Wikipedia talk:WikiProject Molecular Biology/Metabolic Pathways/Archive 1

Project directory
Hello. The WikiProject Council has recently updated the WikiProject Council/Directory. This new directory includes a variety of categories and subcategories which will, with luck, potentially draw new members to the projects who are interested in those specific subjects. Please review the directory and make any changes to the entries for your project that you see fit. There is also a directory of portals, at User:B2T2/Portal, listing all the existing portals. Feel free to add any of them to the portals or comments section of your entries in the directory. The three columns regarding assessment, peer review, and collaboration are included in the directory for both the use of the projects themselves and for that of others. Having such departments will allow a project to more quickly and easily identify its most important articles and its articles in greatest need of improvement. If you have not already done so, please consider whether your project would benefit from having departments which deal in these matters. It is my hope that all the changes to the directory can be finished by the first of next month. Please feel free to make any changes you see fit to the entries for your project before then. If you should have any questions regarding this matter, please do not hesitate to contact me. Thank you. B2T2 23:37, 25 October 2006 (UTC)

Glucose Metabolism template
I found this template made by User:David D. but I don't know how to edit it... I think it'd be useful, but I don't even know how to give it its own template page.Robotsintrouble 15:48, 14 December 2006 (UTC)
 * Could we add the Glyoxylate cycle? It may not happen in animals, but it is very important in the scheme of it all. Adenosine | Talk 19:03, 14 December 2006 (UTC)

Created the template at Template:Glucose metabolism, to use simply type.

- Zephyris Talk 19:33, 30 December 2006 (UTC)

Wikipedia Day Awards
Hello, all. It was initially my hope to try to have this done as part of Esperanza's proposal for an appreciation week to end on Wikipedia Day, January 15. However, several people have once again proposed the entirety of Esperanza for deletion, so that might not work. It was the intention of the Appreciation Week proposal to set aside a given time when the various individuals who have made significant, valuable contributions to the encyclopedia would be recognized and honored. I believe that, with some effort, this could still be done. My proposal is to, with luck, try to organize the various WikiProjects and other entities of wikipedia to take part in a larger celebrartion of its contributors to take place in January, probably beginning January 15, 2007. I have created yet another new subpage for myself (a weakness of mine, I'm afraid) at User talk:Badbilltucker/Appreciation Week where I would greatly appreciate any indications from the members of this project as to whether and how they might be willing and/or able to assist in recognizing the contributions of our editors. Thank you for your attention. Badbilltucker 17:06, 30 December 2006 (UTC)

Metabolic pathway article organisation
I'm very proud to see this discussion page in use! Time to take advantage of it...

The metabolism articles at the moment are a mess, as the template demonstrates, and there needs to be a plan on how to proceed. I have a few ideas (see below), please comment/adapt or propose your own plan. After we decide on an overall structure it will be much easier to systematically improve the articles with appropriate priority.

I suggest 5 'classes' of articles:
 * Fundamental articles, including enzyme, metabolic pathway, etc. which cover the basics and required knowledge of the other articles. These should be accessable to all readers (or as near as possible), aiming for secondary/high school level would be good. These articles are generally good.
 * Process articles, in particular aerobic respiration, anaerobic respiration, and various synthesis pathways. These should cover the roles of metabolism within the cell without diving into unneccecary detail (such as detailed pathways). Again these should be accessable to all readers, but may get more technical in the later stages of the article - think aproaching A level standard. These articles would be particularly important in linking metabolic pathways with the molecular biology processes or protein synthesis, DNA replication and other central cell biology processes.
 * These will include lipid metabolism, carbohydrate metabolism, etc. The associated catabolism/anabolism pages should redirect to the metabolism page. Principles and processes of anabolism/catabolism should be discussed, but specific details belong in the metabolic pathway of anabolism or catabolism.


 * Pathway articles, for example glycolysis and the citric acid cycle. These should detail individual pathways preferably covering role in the cell, history/discovery, the pathway itself, pathway regulation and other relevant information, such as related genetic disorders. These may be less accessable to a general reader, and should direct to simpler process articles to aid understanding. These articles should be well linked to the KEGG pathway database and other similar resources for further reading. Care should be taken throughout to identify what classes of organism the pathway is relavent to, and provide links to alternatives in other organisms. They cannot be entirely human orientated.
 * KEGG pathway database provides a good list of pathways which may be used as an outline for which articles to have. More peripheral pathways, such as the metabolism of individual sugars, may me better grouped together into a single article.


 * Enzyme/Chemical articles, for example glucose 6-phosphate and hexokinase. These should provide basic information on the chemical and some information on the many different versions of enzymes. These pages are not vital, but should at least be provided as a stub with a formula/cartoon structure and a link to the relevant pathway.
 * Technique articles, similar to fundamental articles, but from a practical perspective. Should be as accessable as possible to all readers due to their stand-alone nature.


 * This will give a very tree-like structure for the articles. In addition the articles will be directly tied together with templates such as and  to provide 'horizontal' navigation. A portal page should also be produced, although I believe (if possible) to make a radically different structure to the ones which currently exist. It should promenantly feature a linking diagram of the interlinking metabolic processes of the cell, highlighting major processes such as aerobic respiration and compounds like deoxyribiose.- Zephyris Talk 00:52, 31 December 2006 (UTC)

Metabolism Summary
Comments please! This is still very much a work in progress and any comments of factual accuracy/misconceptions, layout and overall apperance are welcome. I know the names dont fit in the boxes ;) - Zephyris Talk 19:19, 1 January 2007 (UTC)
 * Edit: Draft 2... - Zephyris Talk 11:34, 2 January 2007 (UTC)
 * Edit: I have made a partly linking template version, see Template:Metabolic pathways- Zephyris Talk 13:16, 3 January 2007 (UTC)
 * Nice work, it kind of sets the stage for a lot of articles and work to be done. Could it be SVG? Adenosinetalk 21:00, 3 January 2007 (UTC)
 * Im glad you think that! its exactly what i was aiming for... however unfortunately I dont have a program which can convert from .xpr/.ai to .svg so svg isnt a possibility, unless someone has illustrator and feels like converting it for me. - Zephyris Talk 23:40, 3 January 2007 (UTC)
 * I was just re-admiring this diagram, and wondering the scope of it, and of this group. Which organism(s) is this a map of? It has both lactate and ethanol for anaerobic metabolism, many essential amino acids, and some more exotic polysaccharides that all mean this is not human, was this based on any one particular lifeform? (This is a bit of a tangent, is this group aiming for any biochem pathway or just human or etc..?) . Aesthetically this diagram's great, hard to lay these things out without overlap, duplication, or huge looping arrows - what was the basis/inspiration for it? Would it be beneficial to colour code some of the lines to designate direction, energy production, control points, limiting reaction etc. or color code some of the substrates to show differemces in input vs. output or something? This is stuff I'd do if it was just for me, but they be over complicating it alot, and these suggestions may not be suitable of the 'average' wiki-reader..  Kudos, great work Adenosinetalk 23:08, 10 January 2007 (UTC)
 * It is based on a poster which is available online here, which is, as far as im aware, a general map of metabolism. In making this simplified version I tried to include interesting compounds, it is by no means based on any particular organisms metabolism. I drew it with the intent of being as simple as posible map of metabolism, hence no arrows/color coding, although im very tempted to cover it in arrows to show the general route of loads of fundamental processes.
 * On the subject of your tangent, i think all metabolic pathways should be covered (eventually!) with clear indications of which one happens where... It would make sense to concentrate on human pathways initially because of the wider interest these have, although it is important to cover other important non-human pathways like ethanol production, nitrogen fixation, etc.- Zephyris Talk 23:39, 10 January 2007 (UTC)
 * Oh, and check out the portal if you havnt already portal:metabolism.- Zephyris Talk 23:40, 10 January 2007 (UTC)


 * I don't think it is really possible to include everything. I used to have a chart called Biochemical Pathways that tried to do just that. It was really cool. I have two comments.
 * 1) I'm a botanist, so it might be nice to see a green colored version of this that includes Botanical pathways such as the Calvin cycle.
 * 2) Is there a place in there for C4 metabolism? A biological pathway in photosynthesis starting with PEP?
 * I think that we could make a png of this and map the blocks to link to particular metabolic pathways. maybe.Rozzychan 17:58, 25 February 2007 (UTC)
 * Im no expert but I can easily adapt this diagram to include more pathways if im given guidance... - Zephyris Talk 13:03, 27 February 2007 (UTC)

It's really psychadelic. I love the colors, but I don't like the use of outlined text. I find the white outline text hard to read.Rozzychan 16:56, 25 February 2007 (UTC)
 * I went for the outline for clarity - white text is relitivly hard to read, black text, if it overlaps the pathway lines, isnt suitable, and coloured text would get lost in some backgrounds. Any suggestions are welcome though, the outline doesnt work well at this resolution. - Zephyris Talk 13:03, 27 February 2007 (UTC)

I would just like to point out that, at some point, I would like to make a similar diagrams for electron transfer processes and molecular biology processes - any contributions to the content/layout these could have would be welcome. - Zephyris Talk 13:03, 27 February 2007 (UTC)
 * I'm attempting to contribute to the Biochemistry structure for Wikiversity. I was very impressed visually by your schema as visually appealing, structuring, and with a possibility to break down in further detail by small pieces without getting into the step-by-step pathway description. Xyzt1234 19:36, 9 May 2007 (UTC)

Printable glycolysis pathway
I know that current view is to use the line drawings of molecules in pathways, but I find that when teaching glycolysis to introductory students, it is important to include every atom, so I made an old-fashioned Glycolysis pathway diagram from scratch.

Can you please read it and tell me if I have any errors in it. If it is OK I plan to add a link to the bottom of the glycolysis page saying "printable version" if no one objects. Rozzychan 17:02, 25 February 2007 (UTC)
 * looks good, and i can see it would be useful! Go for it be bold - Zephyris Talk 20:00, 25 February 2007 (UTC)

NOT GOOD, look at phosphoenolpyruvate-carbon 2. there is a double bond and three single bonds on it. that hydrogen should not be there.

Templates
I've noticed the Metabolic pathway template placed in the article. Shouldn't it be placed on the talk page, along with the rest of the project banners? Thanks, RHB Talk - Edits 00:27, 4 March 2007 (UTC)
 * umm, yes it probably should be. thanks for noticing! - Zephyris Talk 11:49, 4 March 2007 (UTC)

You might also want to consider replacing metabolic pathway stub with a talk-page equivalent, i.e. populating rather than a stub category as such. As it stands, it drives a coach and four through the stub guidelines. If not, it'll have to be renamed, reformatted, given a category -- and hence, a well-defined scope: it doesn't seem to me that everything this is used on would go in the  permcat, and the "of interest to" scoping is vague, and not really appropriate for a mainspace-category-feeding template. Alai 20:52, 19 March 2007 (UTC)

Biological Value
This article, on a method for evaluating biological utilizations rates of proteins in human and animal consumption, was started in August and is in desperate need of an expert. We are having trouble locating one and the article desperately needs it. This method is used constantly in bodybuilding magazines and products and is the subject of much misinformation and half-truths. On the other hand it does appear to have some value. Please help if possible. Quadzilla99 22:04, 4 March 2007 (UTC)
 * See my reply at Talk:Biological Value - Zephyris Talk 00:59, 5 March 2007 (UTC)

Peer-review of Metabolism
Hi everybody, this article has been re-written and expanded. Any comments at Peer review/Metabolism/archive1 would be very welcome. TimVickers 04:01, 21 March 2007 (UTC)
 * Now nominated as a FAC here. Comments and suggestion would be very welcome. TimVickers 19:22, 25 March 2007 (UTC)

Project Banner
I have recently created a banner for WikiProject Biology which has assessment parameters. I notice that your existing banner does not. Given the amount of overlap in the biology sector, and the concerns expressed elsewhere about the proliferation of project banners, I was wondering whether the members of this project would be interested in perhaps utilizing the Biology banner, with a "drop down tab" for this project, perhaps similar to the WPMILHIST banner. Doing so would permit for individual assessment for each project, as that is something the Military History banner does, while at the same time reducing the amount of banner "clutter" on talk pages. If you would be interested in such an arrangement, please let me know and I will work to revise the Biology banner to include the "drop-down" tab and make the other arrangements required for your project, as well as theirs, to have assessment data available. Thank you. John Carter 21:01, 27 April 2007 (UTC)

SVG arrows
Hi, I'm not sure, if this is the right place to post. I just noticed some of the PNGs of reaction arrows you're using on Commons and wanted to inform you that I uploaded a set of reaction arrows as SVGs some time ago, which you can find here. I thought they might be useful for your purpose. Regards, --NEUROtiker 11:10, 21 October 2007 (UTC)

FAC of Nicotinamide adenine dinucleotide
Hi there. I've nominated this article as a FAC (here), but have got very few reviews. Would anybody here like to comment? Tim Vickers (talk) 04:26, 11 December 2007 (UTC)
 * Anybody? :) Tim Vickers (talk) 02:29, 16 December 2007 (UTC)

tl|Metabolic pathway stub
The template has been listed at Stubs for deletion for possible renaming or deletion. Of particular concern is that the template does not follow the naming guidelines for stub templates. Caerwine Caer’s whines 17:25, 19 March 2008 (UTC)
 * FYI: It is renamed as . Will change this on the main page as well.Calaka (talk) 10:52, 30 May 2009 (UTC)

Merge this wikiproject as a task force to WP:MCB?
I made a proposal to merge this wikiproject along with two others (WP:RNA & WP:Cell signaling) into the WP:MCB banner as a task force. Any comments would be most welcome in the WP:MCB note that I left. Cheers. Calaka (talk) 03:51, 23 May 2009 (UTC)
 * Merging process will now begin for this project. If there any thoughts, please write on the provided link. Thank you. Calaka (talk) 10:58, 30 May 2009 (UTC)

New map of Metabolic Pathways
I've made a new metro-style map of the major metabolic pathways, which was inspired by the already existing one (Template:Metabolic_pathways) and other excellent online resources (e.g., ). The map encompasses most of the biochem pathways in human, but also include important ones in plants / fungi / microbes (double lines). The metabolites are grouped as general terms (e.g. "Hexose Phosphates") instead of the specific ones in the existing map. I'm also going to make it a clickable map.

Some questions:
 * Is it suitable for wikipedia, in terms of style and complexity?
 * Is it good to replace the existing map with this one (that would change all the pages that includes Template:Metabolic_pathways) or make it a separate work?
 * Any comment on the map as an individual work?

Thanks! (also posted at Wikipedia_talk:WikiProject_Molecular_and_Cell_Biology) Chakazul (talk) 17:33, 30 May 2016 (UTC)
 * I think the map you made is incredible! Good job! As for whether to replace it with the current metabolic map, I would say be bold and do it, if someone has any reasons why not to replace it they can say it. Keep up the great work. :) Calaka (talk) 11:12, 31 May 2016 (UTC)