–6. PMC 309744. PMID 8332535. {{cite journal}}: Unknown parameter |month= ignored (help)), there are 5268 Enzyme Commission entries (record = "ID"). In this particular file, en/em dashes in the accepted name (record = "DE") are represented by a double hyphen "--". There are 226 entries with a double hyphen (see User:Boghog/Sandbox5 for wiki links, two links per line, left link is based on the enzyme name where the double hyphen has been replaced with a single hyphen, "--" → "-", right link double hyphen has been replaced with an em dash, "--" → "—"). It appears that the articles names have em dashes replaced with hyphens whereas the proper enzyme names containing the em dashes are redirects. In my opinion, the direction of these redirects should be reversed. Boghog (talk) 10:38, 20 March 2011 (UTC)

I agree with reversing them, of course. My only concern is moving them all and then realizing, oops! wrong dash.

Evidently because of coding problems, in some names brackets have been replaced with parentheses. An example is (glutamate-ammonia-ligase) adenylyltransferase ~ (glutamate—ammonia-ligase) adenylyltransferase. It would be good to correct those too if we can. I'll see what I can dig up. — kwami (talk) 20:56, 20 March 2011 (UTC)

Ah, see Wikipedia:Naming_conventions_(technical_restrictions)#Forbidden_characters. Square brackets are not allowed, and the templates that modify a title (such as eBay) do not work for them. We can substitute East Asian brackets, but they won't kern properly: ［glutamate—ammonia-ligase］ adenylyltransferase. — kwami (talk) 21:24, 20 March 2011 (UTC)

I done an extensive google search, and I cannot find any documentation about whether em or en dashes should be use in enzyme names. In looking at other databases, there doesn't seem to be much consistency. For Thetin-homocysteine S-methyltransferase:

If double and triple hyphens are considered equivalent to en and em dashes respectively, then three four of the databases use em dashes, two one uses en dashes, and one uses hyphens. Since the official IUBMB database uses em dashes, my opinion is the article names should also contain em dashes. Boghog (talk) 21:30, 20 March 2011 (UTC)

Concerning the brackets, I guess we can keep them as is (i.e., use parentheses) and insert {{Correct title}} templates. Boghog (talk) 21:33, 20 March 2011 (UTC)

What would be the 2nd source using en dashes?

Double hyphens are the usual substitute for em dashes, and single hyphens the substitute for en dashes. (Triple hyphens are occasionally for em dashes used when double hyphens are used for en dashes.) So we have no evidence that anyone uses en dashes, while 3 and possibly 4 use em dashes. That's convincing. I'll start moving. — kwami (talk) 21:47, 20 March 2011 (UTC)

I fixed a dozen or so links on your sandbox (parentheses and clipped names). — kwami (talk) 22:03, 20 March 2011 (UTC)

You are right, there is no 2nd source using en dashes. Thanks for starting the move and for fixing the names in my sandbox. Boghog (talk) 05:57, 21 March 2011 (UTC)

Power went out, but I'll restart AWB in a minute. — kwami (talk) 06:15, 21 March 2011 (UTC)

• There's an AfD discussion for Wikipedia:Articles for deletion/Nkx2-2as that it would be useful to get input from MCBers on.--Paul (talk) 08:06, 26 March 2011 (UTC)

Is there somewhere here discussing why (or if) the self replicating molecule only got created once? 82.137.72.133 (talk) 10:51, 31 March 2011 (UTC) Yes, so I went and posted it on the link for queries at the top of the page and it came back herePpeetteerr (talk) 12:31, 4 April 2011 (UTC)

Hi,

Plindenbaum and I were editing some pages on Orthology databases. We discussed making a subcategory of Biological databases called something like Orthology databases. Of course one could subclassify the biological database articles more completely. Perhaps using the NAR database collection classification:

http://www.oxfordjournals.org/nar/database/c/

Has this been discussed before? Alexbateman (talk) 08:22, 4 April 2011 (UTC)

Is there somewhere here about why (or if) the self replicating molecule only got created once? Ppeetteerr (talk) 12:30, 4 April 2011 (UTC)

Is this self replication my answer? (joke)Ppeetteerr (talk) 12:35, 4 April 2011 (UTC)

There is no proof of a "Shadow Biosphere" at present (although the topic has gained ignominy after the badly phrased Arsenic Felisa Wolfe-Simon paper). I am not sure if anyone has delt with the topic, but if a self replicating molecular machine were to arise twice with similar substrates (therefore were in competition), one would have a much higher fitness than the other (IMO), eg. LUCA's forefathers were one more rubbish (low fidelity and high promiscuity) than the other, until there was little fitness difference resulting in a radiance of 3 domains and the hard polytomy of bacterial phyla. There is a paper where they get junk DNA and make a antibiotic resistance gene in 50 cycles and its improvement per cycle follows a rectangular hyperbola. Interesting topic of speculation... --Squidonius (talk) 20:42, 4 April 2011 (UTC)

A number of editors, both named and anonymous, have been adding external links to GeneReviews. Usually this is from accounts that have never edited before and subsequently make no contributions. Instead of using the {{Infobox disease}}, the editors use the external links section. Often, the links are only to very peripherally related conditions. Today it was 205.152.158.201 (talk · contribs) who did a link adding spree.

Does anyone know why this is happening, and does everyone agree that these links are not always useful? What could we do to streamline these edits? Does anyone know the presumed person who is behind this? JFW | T@lk 17:04, 5 April 2011 (UTC)

I don't think anyone besides the person him/herself knows who this individual is. After some prodding, the individual is doing a somewhat better job of conforming to Wikipedia guidelines. But the format and relevance could certainly be improved further. As you suggest, the individual should use the already existing fields in the {{Infobox disease}}. In addition, this individual has been adding a lot of links to Gene Wiki articles. We don't have any relevant fields in the {{GNF Protein box}} template at the moment, but perhaps we should add a "disease linkage" section where GeneReviews links could be added. Furthermore we could have a bot go through these pages and move the external links to the infoboxes. Boghog (talk) 18:33, 5 April 2011 (UTC)

This came up at the external links noticeboard over a year ago, and I believe that the GeneReviews parameters were added to Infobox disease as a direct result. At the time, the editor was being reasonably careful about the links s/he added. So long as that is still more or less true, and any individually unwanted links aren't being edit-warred over, then I don't think we have a problem—except for my conviction that such a person could be a valuable registered editor, and I'd like to convert him from a "links-only" anon to a solid content contributor if at all possible. WhatamIdoing (talk) 19:29, 5 April 2011 (UTC)

I have no intention of chasing away the editor and would love to pin them down and turn them into content generators. JFW | T@lk 21:44, 5 April 2011 (UTC)

A new editor has asked for help at WP:FEEDBACK with Satellite cell (glial). It sounds like she's a student and has significantly expanded the article. If someone who knows a thing or two about this would please leave a note on the article's talk page at Talk:Satellite cell (glial), then I'm sure she would be grateful. WhatamIdoing (talk) 19:26, 8 April 2011 (UTC)

Monopolin has been an orphan since the winter of 2009. "Mono" means "lonely" in Greek... Will spring 2011 bring hope? You can make a difference. ^walk victor falk ^talk 11:14, 10 April 2011 (UTC)

Don't pass go and don't collect $2000. JFW | T@lk 15:15, 10 April 2011 (UTC)

Here in NZ, it is autumn... it is raining here so the spring comment is very upsetting :-P --Squidonius (talk) 22:24, 10 April 2011 (UTC)

Hi all! I currently have peer reviews running for two articles I have worked on, DNA nanotechnology (review page) and Nucleic acid design (review page). I'd appreciate it if you could take a look and leave any feedback you could give. Thanks! Antony–22 (^talk⁄_contribs) 01:42, 19 April 2011 (UTC)

Just a quick pointer that there is an interesting thread over at WikiProject Chemicals about enabling Jmol on wikipedia. This is something that might be interesting for many pages here, too. --Andreas (talk) 04:08, 8 April 2011 (UTC)

On a related note, would anyone mind if I uploaded the PDB to Wikipedia? All the tools were developed here: http://PDBWiki.Org --Dan|^(talk) 13:09, 12 May 2011 (UTC)

BTW, where is the Jmol discussion? --Dan|^(talk) 13:11, 12 May 2011 (UTC)

The discussion was moved to an archive. Concerning uploading the PDB to Commons, this might make sense if and when Jmol is made available. However there are some significant security concerns in doing that. In the short to medium term, a off-site Jmol server might be a more acceptable solution (see for example chemapps) and it would make sense to store the coordinates on that server. Boghog (talk) 16:04, 12 May 2011 (UTC)

Hi everyone,

My biological clocks class is working on a few circadian biology articles. We've submitted cryptochrome (create review page) and Candolle (create review page) at GAN, but so far no reviewers have shown up; if one of you could help with a review, that would be great. We're also tackling the following articles:

• Timeless (gene)
• Melanopsin
• CLOCK
• Pigment dispersing factor
• Period (gene)
• Casein kinase 1
• Colin Pittendrigh
• Ron Konopka
• Jürgen Aschoff
• Jean-Jacques d'Ortous de Mairan
• Joseph Takahashi
• Ignacio Provencio
• Seymour Benzer

We haven't set up formal peer reviews for the latter articles, so the talk pages for the articles are fine for feedback. General feedback for the class can go here or on my talk page. Thanks! C1ock122 (talk) 21:17, 19 April 2011 (UTC)

Bleb is a (the) member of the non-existent category Category:Cell motility. I'm not sure it belongs there, however I am also inclined to think that would be a useful category. I leave it to the experts. Rich Farmbrough, 23:48, 24 April 2011 (UTC).

The category member is currently Bleb (cell biology), and it seems reasonable. Mikael Häggström (talk) 06:13, 15 May 2011 (UTC)

I wanted to know the consensus for what headers and sections a protein or gene article should have and what are the preferred orders, but both wp:Manual of style (protein articles) and wp:Manual of style (gene articles) are currently red at this time of posting. They should be made blue, either by redirect or by article creation. Mikael Häggström (talk) 06:10, 15 May 2011 (UTC)

That would be really good, there is little consistency for non-human protein and there are many basic anabolic enzymes which are missing, such as 3-isopropylmalate dehydrogenase (leuB or IPMDH). --Squidonius (talk) 06:37, 15 May 2011 (UTC)

Concerning non-human proteins, the {{Infobox protein}} template was used for historical reasons however this is far from optimal since many of the links provided by this infobox are human specific. A new {{Infobox nonhuman protein}} template was created relatively recently that should replace {{Infobox protein}} in articles for proteins without a human ortholog. Missing enzyme articles is of course a separate issue from the MOS. Perhaps a new bot could be commissioned to finish the heroic work started by WillowW (talk · contribs). Boghog (talk) 08:35, 15 May 2011 (UTC)

I also think it would be a good idea. However in the vast majority of cases IMHO, the gene and the protein encoded by that gene should be in the same article, hence I think there should only be one MOS (wp:Manual of style (gene and protein articles)). I will start working on one. Boghog (talk) 07:01, 15 May 2011 (UTC)

Great. That manual of style could have subsections for any specific guidelines for gene aspects or protein aspects. Mikael Häggström (talk) 07:07, 15 May 2011 (UTC)

A major issue that needs a note in any wp:Manual of style (protein article) is in handling Interactions-sections, such as that found in Rb#Interactions or BRCA1#Interactions. A previous suggestion on splitting them to separate articles was apparently not feasible. I think, however, that the problem rather is the current presentation of them as tediously long lists of proteins. After all, it's not the protein interaction itself that is notable, but rather any effect of it, such as stimulation or inhibition of protein activity - and such effects should be given in the Wikipedia article rather than simply referring to external sources like a collection of external links (which Wikipedia should not be). Therefore, I suggest adding the guideline that a protein interaction is notable for inclusion only when there's a comment on any effects of the interaction, such as specific stimulation or inhibition of protein activity, and may otherwise be deleted. The comprehensive lists can still be found in external (and more updated) databases for this purpose, such as CPDB. Mikael Häggström (talk) 06:55, 15 May 2011 (UTC)

The primary reason for including these internal links (emphasis added) is to reduced the number of orphan Gene Wiki articles. Moving these interaction lists to separate articles is certainly feasible, but in my opinion unnecessarily fragments the articles. Paring down the list to interactions where functional significance can be assigned (which I agree has some merit) will increase the number of orphan articles. In addition, converting a long list of interacting proteins to prose might overwhelm the rest of the article. Furthermore converting to prose is probably beyond the ability of any bot, so this work would have to be done manually. A better solution might be to move the interaction list to a collapsible section of the {{GNF_Protein_box}} template. An additional advantage of this solution is that it would be easier for bots to update these lists. Any particularly notable interactions could be expanded upon later by human editors. Boghog (talk) 07:29, 15 May 2011 (UTC)

So, apparently, the lists are useful in themselves too. So the optimal would perhaps be to have both prose and a list, the latter perhaps in a separate place in the {{GNF_Protein_box}} template. At least, it should be encouraged to add practical details on the interactions where any such are known. Mikael Häggström (talk) 11:46, 15 May 2011 (UTC)

Hi, just came across this.. are these two articles about the same thing? Sorry I didn't know where else to ask, I'm not knowledgeable on this subject. -- œ^™ 16:59, 15 May 2011 (UTC)

I have no idea either but I'd say merge. The former seems to be a misspelt version and seems to be a name of a Pokemon. Plus, if it were a real Greek word, it would be ζά + εἶδος (very-like) or a clipped version of something with a zeta (ζ) before the declension suffix, such as trapezoid... --Squidonius (talk) 20:28, 15 May 2011 (UTC)

I'd hold off on a merger. These may need dab hat notes. Zooid (zoöid) /ˈzoʊ.ɔɪd/ and zoid (zoïd) /ˈzoʊ.ɪd/ are old synonyms, dating from the mid 19th century at the latest; it's quite possible that they have been formally distributed among the two meanings they were used for.

The broad historical usage is attested in the OED, which says of zooid:

Something that resembles an animal (but is not one in the strict or full sense): in early use applied somewhat widely, including, e.g., a free-moving animal or vegetable cell, as a spermatozoon or antherozooid; but chiefly restricted to an animal arising from another by asexual reproduction, i.e. budding (gemmation) or division (fission); spec. (and most usually) Each of the distinct beings or ‘persons’ which make up a compound or ‘colonial’ animal organism, and often have different forms and functions, thus more or less corresponding to the various organs in the higher animals.

It may well be that that early use has now been made specific to zoid.

BTW, there's also zoon /ˈzoʊ.ɒn/, pl. zoa, which is,

An organism scientifically regarded as a complete animal, i.e. one which is the total product of an impregnated ovum, whether constituting a single being as in the higher animals, or a number of distinct beings (zooids) as in the successive asexual generations of aphides or the various ‘persons’ that make up a compound or ‘colonial’ animal.

— kwami (talk) 00:17, 16 May 2011 (UTC)

The article Moonlighting protein was created recently as part of a school project. I started applying wiki love but just discovered the Gene sharing article which covers the same topic. Which name is better? Anyone want to help merge these? Discussion at Talk:Moonlighting protein. Quarl ^(talk) 06:14, 17 April 2011 (UTC)

I work on (prokaryotic) enzyme promiscuity — different but still related to gene sharing—, but I have never heard the term Moonlighting protein, is it common? --Squidonius (talk) 07:19, 17 April 2011 (UTC)

I can't say I ever heard of it either. The "moonlighting" term has been used by more than one author (see PubMed). Gene sharing has also been used (see PubMed). Hence I am not sure which term would be preferred. Boghog (talk) 09:26, 17 April 2011 (UTC)

There are a lot more google hits for "gene sharing" than "moonlighting protein", but that reflects the ambiguous nature of the former phrase. I like the unambiguous nature of 'moonlighting protein'; 'gene sharing' requires explanation of what it isn't (horizontal gene transfer). The names also focus differently on the protein vs the gene. User:Kavrod wrote on Talk:Gene sharing in 2008 referencing "Times Literary Supplement, February 29 2008, p.30" in favor of moonlighting. Quarl ^(talk) 17:08, 17 April 2011 (UTC)

I've heard lecturers talk about proteins moonlighting, but hadn't realised it was a term used in scholarly literature. I concur with Quarl: "moonlighting protein" is much better than "gene sharing", because the latter is ambiguous—not only in principle, but also in practice, given that these three papers from this year alone use "gene sharing" to describe horizontal gene transfer. But my most preferred title is actually "protein moonlighting". That puts the emphasis on the underlying concept, in line with the current article. "Moonlighting protein" would be an appropriate title for an article that listed or discussed specific proteins that moonlighted, rather than one that treated the concept as an integrated whole. Adrian J. Hunter^{(talk•contribs)} 13:26, 18 April 2011 (UTC)

Re "protein moonlighting" to emphasize the concept: good idea. Quarl ^(talk) 14:05, 18 April 2011 (UTC)

 Done Since the educational class is over, I have gone ahead and merged Gene sharing into Moonlighting protein and renamed the later into Protein moonlighting. This article has also undergone a extensive peer review. While it needs some more work, especially after the merger, I think it is getting close to GA status. I will continue to work on this and would welcome additional input. Cheers. Boghog (talk) 20:09, 21 May 2011 (UTC)

Wow, this article is now looking really good—nice work on the merge, Boghog! This is the kind of article I'd enjoy going over with a fine tooth-comb, if you wanted someone else to have a look before GA (FA?) submission, though real life will keep me too busy for the next 3–4 weeks. Adrian J. Hunter^{(talk•contribs)} 11:47, 22 May 2011 (UTC)

I feel like I've made this point before, but are there any sources that state gene-sharing and moonlighting protein are synonymous? Alternate splicing, for example, could produce two different proteins which could be said to share a gene. Also, gene sharing could apply to non-coding RNA; e.g. sense and antisense transcripts sharing a gene Jebus989^✰ 12:31, 22 May 2011 (UTC)

The second paragraph of this review talks about both "gene sharing" and "moonlighting" and states that they are equivalent but the later term is preferred over the former. Boghog (talk) 15:01, 22 May 2011 (UTC)

Ah ok thanks, that dispels my concerns Jebus989^✰ 15:48, 22 May 2011 (UTC)

Someone has just pointed out a nice resource called FactorBook to me: http://zhome.umassmed.edu/elgg/ I suggested to the authors that they add links to their resource from the relevant Wikipedia articles. I already did one example for them at the IRF4 article. Does that sound reasonable? Alexbateman (talk) 07:24, 24 May 2011 (UTC)

Interesting site. I don't see any problem with linking to them, especially if they provide links back to Wikipedia. Also I think FactorBook needs to document better what kind of data is provided by their site. The "Enriched Motif" is apparently the consensus DNA binding site for that transcription factor. I have no idea what the "Aggregation Plot" is suppose to represent. Boghog (talk) 20:47, 24 May 2011 (UTC)

There is a merge proposal at Talk:Α+β proteins that could do with some attention. Hans Adler 21:39, 25 May 2011 (UTC)

Hello all,

My circadian rhythms class has finished improving our selected circadian biology Wikipedia articles. We would appreciate if someone from the WikiProject could reassess the articles we've worked on (list here). C1ock122 (talk) 19:36, 26 May 2011 (UTC)

I would appreciate some advice on the talk page of Acetyl-Coenzyme A acetyltransferase regarding some merges. Thanks. Cmcnicoll (talk) 23:01, 31 May 2011 (UTC)

We are currently trying to breath new life into WikiProject Computational Biology. There is been quite a bit of overlap with this project and if there are any editors who are interested we could do with some help and advice in these early days. An important step currently is simply to identify Computational Biology articles and get them assessed so we can work out what needs working on. If you can spare a little time I'm sure we can give this project momentum enough to roll on its own. Thanks Alexbateman (talk) 08:27, 9 June 2011 (UTC)

Hi, there's currently a requested move underway at Talk:SPINK5#Requested move which has been listed for a week and is yet to get any comments. I think the lack of comments is at least partially due to the technical aspect of the request (eg is it a protein or is it a gene? Hard for the lay person like myself to know). So, just wondering if any of this project's members who have any knowledge on the subject could add their thoughts to the requested move. Cheers, Jenks24 (talk) 16:06, 22 June 2011 (UTC)

Replied at Talk:SPINK5. Boghog (talk) 04:24, 23 June 2011 (UTC)

In Space, solar winds, mostly charged particles such as protons, penetrate living tissue and damage DNA, apparently some simple forms of life can survive on the outside of the International Space Station. But I don't know much about this, and you can read the ISS article and still be confused about the topic, I could sure use some help with it. I put some stuff in about tetrigrades? I can't even spell them, small invertebrate anyhow. Anyone got a spare 5 minutes ? Penyulap _talk 15:12, 28 June 2011 (UTC)

I have nominated International Space Station 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 "Delist" the article's featured status. The instructions for the review process are here.

I suspect your "tetrigrades" are Tardigrades. The experiments on their survival in the vacuum of space were actually done on one of the Foton-M flights. A quick skim through isn't revealing a particular link to the ISS beyond a hope that experiments with tardigrades could be carried out there in the future. Did you have a particular reason for wanting to include them in the ISS article? It may be better to add a couple of lines to something like Outer space#Environment just above the section on the effects on the human body. Ka Faraq Gatri (talk) 20:34, 28 June 2011 (UTC)

{{Chemformula}} has been nominated for deletion. 65.94.47.63 (talk) 04:56, 30 June 2011 (UTC)

I thought I might notify that I have gone ahead and split E.coli, which now comprises:

• the E. coli main page (general overview and description of the species)
• Pathogenic Escherichia coli (E.coli from the medical point of view)
• Escherichia coli (molecular biology) (E.coli from the scientists point of view)
• Escherichia coli (disambiguation) for all the strains which have pages

Any help is appreciated in fixing all issues resulting from copy-edits. Thanks --Squidonius (talk) 07:20, 17 July 2011 (UTC)

Dear All,

I would like to add links to the FactorBook database which stores information about transcription factors particularly with respect to the ENCODE project. I have added a test link to IRF4, but have a list of a further 120 links that could be added. Here is the FactorBook pages for CTCF:

http://www.factorbook.org/mediawiki/index.php/CTCF

Do others feel it is appropriate to add these linkd to Wikipedia? Alexbateman (talk) 10:15, 1 August 2011 (UTC)

These links do look useful. In addition, it would be useful to internally document what FactorBook is either by adding a FaceBook section to the ENCODE or creating a new FactorBook article and including a wikilink with the external link. Boghog (talk) 11:06, 1 August 2011 (UTC)

To help with the documentation, I just created the {{FactorBook}} template where for example "{{FactorBook|IRF4}}" produces the link FactorBook IRF4. Boghog (talk) 11:18, 1 August 2011 (UTC)

Hello! We currently have two articles, Bacteriostat and Bacteriostatic agent, both apparently about the same subject, and neither of which have any supporting cites. I'd greatly appreciate it if someone knowledgeable could take a look at these, for fact-checking and possible merging. -- The Anome (talk) 16:35, 3 August 2011 (UTC)

Dear MCB Project. It looks as though the PyMOL article still reflects a pre-Schrödinger version of said software. Does anyone here have the necessary familiarity with the Schrödinger version of PyMOL to update this article? It seems like there should be a way to do this while still preserving references to its open source development and the impact Warren DeLano had on the field. I(q) = User(q)·Talk(q) 01:40, 30 August 2011 (UTC)

Is there a better place for such a request? I(q) = User(q)·Talk(q) 16:21, 4 September 2011 (UTC)

Hi. This is probably as good a place as any. I have used both pre- and post-Schrödinger versions of PyMOL and they are qualitatively the same. The program has undergone continuous improvements (see for example list of new features). In addition, there are two parallel forks. The open source version that requires compiling and the paid version for which ready to run binaries and more complete documentation are supplied. Finally not surprisingly there is tighter integration between PyMOL and Maestro, the Schrödindger GUI for MacroModel and other Schrödinger software. Looking over the current version of the PyMOL, I don't see it as seriously out-of-date, but perhaps more detail could be added about the difference between the commercial and open source versions. Boghog (talk) 16:37, 4 September 2011 (UTC)

Ah, thanks. As I said I'm simply not familiar with the newer builds, thus am not really qualified to update the article myself. It's good to hear they haven't scrapped the basic functionality, and that an open source fork still exists. I(q) = User(q)·Talk(q) 18:05, 4 September 2011 (UTC)

Recently I've had some discussions with the editors at the journal Gene about how to encourage academics to improve Wikipedia articles on human genes. I started a discussion at the Village Pump. Please chime in there if you have any thoughts. Cheers, AndrewGNF (talk) 22:34, 9 September 2011 (UTC)

I commend your efforts here and hope that this occurs in many forums. In my view the not-so-hidden agenda of all these efforts is to further break down the barrier between the perceived value of pre vs post publication review and to highlight the value of living documents. In my area if, in the next few years, folks turn to Wikipedia for all their background reading in computational biology as opposed to expensive and inaccessible textbooks I will be very happy. --Pebourne (talk) 15:53, 10 September 2011 (UTC)

The article Capping enzyme complex has been proposed for deletion. The proposed-deletion notice added to the article should explain why.

While all contributions to Wikipedia are appreciated, content or articles may be deleted for any of several reasons.

You may prevent the proposed deletion by removing the {{proposed deletion/dated}} notice, but please explain why in your edit summary or on the article's talk page.

Please consider improving the article to address the issues raised. Removing {{proposed deletion/dated}} will stop the proposed deletion process, but other deletion processes exist. In particular, the speedy deletion process can result in deletion without discussion, and articles for deletion allows discussion to reach consensus for deletion. Sławomir Biały (talk) 20:20, 10 September 2011 (UTC)

We would like to solicit your feedback on a proposal from PLoS Computational Biology (PCB). The journal proposes to help establish new Wikipedia pages in the field of computational biology that are not currently covered, either at all, or exist only as a stub. The pages would be created in the Wikipedia sandbox. When complete they would be reviewed by a newly appointed PCB Topic (aka Wiki) Pages Editor and folks s/he solicits, and if suitable the authors would be given the opportunity to publish it as a PCB Topic Page which would appear as part of the Education section of the journal. The page would be available from PLoS under a Creative Commons Attribution License. The PCB page would be indexed in PubMed and would provide a service to journal readers. As such it provides author incentive. PCB would only publish the Topic Page when it has been released into the public Wikipedia and the PCB page would become the copy of record. The community would make further enhancements to the Wikipedia page on an on-going basis as per usual.

The upside is that authors would be inclined to provide an initial starting point of high quality material as they get a PLoS publication and are indexed in PubMed. Wikipedia gains good content.

The downside is that if this became popular (more than 2-3 per month) PLoS would need to charge to recover publishing costs, but this would not be the case initially.

Phil Bourne EIC PLoS Computational Biology — Preceding unsigned comment added by Pebourne (talk • contribs) 14:30, 7 September 2011 (UTC)

This certainly sounds like a win-win proposal benefiting both PCB and Wikipedia. We first need to make sure that the Creative Commons Attribution License used by PLoS is compatible with WP:COMPLIC. From my reading of the two licenses, it appears they are compatible, but we should get the opinion of someone who is more knowledgable. The only other potential complication I can see is that the audiences and therefore writing styles differ some what between scholarly journals and Wikipedia. Hence it may take additional work to produce an article that would be suitable for both publishing in PLoS and in Wikipedia. It would therefore be helpful to solicit input from experienced Wikipedia editors (for example by submitting a WP:PR request before the article is moved from the sandbox to Wikipedia main space) to make sure that the articles that are produced conform to generally accepted Wikipedia standards (especially with regards to WP:TECHNICAL). Boghog (talk) 16:47, 7 September 2011 (UTC)

Seems the Licenses are compatible. PCB is using CC BY 2.5 which is listed as compatible at WP:COMPLIC. --Andreas (talk) 16:55, 7 September 2011 (UTC)

Sounds like an interesting proposal. I'd be happy to help and answer questions from those contributing to this project who may be new to wikipedia. Also, you may wish to contact WikiProject Computational Biology Jebus989^✰ 17:14, 7 September 2011 (UTC)

Opps, sorry for not suggesting this earlier. Of course WP:COMPBIO sound be contacted since that is the project that most closely overlaps with this proposal. I therefore propose that we move this discussion over to the COMPBIO talk page. Thanks for the suggestion Jebus989. Boghog (talk) 18:02, 7 September 2011 (UTC)

This looks like a good opportunity, both for Wikipedia and for the potential authors. I would be happy to help review articles if this program becomes a reality. Antony–22 (^talk⁄_contribs) 06:07, 8 September 2011 (UTC)

This is an exciting idea. What sort of granularity are you thinking? Will they be strictly computational biology related or would general biology articles qualify? It might be worth looking at a few MCB featured/good articles to see if any would fit your idea of an adequate PCB article. --Paul (talk) 10:47, 8 September 2011 (UTC)

I echo every one else's enthusiasm. (Struck by how coincidentally similar the set up is to the Gene Wiki partnership I mention in the next section.) If the articles will start on Wikipedia where anyone can contribute and edit, then I imagine authorship for the PCB article may be a sticky issue to deconvolute. You could use a system like WikiTrust to assign rough authorship percentages based on text contributed, but it would be pretty approximate (and it is possible to game the system). Did you have any thoughts on how to handle that? Cheers, AndrewGNF (talk) 22:41, 9 September 2011 (UTC)

Thank you for the positive feedback on the proposal, we are planning on proceeding based on this. As a point of clarification. The original authors of the Wikipedia page, which is developed in the sandbox, would be the authors of the PLoS CB Topic Page. The living version in Wikipedia would gain authors in the usual way, but they would not be authors of the copy of record in the journal. However, given the comments feature supported by al PLoS journals, Wikipedia page authors, or others, can add commentary to the journal copy of record should they wish too. At this point we are open to suggestions for computational biology topics and possible authors to be approached to begin the work. --Pebourne (talk) 15:39, 10 September 2011 (UTC)

I echo the broad support for this proposal, though User:U+003F is right in pointing out that drafting the text here under CC-BY-SA would result in it not being publishable under CC-BY. As for assigning and crediting authorship, these issues are discussed in doi:10.3897/zookeys.90.1369. -- Daniel Mietchen - WiR/OS (talk) 23:49, 20 September 2011 (UTC)

Could someone please turn alanine scan into a bluelink? It seems like a pretty important technique and easily understandable (at least in understanding its results, even if not the process of doing it) to the lay public. DMacks (talk) 14:02, 20 September 2011 (UTC)

Agreed - There is an article at Alanine scanning, but it's currently a two paragraph long stub so it could stand to be expanded. (+)H₃N-Protein\Chemist-CO₂(-) 17:00, 20 September 2011 (UTC)

Thanks for finding that! DMacks (talk) 17:40, 21 September 2011 (UTC)

Has there been any past discussion of creating a set of pages for the biosynthesis of each amino acid and cofactor? Each amino acid has a small section, but they vary enormously in style. methionine, for example, has one of the more detailed section, but it is really hard to read and describes how E. coli does it (only enterobacteria and yeast trans-sulfurylate, use succinyl and not acetyl and few organisms need/make cobaltamine (B12 for humans)). I would be willing to spend some time on this matter, but I think a universal layout style should be present to make it navigation-friendly. Maybe it could even have a template similar to {{cladogram}} for a metabolic map. Ecocyc/metacyc has a lot of info and would make work easier, so it is not an overly hard task: the problem would be consistency. --Squidonius (talk) 07:04, 21 September 2011 (UTC)

I not aware of any previous discussion about creating amino acid biosynthesis articles. It might be better to start working on the biosynthesis sections of the existing amino acid articles and then consider splitting out if these sections become very long. A possible alternative to cladogram templates is to incorporate WikiPathways stye templates (see Citric_acid_cycle#Interactive_pathway_map as example). The WikiPathways web site already contains a pathway for methionine biosynthesis (see "Find Methionine pathways". WikiPathways. {{cite web}}: Cite has empty unknown parameter: |coauthors= (help)). However sticking to the old-fashion schematics (see File:Tryptophan biosynthesis.png for example) still might be the best solution. Boghog (talk) 20:47, 21 September 2011 (UTC)

There is also this:

The Wikibook Principles of Biochemistry has a page on the topic of: Synthesis of aminoacids

Boghog (talk) 09:48, 25 September 2011 (UTC)

Thanks that is great: in that wikibook (collage of the wikipedia articles) the style changes for each amino acid and is excellent to see which works best (in my opinion lysine). --Squidonius (talk) 09:21, 27 September 2011 (UTC)

According to the ACS style guide (ISBN 9780841239999, p. 244), the correct nomenclature is "nucleoside monophosphate", "nucleoside diphosphate", and "nucleoside triphosphate", with the term "nucleotide" referring only to the monophosphate. The template, and articles in, Template:Nucleobases, nucleosides, and nucleotides do not conform to this nomenclature, so I wanted to ask if there are differing guidelines, or whether all the articles really do need to be fixed. Antony–22 (^talk⁄_contribs) 20:07, 3 October 2011 (UTC)

Well, I'm going to go ahead and start making changes. Antony–22 (^talk⁄_contribs) 21:43, 4 October 2011 (UTC)

The citric acid cycle seems like a mature article, and knowledgeable editors seemed to have moved on, leaving a number of unanswered questions, as often happens. See "metabolism" above.

My question (there are others that may be more sophisticated) is that the article seems to say that all Krebs cycles are the same (identical) for all of the Animal Kingdom. That is a shocker. Including ants? Dust mites?

I read that "cats create their own Vitamin C." I know, "citric acid." But the writer was intending the information to be unique to cats and this article definitely makes no distinction except for plants. Is that correct? Thanks. Student7 (talk) 19:04, 26 October 2011 (UTC)

Basic metabolic pathways such the citric acid cycle were established quite early in evolution and are extremely well conserved throughout life from bacteria to humans. So yes, ants, dust mites, aardvarks, etc. all rely on the citric acid cycle to generate energy. Vitamin C = ascorbic acid ≠ citric acid, so Vitamin C is not synthesized through the carboxylic acid cycle. For future reference, these types of questions are propably more appropriate for WP:RD/S. Cheers. Boghog (talk) 19:28, 26 October 2011 (UTC)

Hi. I just noticed this new article from a new editor. Could someone please assign an importance and quality rating on the article's talk page? Maybe a welcome and introduction to this WikiProject would be appropriate, but I'll leave that up to you to decide. I've done a fairly thorough online search for copyvio and it appears clean to me. --Anthonyhcole (talk) 07:58, 20 November 2011 (UTC)

Thanks for the heads up. An impressive article for sure. I have added some project ratings, done some additional editing, and rolled out the welcome wagon. Cheers. Boghog (talk) 15:06, 20 November 2011 (UTC)

Immune system is an FA; it was suddenly rewritten, and this needs discussion here. Materialscientist (talk) 05:12, 8 December 2011 (UTC)

Merge Methylase and Methyltransferase--92.203.50.213 (talk) 14:21, 5 January 2012 (UTC)

 Done Boghog (talk) 16:32, 5 January 2012 (UTC)

On the Talkpage:Pomegranate and the Talkpage:Cranberry a discussion is taking place pertaining to 1) the health effects of the aforementioned fruit and berry, and 2) whether the reviews could belong to the ‘further reading’ – section? I am hoping for a larger community input. Do you have time to take a look? Thank you. Granateple (talk) 19:19, 7 January 2012 (UTC)

Stated Low Prolactin Levels are associated with the precursor cells to oligodendrocytes that are responsible for creation of Myelin. Lesions in Myelin in time and place is Multiple Sclerosis (MS). There are too many associations with low prolactin levels and MS. Prolactin secretion levels are affected by pineal gland (the third eye sensing levels of light and regulation of circadian cycle. This corresponds to epidemiological data showing high levels of MS in the most northern latitudes, UK, Finland, etc.)at a youthful age in development. If the individual’s youthful development is in the lower latitude levels say South Africa and moves to say UK at the adult age, the individual takes his low risk with him. If the individual moves to the higher latitude locations at the youthful age, he adopts the high risk of MS of the high latitude location. This shows a link with the amount of sunlight availability and the endocrinological control system responsible for creating prolactin.

MS incidence appears to have some relation to post-pregnancy. Again prolactin at play.

My personal observation of dopamine surge activities lacking physical exertion such as gambling and drug use have some association with incidence of MS. It can be explained by the patho-mechanism of excess dopamine levels inhibiting prolactin secretions thereby having the low prolactin levels cause the dying off of the precursor cells to the oligodendrocytes and thereby causing MS.

Another relation between MS and prolactin is ACTH. ACTH secreted by anterior pituitary causes adrenal secretions of cortisol. Personal experience recalls use of ACTH to reverse remissions in MS? Prolactin is also released at the anterior pituitary.

More thought and research to the hormonal, humoral and neural control properties of prolactin may help in better understanding the patho-mechanism of MS.

166.250.44.189 (talk) 08:04, 11 January 2012 (UTC)

I refer the group to this thread on the Talk page at Major Depressive Disorder concerning the use of Vincent van Gogh's painting "At Eternity's Gate" in that article and to this comment of mine pointing out it has no place in the article and should be removed.

The essence of the complaint is that is fully documented that van Gogh's painting is not at all, nor was ever meant to be, a portrayal of depressive disorder but is rather merely a study of an old man. For that reason alone it should be removed for reasons of encyclopaedic accuracy.

As it stands it necessarily makes a judgement about the nature of depressive disorder, that it necessarily implies despair, even that it necessarily implies suicidal ideation (because of its title and van Gogh's own well known suicide). It is very much to be regretted indeed in my opinion that a Wikipedia administrator, Casliber, a practicising psychiatrist it seems but a poor historian of art, appears to be the prime mover behind perpetuating these poor judgements.

It also mythologises Vincent van Gogh himself who took the greatest care to separate his difficulties in life from his work; the nature of whose illness is not settled but which is not certainly typical of a depressive disorder; who is not documented as suffering from suicidal depressive moods in the last months of his life when this painting was completed and whose suicide itself has in the past year been plausibly questioned by a respected source as rather a manslaughter.

I ask that the image be removed. If it is felt necessary, and I cannot imagine why it should be, that the article be illustrated by a fine art image, then I suggest the original image, Durer's Melancholia, be reinserted. Skirtopodes (talk) 22:33, 13 January 2012 (UTC)

This is the wrong forum. If you have a disagreement about something, consider trying dispute resolution. JFW | T@lk 23:51, 14 January 2012 (UTC)

Last September, there was a discussion (archive) on whether and how academic journals - namely PLoS Computational Biology - could partner up with Wikipedia to improve coverage of areas within their scope. An update has just been posted here, and your feedback is invited. -- Daniel Mietchen - WiR/OS (talk) 16:44, 17 January 2012 (UTC)

A request for comment has been made at the above link. Your input is welcome. Boghog (talk) 20:55, 28 January 2012 (UTC)

Per Talk:Protein homology#discussion1. I'm inclined to agree regarding the need for a distinction, assuming this isn't already covered in another article. It also appears that we don't have an article that talks about structural homology at all really. Although we do seem to have an article on homology modeling, perhaps portions of that could be spun off into a putative structural homology (protein) article? (+)H₃N-Protein\Chemist-CO₂(-) 16:26, 6 February 2012 (UTC)

I'm running a WikiPedia/Wikimedia Commons workshop at the Biophysical Society in a couple of weeks, with expert help from User:Phoebe and sponsorship by the Education and the Early Careers committees of the society. We anticipate a large audience -- perhaps 50-75 working scientists who want to help edit articles and contribute media, and possibly involve their students also. I have truly enjoyed my own Wiki participation, and spreading this idea is one of things I'd like to accomplish as incoming president of the society.

We are thinking about starting a new WikiProject Biophysics as a subproject under Molecular and Cellular Bioogy to provide a collaborative workspace for them and future biophysicists, but would really appreciate feedback on the best way to proceed. Clearly the physics wikiproject is also suitably relevant; also a task force would be a possible alternative to a WikiProject. Thoughts? Would there be interest in this community in working on a dedicated biophysics project? Would it be sensible to have a subproject here and a task force under Physics (which could perhaps concentrate on topics, or aspects of an article, related to theory and to experimental techniques)? Dcrjsr (talk) 14:39, 12 February 2012 (UTC)

After various consultations, WikiProject Biophysics has now been started, under Biology -- it has a skeleton main page, and we will be recruiting new participants at next week's Biophysical Society meeting. Any interested Wikipedians would be extremely welcome!! Dcrjsr (talk) 18:35, 20 February 2012 (UTC)

So, there's a new project which may be of interest to some here. It arises out of Wikipedia:Village_pump_(proposals)#UID_interface_to_Wikipedia, a proposal to make wikipedia articles available by their UID - for instance by their UNIPROT number. Umm. And those two pages are all I have to show you, but I live in hope of input from you to take it all further. --Tagishsimon (talk) 20:48, 14 February 2012 (UTC)

Hello! As a new page patroller I have just come across the following articles, created by User:Rcrzarg on 10 February. They could use some attention and I am not even sure if they are suitable for inclusion here, so I thought I would give you guys a heads up and see if you had any advice on how to handle them :). They are:

• Small non-coding RNAs in the endosymbiotic diazotroph α-proteobacterium Sinorhizobium meliloti
• Αr7 RNA
• Αr9 RNA
• Αr14 RNA
• Αr15 RNA
• Αr35 RNA
• Αr45 RNA

Thanks! --Cerebellum (talk) 16:32, 21 February 2012 (UTC)

I am about to embark on improvements to articles relating to circadian clocks, with a particular interest in improving content related to plant circadian clocks. So far I have edited the lede for circadian rhythm, and have moved circadian oscillator to circadain clock. Anyone with any sort of background or interest in chronobiology or circadian clocks in any way, feel free to give me a hand =) the state of affairs at the moment is a bit dire! Gorton k (talk) 21:41, 1 March 2012 (UTC)

Hi, Molecular and Cellular Biology Wikiproject. Thanks for all the work you do. I have one thing I'd request. I've noticed that many of the articles under the scope of this group have problems with the ordering of the standard "appendix" sections (i.e., "See also", "References", "Further reading", "External links", and so on). Generally those sections go in the order just given. The MOS:APPENDIX page gives further information as well as the rational. I do mostly just MOS:APPENDIX edits and over the years, I have noticed that the chemical, human protein, and genetics articles have the order of the appendices incorrect more than average. Just a moment or two of member's time to read the MOS:APPENDIX page may help to eliminate this issue. Jason Quinn (talk) 22:17, 9 February 2012 (UTC)

Thanks so much. I fixed it for Folding@home, and perhaps I'll take the time to see about some others. Best, Jesse V. (talk) 07:13, 7 March 2012 (UTC)

Scanned all FA/A/GA-class articles. Out of the 59 articles I looked at, I made 5 fixes. Thus this is narrowed down to B, C, Start, or Stub articles, of which there are a lot. Care to narrow it down? Is there a bot for this or something? Jesse V. (talk) 07:46, 7 March 2012 (UTC)

There's a bit of confusion on Commons about the graphs to the right. They say that they show two different genes, and are used in two different articles. However the files themselves are identical. Would 2 different, but related, genes show up identically on this sort of graph? If so - do we need different graphs for each of the genes in question?--Nilfanion (talk) 09:08, 3 March 2012 (UTC)

A stub was recently created for Fastidiousness among microbes. I was curious if some of the expertise here could weigh in on moving it to Fastidiousness or Fastidious microbes, or some other title. It seems odd to have a title of an article be an adjective, but I don't have the knowledge of this area to determine the best title. Thoughts? --TeaDrinker (talk) 01:46, 26 March 2012 (UTC)

Thanks for the alert, I would have never noticed otherwise. Left my comment over at Talk:Fastidious Jesse V. (talk) 03:50, 26 March 2012 (UTC)

Left a message there Flowright138 (talk) (contributions) 03:05, 30 March 2012 (UTC)

I just posted a major update to Circular permutation in proteins. The page is currently listed a stub. Would someone please evaluate the new article for quality and importance?

I wouldn't normally ask directly, but the update is the first wikipedia article published in collaboration with PLoS as part of their new Topic Page track. As such it will likely receive a significant amount of attention from blogs and the press.

--Quantum7 23:14, 29 March 2012 (UTC)

 Done A rating of B sounds good to me, and I based it off of the grading criteria of course. Someone else can certainly change that if I've been too generous or something, but I think its fair. Jesse V. (talk) 00:07, 30 March 2012 (UTC)

Thanks, Jesse. We'll try to make some improvements and get it up to at least an A. --Quantum7 17:47, 30 March 2012 (UTC)

Should this page (MART-1) merge to MLANA? Please comment at Talk:MART-1. Thanks, D O N D E groovily Talk to me 02:28, 2 April 2012 (UTC)

 Done – Thanks for the heads up. These two articles are obviously about the same gene/protein. Therefore I have been WP:BOLD and completed the merger. Boghog (talk) 03:40, 2 April 2012 (UTC)

If anyone is still active here (no more Tim Vickers?), two new articles were created on this today-- I proposed merger to the main article after cleanup. See Talk:Apoptosis#Merger proposal. SandyGeorgia (Talk) 15:08, 3 April 2012 (UTC)

I'm here, and I see from the other sections just above that there are a few others. I support the merge. Jesse V. (talk) 15:18, 3 April 2012 (UTC)

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

I've taken care of several of the diseases, and I'm trying to figure out the rest. There's a checklist on the Talk page. Advice/comments on them and the rest of the article would be greatly appreciated, now more than ever. I feel that GA nominations are very close! Please let me know what you think or if there are issues that need to be addressed. Jesse V. (talk) 19:23, 17 March 2012 (UTC)

Its now a GA nominee. I'd appreciate it if someone could review it. :D Jesse V. (talk) 20:43, 5 April 2012 (UTC)

Hi all, I am trying to get the support to set up a WikiProject for immunology. My reasons are stated at the proposal page, a discussion has also be initiated. Currently, I am just trying to get a feel of how many editors are interested, and whether we have enough to build a task group for a one-month drive, or to improve on one major article, to see how feasible it is to have a WikiProject. Any input, whether opposing or supporting, would be very much appreciated. Again, the link to the proposal is here. Many thanks. Kinkreet^{~♥moshi moshi♥~} 13:22, 5 April 2012 (UTC)

Wikipedia:HighBeam describes a limited opportunity for Wikipedia editors to have access to HighBeam Research.
—Wavelength (talk) 15:51, 5 April 2012 (UTC)

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Thanks. — Headbomb {^ταλκ_{κοντριβς} – WP Physics} 09:22, 15 March 2009 (UTC)

I have made a new article on genetics... could i get all to add the article to your watch list! Indigenous Amerindian genetics we need to watch for vandalism..new with no watchers .. Tks guys!!!!! 01:00, 01 March 2011 (UTC)

→ Wikipedia talk:WikiProject Chemistry#List of vegetable fats. 01:00, 01 March 2011 (UTC)

I just wanted to add my two cents. It is great that the articles have theoretical molecular weights, but is it possible to start adding the isoelectric points (pI) on the side bar for protein pages? This is a valuable resource in proteomics especially, and helps define a protein in greater detail. Thanks. — Preceding unsigned comment added by 24.97.96.113 (talk) 20:20, 5 April 2012 (UTC)

I am not so sure that this is a practical idea. Please note that Gene Wiki articles are not only about the human gene/protein but also orthologs that exist in other species. Even restricting the discussion to one species, there are often different isoforms arising from alternative splicing from the same gene. The isoelectric point may differ substantially depending on which isoform from which species is measured. Boghog (talk) 07:57, 29 April 2012 (UTC)

Are SPR (gene) and Sepiapterin reductase the same thing? Please either comment at Talk:Sepiapterin reductase or boldly merge them. Thanks, D O N D E groovily Talk to me 03:46, 29 April 2012 (UTC)

 Done According to ExPASy EC 1.1.1.153, there is only one human gene (SPR) encoding an enzyme with this activity. Hence there is a one to one correspondence between enzyme and genes and therefore these two pages can be merged. (Sometimes there is more than one human gene with a given enzyme activity and in these cases the pages should not be merged). I have been bold and completed the merger. Boghog (talk) 07:51, 29 April 2012 (UTC)

Please comment at Talk:Chimera (EST) as to whether to merge the page into Fusion protein. Thanks, D O N D E groovily Talk to me 01:59, 2 May 2012 (UTC)

Responded there. Boghog (talk) 04:52, 2 May 2012 (UTC)

Hi all, I am simply an editor who thinks some of the immunology articles on Wikipedia are far from complete and the quality can be easily improved. I'd love to do it all by myself, but it'd be even better to do it in a team, to be more efficient as well as to get a wider viewpoints (from the medical, molecular and cellular viewpoints for example). If you are interested, please go to here and just start editing. The purpose of the page (it's a new page) is simply to get everyone together and collaborate, as to ensure there's editors for different topics. I look forward to working with you soon, any help would be greatly appreciated. Kinkreet^{~♥moshi moshi♥~} 01:15, 6 May 2012 (UTC)

Should Glycyl—tRNA synthetase merge with Glycine—tRNA ligase? Please comment at Talk:Glycyl—tRNA synthetase. Also, thanks to everyone at this Wikiproject for promptly commenting on my questions. D O N D E groovily Talk to me 19:21, 7 May 2012 (UTC)

 Done And thank you for the heads up. I have gone ahead and boldly merged the two articles. Boghog (talk) 20:02, 7 May 2012 (UTC)

I propose to merge N-linked glycosylation and O-linked glycosylation back with the main Glycosylation page. They were split from that page a few years ago, probably to build them out more. But little has been done to either page, and the O-glycosylation page can be moderately reorganized. When merged together, they create a more complete page that provides content in the correct context. What do you think? Potcherboy (talk) 17:25, 9 May 2012 (UTC)

I am not so sure about this merger. Clearly both articles need to be cleaned up which I have started to do. Furthermore quite a few review articles have been published on both subjects indicating each is an important subject worthy of its own article:

• N-linked glycosylation reviews (10 hits)
• O-linked glycosylation reviews (6 hits)

Boghog (talk) 19:00, 9 May 2012 (UTC)

It's a while since I reviewed the relevant literature, but my impression was that N- and O-glycosylation are completely different processes (N is restrictive and O is additive or vice versa) that deserve to have their own pages. JFW | T@lk 20:35, 9 May 2012 (UTC)

Thanks for the comments, and thanks for starting the update process, Boghog. I'll also work on these pages too. Potcherboy (talk) 17:08, 10 May 2012 (UTC)

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

I'm a newbie on wikipedia and had students edit pages for a graduate class. Trithorax-group proteins has now been improved and it seems it should be included in this WikiProject, along with its sister page, Polycomb-group proteins. Do they need review by someone who reads this page to be added? I'm not clear on how on how this process works and don't feel qualified to assign class and importance ratings. Many thanks. Biolprof (talk) 01:43, 20 May 2012 (UTC)

Nice job on the Trithorax-group proteins article. There is no specific guideline for accessing MCB articles. One can refer to the general Wikipedia assessment guidelines. I have gone ahead and assessed both articles. I have rated them start, since both could use some expansion. I have also rated them mid importance since both articles are about families of proteins. Boghog (talk) 08:22, 20 May 2012 (UTC)

Comments on Wikipedia:Village_pump_(idea_lab)#Static_vs_dynamic_topics:_seriously_outdated_articles will be appreciated, so we can get a general perspective on this. Thanks. History2007 (talk) 13:28, 22 May 2012 (UTC)

see Wikipedia:Templates for discussion/Log/2012 May 31#Template:Protbox. Frietjes (talk) 20:27, 31 May 2012 (UTC)

Non-helical DNA structure (Talk:Non-helical DNA structure) is a relatively new article and one which has a lot of content, but is written in an essay style and is mainly written by one editor. I don't feel familiar enough with the subject to properly understand everything in the article, but perhaps someone else from here could review it and make some suggestions? -Zynwyx (talk) 02:10, 26 May 2012 (UTC)

Side-by-side models of nucleic acid have some historical relevance, as they were a candidate for the structure of DNA prior to the Watson-Crick model, but have not been taken seriously since about the 1970's. There are a couple of people who still hold that biological DNA is not a double helix, which is not at all a mainstream viewpoint; they show up on Wikipedia from time to time to push their theories. See this discussion and this discussion for some details.

So as a chapter in the early history of molecular biology, these theories have some notability, but the article will have to be checked and possibly thoroughly edited to conform to due weight and NPOV given the likely COI of the authors. I need to take a more thorough look at the article itself, but I think it could be salvageable. Antony–22 (^talk⁄_contribs) 03:44, 26 May 2012 (UTC)

I definitely think there is a NPOV issue, see Talk:Non-helical DNA structure for the author's viewpoint. The content is interesting though, and a lot of it (especially regarding the chemistry of alternate DNA structures) may be relevant on wikipedia from a purely chemical even if not an MCB point of view. -129.234.93.35 (talk) 19:33, 26 May 2012 (UTC)

We'd really appreciate some help from someone familiar with topoisomerases and/or bacterial chromosome replication. Please see Talk:Non-helical models of nucleic acid structure#Balancing information needed. Thanks! Antony–22 (^talk⁄_contribs) 04:46, 2 June 2012 (UTC)

I have not been able to spend as much time on Wikipedia to keep my watched articles from rotting and I just noticed that Escherichia coli is a patchwork of un-reverted vandalisms and good-faith naive edits that have accumulated since I did some cleaning in January (namely splitting into three articles), but I do not have the time right now to fix it. Does anyone want to adopt a indole-smelling dirty-yellow--coloured friend? --Squidonius (talk) 21:36, 5 June 2012 (UTC)

I would be willing to attempt some cleaning up, do you have anything specific in mind? -Zynwyx (talk) 12:31, 12 June 2012 (UTC)

See Template_talk:GNF_Protein_box#Categories. -- Alan Liefting (talk - contribs) 00:19, 13 June 2012 (UTC)

I have responded in more detail there, but in short, I do not see why the change is necessary. Boghog (talk) 05:19, 13 June 2012 (UTC)

While I was looking for information to expand and rewrite the Northland Pyrite Mine article I came across the term arcellacean, which I have never herd of before. The term is used in the following sentence: "Oxidation of waste rock dumped along the edge of James Lake resulted in development of acidic lake waste waters adjacent to the pile (< pH 5.0), causing arcellacean taxa to die out with the exception of A. vulgaris." Can someone please make an article for this form of taxa? According to this, arcellaceans are a major group of testaceous rhizopods. However, that is probably not a reliable source because it is a blog. It would also be helpful if someone could me what A. vulgaris stands for. Thanks. Volcanoguy 06:51, 18 June 2012 (UTC)

That sentence doesn't occur in the article, but this seems to be place you found the phrase I presume. I have no idea what arcellacean means though. Jesse V. (talk) 07:06, 18 June 2012 (UTC)

According to this, Arcellacean is synonymous to testate amoebae, which redirects to Arcellinida. Volcanoguy 12:44, 18 June 2012 (UTC)

The Eukaryote article says: "All species of large complex organisms are eukaryotes", however the linked article multicellular organism says "Multicellularity exists in both prokaryotes and eukaryotes, and first appeared several billion years ago in cyanobacteria."

If the statement in the second quote is correct, then I think the phrase large complex organism should link to an article of its own and not to multicellular organism. Lifkwe (talk) 12:58, 24 June 2012 (UTC)

I think the claim "All species of large complex organisms are eukaryotes" is correct, but I didn't like the way "large complex organisms" linked to Multicellular organism, as though the two terms were synonymous. So I've removed that link. Whether there really are multicellular prokaryotes I think depends on your definition of multicellularity, a point which our article doesn't really explain. I don't think "large complex organisms" merits its own article as its meaning is self-explanatory. Adrian J. Hunter^{(talk•contribs)} 07:06, 25 June 2012 (UTC)

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

Hello all! I’m working with the Saylor foundation to create a series of original, crowd-sourced textbooks that will be openly licensed and freely available on the web and within Saylor’s free, self-paced courses at Saylor.org. We are using Wikibooks as a platform to host this project and hope to garner the interest of existing members of the Wikibooks and Wikipedia community, as well as bring in new members! We thought that some of your members may be interested in contributing to our book Saylor.org's Cell Biology. Azinheira (talk) 17:40, 18 July 2012 (UTC)

A request for comment has been made at the above link. Your input is welcome. Boghog (talk) 19:01, 19 July 2012 (UTC)

Hi,

A new article was just added on the cell biologist David L. Spector of Cold Spring Harbor Laboratory. Please feel free to take a look at the article make comments, edits, corrections, or to add content.

Jjjjjjjjjj (talk) 02:13, 6 August 2012 (UTC)

I couldn't find any trace of this wikiversity project. The link redirects to Wikia, which says "Bad title". I also found this Wikia category page that has been deleted. Shall I delete this link, or has it moved somewhere? Klortho (talk) 02:07, 17 August 2012 (UTC)

I vote that you go ahead and delete the link. If anyone really cared, they can always put the link back, but it would be nice to have things cleaned up. • Jesse V.^(talk) 03:55, 17 August 2012 (UTC)

Done. Klortho (talk) 16:21, 17 August 2012 (UTC)

Can someone check this article and mark it as reviewed. After looking through it, I don't see any problems, except I'm unsure of its title. Ryan Vesey 16:08, 17 August 2012 (UTC)

Thanks for the heads up. Since most of the prose in the article discusses the properties and function of the entire protein, I have renamed the article to enterotoxin type B and added an infobox for the C-terminal domain to compliment the N-terminal domain infobox that was already present. Boghog (talk) 10:36, 18 August 2012 (UTC)

Thank you. Ryan Vesey 03:49, 19 August 2012 (UTC)

Hi, I am working with Sherry Ogg, a professor at JHU, and with the Wikipedia Education program, to prepare a Wikipedia project for her upcoming online Molecular Biology class (two sections; the course pages are here: one, two). We have in mind providing the students with a list of articles that need work, on topics relevant to the course, and have the students, working in pairs, select among this list, and then work throughout the semester to provide substantive improvements to those articles. We're designing the assignment itself on one of my user pages, if anyone is interested to take a look (and/or make suggestions).

So, first of all, I wanted to make sure that we introduce ourselves, and let you know that we are coming, so hopefully there won't be a huge surprise when a lot of newbies start making major edits to pages in this project's purview. Hopefully if the edits are initially of poor quality, then editors here can help guide the students in ways that don't discourage (I'm sure you all do that anyway!)

Next, we're hoping we can get some suggestions for articles that need work that we could add to our list. We are planning to look at your how you can help section, the Category:Molecular and cellular biology stubs, and your article worklist, but I thought I would first throw this out, in case there are any other suggestions for places to look, or for particular articles that are in dire need of some work. The course uses Watson's Molecular Biology of the Gene, and covers the whole book, so the scope is quite broad. Klortho (talk) 02:06, 19 August 2012 (UTC)

Hi. We certainly welcome your students contributions to Wikipedia. First, it would help to know a little more about the course. Digging around, it appears that this syllabus describes the course. Is this correct? If so, more general articles on molecular biology as opposed to specific gene/protein articles might be most relevant. More general articles that are still rated stub or C-class are a good candidates. A far more extensive list of MCB stub articles may be found here.

Many MCB articles cite sources using citation templates and a Vancouver System author list. In order to promote consistency with citations that are already present in many of these articles, I would strongly recommend using User:Diberri's Wikipedia template filling tool (instructions). Given a PubMed ID, one can quickly produce a full citation that can be copied and pasted into a Wikipedia article. This tool can save you a lot of work and ensure that the citations are displayed in a consistent manner.

If you have any additional questions or if I can be of additional help, please don't hesitate to ask. Cheers. Boghog (talk) 05:35, 19 August 2012 (UTC)

Hi, this sounds like a great idea. Choosing the articles to edit is a really important aspect to this. There are quite a lot of stubs that describe individual human genes. These might be good to use because they are quite self contained. If you choose pages that cover a large subject it can be difficult to get started. The page on chromothripsis is in need of work and is a really interesting growing area in molcular biology of cancer. So would not appear in current text books but requires reading the primary literature. It is also quite difficult to identify molecular biology subjects tha google doesn't cover. You could ask your students to try and identify some as a classroom exercise. If they can then you can include some new articles to start. For some reason students always seem to prefer creating completely new articles :) Hope that is useful. Alexbateman (talk) 07:15, 19 August 2012 (UTC)

Thanks Alex for your suggestions. If the students do choose to expand gene/protein articles, consulting this proposed style guideline may be helpful. (BTW: I have been working on this proposed guideline off and on for the last couple of months. I would appreciate input of others on this proposal with an eye to eventually promoting this proposal to an official guideline.) Boghog (talk) 09:25, 19 August 2012 (UTC)

Thanks a lot for the welcome and the suggestions. I've been fleshing out my notes and working on the course pages, and will try to incorporate the various links you sent me. If any of you would like to help with the design of the assignment, or helping out the students while it's going on -- welcome! I want the student discussions to take place on the course talk pages, so just come watch one or both of them: one / two. Klortho (talk) 20:01, 19 August 2012 (UTC)

Hi, Alex, I am a big fan of what you are doing with Wikipedia and bioinformatics. I saw a very good presentation by Robert Finn at NCBI/CBB on Rfam, Pfam, and Wikipedia, over a year ago, and that is one reason why I find myself doing this now. I was inspired by that talk to suggest to my advisor and a few faculty at JHU, where I'm a student, to try to incorporate Wikipedia into their courses. It is finally bearing fruit because Dr. Ogg is willing to go out on a limb and give it a try. — Preceding unsigned comment added by Klortho (talk • contribs) 23:56, 19 August 2012 (UTC)

For months now, I've been working on improving the quality of the Folding@home article. However, I'm having an increasing amount of difficulty finding things to fix or things to add, and I'm running out of what little technical knowledge I have. I hope there are some experts here who can offer an insight on what the article needs next and how to go about taking care of it. Any ideas? • Jesse V.^(talk) 05:58, 28 August 2012 (UTC)

Also, can someone please review it and see if it qualifies for A-class? If it's not A-class, please advise on how I can get it up there. • Jesse V.^(talk) 14:26, 28 August 2012 (UTC)

Please take a look at our Molecular Biology course page for the upcoming semester, as I described above. If any of you have time and would like to suggest improvements (or just be bold and make them), please do! Klortho (talk) 12:24, 28 August 2012 (UTC)

Wow! I am impressed with the thoroughness of the course page and from my first reading, I do not see any major short comings. Well done! This should serve as an excellent model for future courses. I also see that you have also incorporated our suggestions which I very much appreciate. I look forward to the students contributions! Boghog (talk) 19:27, 28 August 2012 (UTC)

Portal:Xray Crystallography, a portal in which you may be interested, has been nominated for deletion. Your opinions on the matter are welcome; please participate in the discussion by adding your comments at Wikipedia:Miscellany for deletion/Portal:Xray Crystallography and please be sure to sign your comments with four tildes (~~~~). You are free to edit the content of Portal:Xray Crystallography during the discussion but should not remove the miscellany for deletion template from the top of the page; such a removal will not end the deletion discussion. Thank you. ···日本穣^? · 投稿 · Talk to Nihonjoe · Join WP Japan! 17:10, 15 September 2012 (UTC)

The article for pulse labelling is in need of some attention. A quick Google search does not bring up any useful definitions of what pulse labelling is, and the Wikipedia article is the first result but not at all helpful. I think it may be the same thing as pulse-chase analysis but I'm not sure, so hopefully someone with relevant knowledge will be willing to improve the page. — Preceding unsigned comment added by Zynwyx (talk • contribs) 00:07, 18 October 2012 (UTC)

I just wanted to let everyone know that I've nominated Folding@home as a Featured Article candidate. Comments or editing assistance would be most welcome. • Jesse V.^(talk) 02:37, 17 September 2012 (UTC)

Lead section is too long and too technical IMHO, 2nd-3rd paras could be split off to a new section. Otherwise a decent piece of work. kashmiri 18:37, 18 October 2012 (UTC)

Hmm. I thought it summarized the article rather well and that it avoided any technical language. Could you be more specific? What are the technical parts that you have problems with? • Jesse V.^(talk) 18:53, 18 October 2012 (UTC)

To my understanding, the lead section specifically should avoid technical language unless necessary and explain the subject in a very accessible manner (WP:MOSINTRO: "specialized terminology and symbols should be avoided in an introduction"). "Distributed computing project for simulation of protein folding, computational drug design, and other molecular dynamics for disease research" is perhaps a very correct and precise definition – but it carries hardly any meaning to a layman. I would try to phrase it, for example, like this: "... is a large project that uses the idle power of connected personal computers of anyone wishing to participate in the project to perform complex calculations in medicine and biology. Specifically, ordinary personal computers and Playstation-3 devices, connected to the Internet and running special software, calculate parameters of protein folding and other molecular phenomena." I am not a native English speaker so I am sure this could be phrased more neatly.

Similarly, "The project uses statistical simulation methodology that represents a paradigm shift from traditional computational approaches. As part of the project's client-server architecture, the volunteered machines receive simulation work units, complete them, and return them to database servers where they are compiled into an overall simulation." This could go very well in the main body. In the lead, however, this could be either entirely omitted or summarised in, say, such words: "The project uses a new approach in statistical data computing: participating computers receive individual calculations to perform and then send the results back to the project's server which in turn compiles and analyses them."

Same with the last sentence of the lead which in my opinion is not clear even to the majority of university graduates (except in certain technical fields) unless they feel like googling up "protein folding times", "protein pathways", and "equilibrium constants" (they are not even wikilinked).

Thus, I tend to believe the lead could easily be made more accessible. Some time ago I wrote a short lead to the spinal muscular atrophy article. It is not overly technical – hope you agree on that; even so, I heard from an editor that the lead should be made even simpler. kashmiri 20:15, 18 October 2012 (UTC)

Hmm. I just really like the lead the way it is, but I'll have to think more about that and ask some non-experts what they think. In part I was following Rosetta@home as an example, which uses very precise language. I was trying to avoid being over-simplified and wordy, but there is a possibility that I need to tone it down a bit. I see if I can resolve that last line in particular. • Jesse V.^(talk) 21:01, 18 October 2012 (UTC)

I like it too – but for a specialist encyclopaedia rather than for Wikipedia. Currently the lead uses the same technical language, and assumes the same level of reader's familiarity with the subject, as the body. It shouldn't (yeah, unless truly unavoidable). Excellent guidance here: WP:TECHNICAL. Rosetta@home should follow? kashmiri 21:50, 18 October 2012 (UTC)

I respectfully disagree, Kashmiri. The lead is not too long, and there is no way to not have some technical language in an article like this. I will take a brief whack at the lead to see if I can clean up anything overly techie, but this is what wikilinks are for. I know nothing about the topic, so if I can understand it, it's understandable. Montanabw^(talk) 02:52, 19 October 2012 (UTC)

I do understand the lead, too (well, I would need to look up "equilibrium constants" and "protein pathways" to get a full understanding). If I understand it, it's not necessarily understandable to others – as per WP:TECHNICAL, Wikipedia articles, or at least the lead sections, should be understandable to several other categories of readers (see there), not only to well-educated editors as you appear to be (judging from your contributions). Also, I guess lead sections should not require googling. As to the length, it's generally ok as regards plain word count; but since it goes too deep into the topics IMHO, it could easily be made more concise. But that's just a personal opinion. kashmiri 09:53, 19 October 2012 (UTC)

I think Folding@home's lead is much more accessible than that of most technical mid-importance FAs in biology, chemistry and computing, like Enzyme inhibitor, RNA interference, Rosetta@home, and even some core technical FAs in those areas like DNA, Evolution and Parallel computing. The recent edits to the lead improved things noticeably.

I agree with kashmiri that the last sentence is too advanced and should be simplified. Other than that, though, I think the lead as it currently stands is a good example of how the accessibility barrier created by introducing central technical terms can be lowered by providing context and appositives that explain what those terms mean. Other than the last sentence, which terms still require context/explanation? Emw (talk) 11:57, 19 October 2012 (UTC)

Thanks for simplifying the last sentence. • Jesse V.^(talk) 16:24, 20 October 2012 (UTC)