Wikipedia talk:WikiProject Molecular Biology/Molecular and Cell Biology/Proposals/Archive 1

Archive 1

Proteins

Protbox start - split image?

Does anybody object if I split out the image field from Template:Protbox start into its own subtemplate (probably something like Template:Protbox image? The way it is set up right now, we can't use the template at all unless we have an image, because the image field is embedded in the same subtemplate that has the table headers. --Arcadian 01:46, 23 November 2005 (UTC)

Go for it. There should be a protein info box that does not need an image. --JWSchmidt 02:02, 23 November 2005 (UTC)

I've got a rough cut working at Lactotransferrin. If there are any objections/feedback let me know, otherwise I'll start working it into some of the protein pages. --Arcadian 01:02, 24 November 2005 (UTC)

Small molecules

Info boxes

We definately need infoboxes that can satisfy both us, the molecular biologists, and the chemists. There are currently two code distinct infoboxes on the "market" - format styles I and II.

2. Format style I, used in several variations, has the following code (on the left) and result (on the left):

{| align="right" cellspacing="0" cellpadding="3" style="background: #FFFFFF; border: 1px solid #C0C090; border-collapse: collapse; margin: 0 0 0.5em 0.5em; width: 320px;" ! {{chembox header}}| '''{{PAGENAME}}''' <!-- replace if not identical with the article name --> |- | align="center" colspan="2" bgcolor="#ffffff" | [[Image:{{PAGENAME}}.gif|{{PAGENAME}}]] <!-- replace if not identical with the pagename --> |- | style="vertical-align: top;" | [[IUPAC nomenclature|Chemical name]] | style="width: 100%;" | 2-(carbamimidoyl-methyl-amino)acetic acid |- | style="vertical-align: top;" | Synonyms | (α-methylguanido)acetic acid<br/>Creatin<br/>Kreatin<br/>methylguanidinoacetic acid<br/>N-amidinosarcosine |- | style="vertical-align: top; white-space: nowrap;" | [[Chemical formula]] | C<sub>4</sub>H<sub>9</sub>N<sub>3</sub>O<sub>2</sub> |- | [[Simplified molecular input line entry specification|SMILES]] | CN(CC(=O)O)C(=N)N |- | [[Molecular mass]] | 131.133 g/mol |- | style="vertical-align: bottom;" | [[Density]] | ? g/cm<sup>3</sup> |- | [[Melting point]] | ? °C |- | [[Boiling point]] | ? °C |- | style="vertical-align: top;" | [[Acid dissociation constant|p''K''<sub>a</sub>]] | style="vertical-align: top;" | ? |- | [[CAS registry number|CAS number]] | 57-00-1 |- | [[EINECS number]] | 200-306-6 |- |}

WikiProject Molecular Biology/Molecular and Cell Biology/Proposals/Archive 1 WikiProject Molecular Biology/Molecular and Cell Biology/Proposals/Archive 1 Chemical name 2-(carbamimidoyl-methyl-amino)acetic acid Synonyms (α-methylguanido)acetic acid Creatin Kreatin methylguanidinoacetic acid N-amidinosarcosine Chemical formula C4H9N3O2 SMILES CN(CC(=O)O)C(=N)N Molecular mass 131.133 g/mol Density ? g/cm3 Melting point ? °C Boiling point ? °C pKa ? CAS number 57-00-1 EINECS number 200-306-6

2. II, which i am "advocating", and which uses ideas from other info boxes, has the following:

{{BioChemInfoBox | name=Arginine | image=Arginine.png | width=100 | IUPAC=2-Amino-5-guanidino-pentanoic acid | formula=C<sub>6</sub>H<sub>14</sub>N<sub>4</sub>O<sub>2</sub> | mass=174.2 | density= | Tb=? | pI=10.76 | pKa=2.03<br/>9.00<br/>12.10 | accept= | tautomers=3 | CAS=74-79-3 | PubChem=232 }}

{{BioChemInfoBox | name=Arginine | image=Arginine.png | width=100 | IUPAC=2-Amino-5-guanidino-pentanoic acid | formula=C<sub>6</sub>H<sub>14</sub>N<sub>4</sub>O<sub>2</sub> | mass=174.2 | density= | Tb=? | pI=10.76 | pKa=2.03<br/>9.00<br/>12.10 | accept= | tautomers=3 | CAS=74-79-3 | PubChem=232 }}

I initially used format style I, but as i was tryig to make the tables look standard and all i realized that i couldn't do it this way, b/c if i needed to add a new change to the way the table looked in all of the articles that had it so far (say add a link, or border, or anything) i had to go and edit each one of them. When the number of these articles is low that's not a problem but if this standard table is to be used for all the compounds produced by the cell - tens of hundreds if not thousands, then that's a major headache. So i learned about the templates and created format style II, which design by the way looks similar to the one used for the chemical element's "info table". Now if i need to make any change all i need to do is to change the appropriate template and that will affect all the articles that use it. Certainly, Style II is not in its final edition, more changes will be added to it to suit both the biologists and the chemists, as i would realy, hmmm dislike, if the info table contains chemical data only and lacks any biological one - the info for the melting and boiling points, or for any of the solid properties (i'm going to add these later) don't really "heat the soup" for the biologists, we also need stuff like - H-bond donor count. About "EINECS", i added it b/c it was already in the info, i didn't know what it ment. If it is not used anymore then i'll stop using it too. I didn't write the code that adds the article's name on the top of the table b/c having a table named "Creatine" in an article called "Creatine" is redundant. But if you insist i will add it and here is the exmple of the power of the templates - i will change the template {{NatOrganicBox_header}} and all the articles that use it will be affected. BorisTM 19:28, 2 November 2005 (UTC)

Although a good start, it still has some issues. Yes, i suppose most people would like to see a title to the table with the name of the compound. Second, images inserted in this box cannot be resized, so it stretches the box to the size of the image, which disturbes layout. Third, I prefer to leave out unknown information at all in a given article, instead of inserting questionmarks '?' in a table. Leaving out certain things is difficult in your case, because it has several properties next to each other instead of below each other.Cpt. Morgan 22:06, 8 November 2005 (UTC)

Ok, i will have the name.
I desperately tried to create a template where the width of the image is a variable, but either because of a wrong template logic or because Wiki doesn't allow the width as a variable, it just didn't work.
Yeah, i know it needs many improvements. You are right, if we don't have certain info, it should not be displayed at all, i don't like the "?" either. The properties that are next to each other form a group, and these 4 used to be bellow each other but that way they were on 4 rows with a lot of empty space, now they are on three wich i will change to two. Wasn't you who said that the table was too big? And i agree with you. I am working on a template style that will allow displaying of the info rows that have their info and not displaying those that don't have it. BorisTM 11:56, 9 November 2005 (UTC)

Yes i was the one who thought it was too large. Once the issues has been sorted out, I would be happy to use your template. I am still bothered by the resizing image issue, however, I am not familiar with creating templates, but I know the regular chembox (as is now in use for the amino acids) allows images to be resized. Before your box can be used there, it should either allow resizing or the images themselves should be resized. But using the current big images is impossible with your template. Keep up the good work though. Cpt. Morgan 16:58, 9 November 2005 (UTC)

There you go, guys. The with of the image is resizable, only the mandatory properties are seen, even when they don't have values. Only "PubChem" and "SMILES" are not complete, "PubChem" is a hard nut, while i need Peak's permition to change the template for "SMILES". You can use BioChemInfoBox if you want, i've made an "allel" of it BioChemInfoBox_check where i can play around, without affecting the articles. BorisTM 20:48, 10 November 2005 (UTC)

• Please can you make sure that you discuss any changes with Wikipedia:WikiProject Chemicals before you make any new policy on small molecule articles? The Chemicals WikiProject uses one of three infoboxes as listed at Wikipedia:Chemical infobox, with a supplementary data page for less important data items. There is a tranclusional version (is that the right term?) of the main infobox, too. Also, we regularly monitor and assess around 380 chemical substance pages on our worklist, including 50 biologically important compounds. You may also want to look at the section right after this one, "other important compounds," which includes some terpenes etc. We need to make sure that your data boxes mesh well with ours. From our group, User:Borb has been the main person working an amino acids, while I have done a bit of terpene work. I'm sure we chemists will be pretty flexible about what goes in the infobox, but if we just see changes to infoboxes they might get reverted as being "non-standard"! Thanks, Walkerma 06:15, 10 January 2006 (UTC)

I totally agree. We should coordinate out work not only for the infoboxes but for the whole article as well. -- Boris 14:19, 10 January 2006 (UTC)

• Great, thanks! You can see from our worklist what we're aiming at for each, an A-Class article. Ideally we could write chemistry sections, and you guys could supply biochemistry/mol. bio sections. If you're very active on specific aspects (e.g., a new infobox) or a specific article (e.g., for FAC) please post a comment here, and I'll try to make sure we do the same. I know we would really appreciate your help in cleaning up folic acid. This could be the start of a beautiful friendship! Walkerma 17:46, 10 January 2006 (UTC)

Question - is everyone satisfied on this issue? Can it be archived? --Username132 (talk) 09:38, 1 September 2006 (UTC)

Wikiproject MCB: Some small suggestions for our improvement

I was strolling across the Wiki today, taking a look at the pages for some of my favorite subjects, and I found that some of the pages for some very basic subjects in molecular and cellular biology (adenosine triphosphate, cell cycle, among others), are not nearly what they should be. Considering the potential editing power that we can collectively bring to bear on any subject, it seems to me that all we really lack is the organization.

For that purpose, I'm going to be bold and take the initiave and begin the following practices, modelled in part on the very effective practices of Esperanza.

1. I will initiate an "MCB Article Improvement Drive" (not unlike the Wikipedia:Article Creation and Improvement Drive) to choose an article for our focus with the goal of improving the chosen subject to at least Good Article status. A new focus will be chosen every two weeks.
2. I will begin a monthly "MCB Newsletter" that I will post to all WP:MCB members. Although the superficial purpose of this newsletter is to inform members of the MCB going on, its real purpose is to introduce a small aspect of community to the MCB project.
3. Finally, I would like to propose an election for an "MCB Project Director" (boss, captain, chairperson, chief, controller, superintendent, supervisor? Actual title to be decided by the community). This person would be responsible for the administrative for the MCB project, including but not limited to coordinating recruiting efforts, spamming the newsletter, and maintaining the Article Improvement Drive and MCB Portal.

I don't want to step on anybody's toes, so please let me know if you think I'm out of line. However, I sincerely believe that with a little organization we could advance from a relatively obscure wikiproject into a model of efficiency that other projects will seek to emulate. – ClockworkSoul 22:22, 26 August 2006 (UTC)

Out of line? Are you crazy? Sounds like a bunch of great ideas. David D. (Talk) 05:04, 27 August 2006 (UTC)

I'm glad you like them. I'm putting together the first newsletter now, which has all of the links to the propositions and new pages that I'm in the process of creating. Please feel free to take a look and/or edit mercilessly. Really, I could use the help. – ClockworkSoul 05:39, 27 August 2006 (UTC)