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Archive 1 | ← | Archive 3 | Archive 4 | Archive 5 | Archive 6 | Archive 7 | → | Archive 10 |
>Why are you leaving me personal messages on my talk page about a CfD? If your comment is related to the CfD keep the discussion there.
[email protected] (
talk)
20:42, 11 January 2011 (UTC)
See also this comment which I left on Protonk's talk page. Richwales ( talk · contribs) 17:27, 16 January 2011 (UTC)
Hi Boghog, could you please have a look at my AfD and comment (either way)? It has just been re-listed the 2nd time. thanks, MichaK ( talk) 08:19, 24 January 2011 (UTC)
Template:IUPHAR ligand has been nominated for deletion. You are invited to comment on the discussion at the template's entry on the Templates for discussion page. — This, that, and the other (talk) 09:46, 25 January 2011 (UTC)
Hi! Thanks for signing the Online Ambassador interest list. We're gearing up for the next term right now, and the Wikipedia Ambassador Program will be supporting considerably more courses, with considerably more student activity... possibly upwards of 500 students who will need mentors.
If you're still interested, I encourage you to take a look at the Online Ambassador guidelines; the "mentorship process" describes roughly what will be expected of mentors in the coming term. If that's something you want to do, please apply!
You can find instructions for applying at WP:ONLINE. The main things we're looking for in Online Ambassadors are friendliness, regular activity (since mentorship is a commitment that spans several months), and the ability to give detailed, substantive feedback on articles (both short new articles, and longer, more mature ones). If you have any questions, please let me know.
I hope to hear from you soon.-- Sage Ross - Online Facilitator, Wikimedia Foundation ( talk) 20:29, 3 January 2011 (UTC)
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Delivered by EdwardsBot ( talk) 00:31, 29 January 2011 (UTC)
Hi! I've noticed that you fixed my links to Pubmed articles, making them standard and nice-looking. Could you please help me to understand, what is the best way to do it? Is it some kind of a special add-on program? I'll reference Pubmed in the future for sure, and I'd like to it properly =) Khakhalin ( talk) 18:22, 27 January 2011 (UTC)
The WikiProject Barnstar | ||
For your open, friendly, and helpful response to the comments at Wikipedia talk:WikiProject Molecular and Cellular Biology#Squint_talk, and for your subsequent diligent efforts to resolve the concerns presented by the user. People like you make WikiProjects a delight to work with, and help us focus on solving the problem, rather than assigning the blame. WhatamIdoing ( talk) 22:20, 10 February 2011 (UTC) |
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Delivered by EdwardsBot ( talk) 18:21, 11 February 2011 (UTC)
Thank you so much for what you're doing on Pain, and for your calm, constructive rationality. -- Anthonyhcole ( talk) 11:01, 13 February 2011 (UTC)
A) I just did that edit I'd mentioned - turned out to be many - cleaned it right up - 'Beta clamp: sandbox:", and B) is there an elucidation [for me] of 'Boghog'? Many thanks! ~ Betaclamp ( talk) 08:03, 15 February 2011 (UTC)
Hi Boghog!
If you're still interested in being a mentor this term, please add your profile to Wikipedia:Online Ambassadors/Mentors. If you have any questions about the ambassador role or what you're interested in doing as an Online Ambassador (whether mentoring, pitching in in other ways, or something else), please let me know.-- Sage Ross - Online Facilitator, Wikimedia Foundation ( talk) 17:36, 14 February 2011 (UTC)
This message is going out to all of the Online Ambassadors who are, or will be, serving as mentors this term.
Hi there! This is just a friendly reminder to check in on what your mentees are doing. If they've started making edits, take a look and help them out or do some example fixes for them, if they need it. And if they are doing good, let them know it!
If you aren't mentoring anyone yet, it looks like you will be soon; at least one large class is asking us to assign mentors for them, and students in a number of others haven't yet gotten to asking ambassadors to be their mentors, but may soon. -- Sage Ross - Online Facilitator, Wikimedia Foundation ( talk) 20:05, 21 February 2011 (UTC)
You prolly already are aware of this algorithm flaw, but in case not, I thought I'd mention that the Further Reading lists I see on many science pages many times contain publications that do not provide meaningful information with the wiki page.
For instance, on the STARD8 page, one reference is the DNA sequence of chromosome X. Well, true, STARD8 is there, but this does not increase any understanding of the protein. Moreover, an existing reference on the page already cites its localization to that chromosome.
STARD13 has a Further Reading article (Strausberg RL, Feingold EA, Grouse LH, et al. (2003)) that is entirely about a new way to generate cDNAs vs actually having anything to do with STARD13.
Is the Further Reading usually added for readers to supplement Stub class articles which either no one has fleshed out yet or there is still too little scientific info on? Skingski ( talk) 21:49, 21 February 2011 (UTC)
Hey Boghog. One of the classes working with the Wikipedia Ambassador Program, Jonathan Obar's Media and Telecommunication Policy, is working in small groups and would like us to assign a mentor to each group (rather than having students request the mentors they'd like, as other classes are doing).
I invite you to sign on as the mentor for one or more groups, especially if any of the topics catch your interest. To sign up, go to the course page and add yourself as "Mentor: you" in the section for that group. They students and/or professor or campus ambassadors should be cleaning things up soon to list all the usernames for each group and add a few more groups. Once you know who the students are in the group, you can leave them each a quick introduction to let them know you'll be mentoring their group.
Thanks!-- Sage Ross - Online Facilitator, Wikimedia Foundation ( talk) 19:07, 22 February 2011 (UTC)
Hi Boghog. Just a quick reply to the question in your edit summary. I put the image under hidden text as at the time it was a redlink, but the uploader expressed concern over the deletion. So, no I personally have no reason to doubt User talk:Spitfire ch. By the way (as I see you are a mentor and have been around for a while) would you be able to keep an eye on the file. I offered to help, but my experience, especially around images is low. I am guessing an email would clear it up?
Nevermind, I see you have it under control. AIRcorn (talk) 10:18, 27 February 2011 (UTC)
Thank you for the excellent job you've done on converting Pain to vcite. (It looks like you've finished.) I really appreciate it. You found a resolution to a conflict and worked diligently to implement it. You're gold. -- Anthonyhcole ( talk) 18:21, 27 February 2011 (UTC)
Please take a look at this project page and see if you can be a mentor to one of the many Areas of Study. If you can, please put your name in the "Online Mentor" area of the Area of Study of your choice and then contact the students you will be working with. As the Coordinating Online Ambassador for this project, please let me know if I can be of assistance. Take Care... Neutralhomer • Talk • 04:31, 3 March 2011 (UTC)
Dear Boghog, Thanks for your many contributions to the gene wiki articles! I set up a twitter feed that summarizes edits to the gene wiki pages and am curious what you think of it? Is it useful to you? I'm very much open to suggestions for alterations if you have any ideas. See twitter/GeneWikiPulse . Thanks again for making so many great contributions! Benjamin Good ( talk) 23:46, 1 March 2011 (UTC)
That is what I think: [1]. I will be back in a week and would be happy to discuss this in more detail. Thanks, Hodja Nasreddin ( talk) 23:28, 4 March 2011 (UTC)
Howdy, Online Ambassador!
This is a quick message to all the ambassadors about marking and tracking which articles students are working on. For the classes working with the ambassador program, please look over any articles being worked on by students (in particular, any ones you are mentoring, but others who don't have mentors as well) and do these things:
And of course, don't forget to check in on the students, give them constructive feedback, praise them for positive contributions, award them {{ The WikiPen}} if they are doing excellent work, and so on. And if you haven't done so, make sure any students you are mentoring are listed on your mentor profile.
Thanks! -- Sage Ross - Online Facilitator, Wikimedia Foundation ( talk) 18:10, 15 March 2011 (UTC)
Rubredoxin—NAD(P)(+) reductase has one more set of parentheses than Ferredoxin—NADP(+) reductase. Could you check if one is an error? (Also NADPH—hemoprotein reductase, NADPH—cytochrome-c2 reductase.) — kwami ( talk) 06:59, 21 March 2011 (UTC)
Long-chain-fatty-acyl—CoA synthetase: acyl or acid? Synonyms?
Methylenetetrahydrofolate—tRNA-(uracil-5-)-methyltransferase: should that last hyphen be there?
Glucose—1-phosphate uridylyltransferase may have been an error: no em dash?
Nother merge at ubiquinol-cytochrome-c reductase, plus ones at galactose—1-phosphate uridylyltransferase & lecithin—cholesterol acyltransferase where I just guessed at the em dash.
Okay, in all the remaining links (which are 134, down from 200+), it's the last hyphen before the last space that's the em dash. A bot could do that. Though some are redirects, and I don't know about the names they redirect to.
[Okay, now the only hyphen.] — kwami ( talk) 07:18, 21 March 2011 (UTC)
Sure thing. All moves (from that sandbox) finished.
I see you merged 2',3'-cyclic-nucleotide 3'-phosphodiesterase to the form w the capital Cyclic. Yet the box is still l.c. Shouldn't it have been the other way around? (If it's just a problem of the page histories, I can shuffle them around.)
BTW, I have not copy edited the articles to match their new titles. — kwami ( talk) 08:25, 21 March 2011 (UTC)
plastoquinol-plastocyanin reductase rd's to plastocyanin, but plastoquinol—plastocyanin reductase rd's to cytochrome b6f complex.
Boggy, please look at Template talk:Chromosomal abnormalities - I'm not sure whether it needs expansion by another example of abnormality. Cheers, -- CopperKettle 21:29, 25 March 2011 (UTC)
Hi Boghog! I'm trying to find mentors for each of the groups in the Energy Economics and Policy course. Would you be willing to mentor this group? If so, please sign up on the course page and introduce yourself to the students in the group. If not, let me know so I can find someone else. Thanks!-- Sage Ross - Online Facilitator, Wikimedia Foundation ( talk) 14:43, 28 March 2011 (UTC)
Thanks for taking the time in correcting my errors in the reference formatting, I didn't realize that that I added a reference that was already there. 7mike5000 ( talk) 17:45, 29 March 2011 (UTC)
I'm speechless. ~ Betaclamp ( talk) 05:32, 5 April 2011 (UTC)
Hi Boghog
I am working on producing a Wiki page on Mercury Regulation for an Environmental Economics and Policy course at Indiana University and I was wondering if you would like to be my mentor. Thanks!
Ejking311 ( talk) 18:34, 27 February 2011 (UTC)Ejking311 (Lizzie)
Ejking311 ( talk) 03:55, 7 March 2011 (UTC)Ejking311
Hi Boghog. I've been thinking about changing my outline to reflect different categories of Mercury Regulation (ie - Direct Effects (use and release) and Indirect Effects (Environmental Standards)). I like this new approach but I'm worried that it may not be easy for a reader to get to laws such as the "Mercury Export Ban Act of 2008". Do you think I should try to work with this new outline or stay with the old one that focuses more on the individual regulations as opposed to grouping them? My page reflects some of these changes but I haven't deleted anything so I apologize if it is hard to read currently. Also, I've found some wonderful pdfs of tables on the web and I'd love to use them but I seem to recall that it can kind of be an ordeal to upload pictures on wikipedia. Do you think I could just redo the table in wikipedia and cite the source? Let me know what you think about this as well. As always, thanks for your help! Ejking311 ( talk) 22:47, 5 April 2011 (UTC)ejking311
Good work so far on DHSA. Please add appropriate categories to the article. I added two templates to the talk page. WP:ARS member -- DThomsen8 ( talk) 17:15, 10 April 2011 (UTC)
I noticed that you like to strip URLs in references if a DOI is supplied. I agree there can be justification for that but you shouldn't be so quick to do it automatically. In the particular reference I supplied, the URL points to a full text, open-access journal. It is easier for a wikipedia reader to simply click on the link and be taken to the article than to make extra effort to search for the article by DOI... which in most instances leads to articles that are behind subscription paywalls. Not everyone is in a university with a massive e-journal subscription list, so as a result they become conditioned to NOT doing further searching. Moreover, DOIs frequently lead to publishers' sites that only post the *abstract* of an article, instead of the full text... and many people are turned off by this, further leading to a disincentive for searching DOIs.
In this wikipedia article, some of the DOIs lead to open-access journal articles, but some don't (e.g., the Annu Rev Genetics reference). The reference I supplied has a URL for a full-text article that's not hidden behind a paywall, and it's a primary review article that covers the entire content of this wikipedia article in better detail, so I think you'd agree that it's best with the URL back in.
If you like to clean things up by stripping away URLs (which can change) in favor of DOIs (which are not supposed to change), I see the rationale. But consider modifying your practice so you don't do it automatically. While the DOI in this reference does in fact lead to the full-text, open-access article, again, that is atypical and I assure you that many people (e.g., at home, in public libraries, in high schools) don't bother with DOIs because they've been repeatedly burned by links to things behind paywalls, so they will appreciate a direct URL link to the article.
Whatever you decide to do in the future, I suggest you leave this reference alone (with URL intact) for the reasons stated. That said, I realized I made a typo in the URL... adding a period and digit... the correct URL (which you can confirm yourself) is: http://genomebiology.com/2002/3/10/reviews/3013
Lapabc ( talk) 15:33, 11 April 2011 (UTC)
Hey Boghog. You seem to be very good with these templates. Wondering if you could combine {{Infobox drug}}, {{Drugbox}}, and {{Chembox}}? Thanks. Doc James ( talk · contribs · email) 23:35, 14 April 2011 (UTC)
Howdy Boghog,
I'm working on a new version of the Protein Box Bot for Gene Wiki articles. As I understand it from
Andrew, the old version of the bot hasn't been running in some time, and as pages are edited, the PBB controls and templates are generally removed (makes sense).
I imagine that the new bot's role would be more suited to updating small details easily pulled from existing databases, like EC numbers and homologene IDs, so that higher-contributing editors (like you) can spend more time editing the text of the articles and less time on the minutiae. I've read some discussions relating to the bot's updating of the summary text on various talk pages, so I think the new version will be restricted updating the sidebar GNF_Protein_box template and the information it contains (and, of course, subject to any control flags). In any case, I was hoping to get your input as I went forward. Is there anything you would want to ensure for this version particularly, or any behaviors to include?
Pleiotrope (
talk)
00:30, 7 April 2011 (UTC)
{{
nobots}}
flag, something I saw requested on the ideas page. We're having a code review on Monday, but in the meantime I thought I'd just run through the current workflow of the bot and see what you think. (I won't be updating any other templates besides the one on my sandbox for a while)
Hi Boghog, thanks for the assistance on the section I altered yesterday. Please let me know if there is anything else you think I can do to improve that section. Thanks! Aventre3 ( talk) 13:07, 22 April 2011 (UTC)
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Delivered by EdwardsBot ( talk) 16:31, 22 April 2011 (UTC)
This is an automated message from VWBot. I have performed a search with the contents of KIAA0895, and it appears to be very similar to another Wikipedia page: KIAA0895L. It is possible that you have accidentally duplicated contents, or made an error while creating the page— you might want to look at the pages and see if that is the case. If you are intentionally trying to rename an article, please see Help:Moving a page for instructions on how to do this without copying and pasting. If you are trying to move or copy content from one article to a different one, please see Wikipedia:Copying within Wikipedia and be sure you have acknowledged the duplication of material in an edit summary to preserve attribution history.
It is possible that the bot is confused and found similarity where none actually exists. If that is the case, you can remove the tag from the article. VWBot ( talk) 05:18, 25 April 2011 (UTC)
Greetings, Boghog. I've noticed that Swmmr1928 ( talk · contribs) has been having difficulties at Moonlighting protein, seemingly due to a lack of familiarity with Wikipedia norms and conventions. I wonder if I could trouble you to help accommodate their alterations in a revised form, or if that is not in the article's interest, explain to them in a bit more depth why? They seem a little frustrated with the situation at present, and could use some help from us ambassadors. Regards, Skomorokh 17:03, 28 April 2011 (UTC)
April 30, 2011
Hi Boghog. Thanks for your comments. I re-read what are to be included in Wikipedia. Wikipedia is not the place for New Discoveries. Thanks VRodrig110 ( talk) 17:28, 30 April 2011 (UTC)
Hi Boghog. Thanks for reformatting my reference on the Arginine vasopressin page; I didn't realize that I had cited the earlier EPub. With regards to the reference that was originally present there, I removed it simply because the newer reference was more current and was unequivocal about the effect of AngII on AVP secretion. I don't want to make a big deal out of it, but I don't see the point of including the older reference as well. Please let me know what your thoughts on this are. Thanks, Techfiend ( talk) 06:31, 2 May 2011 (UTC)
Hi Boghog/Archive 5,
Your work as an Online Ambassador is making a big contribution to Wikipedia. Right now, we're trying to measure just how much student work improves the quality of Wikipedia. If you'd like contribute to this research and get a firsthand look at the quality improvement that is happening through the project, please sign up to assess articles. Assessment is happening now, just use the quantitative metric and start assessing! Your help would be hugely appreciated!
Thank you, ARoth (Public Policy Initiative) ( talk) 17:10, 6 May 2011 (UTC)
Thankyou for your Great Edits!
I think according to this, we still need an In-text attribution for the table in this section.
I added the align right tags to the tables in the Moonlighting protein article per these requests. However, the requests are from inexperienced users and maybe that is why you reverted the edit/did not discuss. Do you agree that the tables disrupt the flow when they are aligned in the center?
Also, can you explain why most proteins are not enzymes? Do you have numbers to back your claim? I am a bit confused after searching. Swmmr1928 talk 23:51, 4 May 2011 (UTC)
Is there anything wrong with quoting from a journal article's abstract? Swmmr1928 talk 01:59, 13 May 2011 (UTC)
Thank you for your friendly form letter of welcome to WikiProject_Molecular_and_Cellular_Biology.
I noticed a protein-box-bot template on another protein, and tried adding one on the same pattern to KLF14. It doesn't work, unsurprisingly. Is the bot still active, and if so how do I get it to give me a box? -- Dan Wylie-Sears 2 ( talk) 23:00, 17 May 2011 (UTC)
Hi! This is the last call for signing on for a Wikipedia Ambassador hooded sweatshirt (in case you missed the earlier message in one of the program newsletters about it). If you would like one, please email me with your name, mailing address, and (US) sweatshirt size. We have a limited number left, so it will be first-come, first-served. (If more than one size would work for you, note that as well.)
Cheers, Sage Ross - Online Facilitator, Wikimedia Foundation ( talk) 19:40, 19 May 2011 (UTC)
Hi Ambassador,
We are at a pivotal point in the development of the Wikipedia Ambassador Program. Your feedback will help shape the program and role of Ambassadors in the future. Please take this 10 minute survey to help inform and improve the Wikipedia Ambassadors.
WMF will de-identify results and make them available to you. According to KwikSurveys' privacy policy: "Data and email addresses will not be sold, rented, leased or disclosed to 3rd parties." This link takes you to the online survey: http://kwiksurveys.com?u=WPAmbassador_talk
Feel free to contact me with any questions or comments, Thank You!
Amy Roth (Research Analyst, Public Policy Initiative) ( talk) 20:36, 24 May 2011 (UTC)
Is no merge of these two articles necessary?
Swmmr1928 talk 01:13, 28 May 2011 (UTC)
Wondering if you could implement a number of improvements to this infobox as suggested here Template_talk:Interventions_infobox I just cannot get it to work. Doc James ( talk · contribs · email) 23:45, 1 June 2011 (UTC)
I have recently created the above infobox which I have used here at Complete blood count. Still not working perfectly. Wondering if you could help fix a few things mentioned here Template_talk:Diagnostic_infobox#Things_that_need_fixing? Doc James ( talk · contribs · email) 09:24, 3 June 2011 (UTC)
Are we able to move forwards with the changes to the drugbox? I have no strong feelings about transclusion but it would be nice to get the clinical data added. Doc James ( talk · contribs · email) 09:30, 3 June 2011 (UTC)
The Medicine Barnstar | ||
For the incredible work you have done on the medical templates. Doc James ( talk · contribs · email) 09:18, 4 June 2011 (UTC) |
Hey Boghog Have brought your changes to the drugbox live. I think I have it set up correct but wondering if you could double check. Will work on updating the top 20 most common prescriptions with the new info. Doc James ( talk · contribs · email) 07:14, 6 June 2011 (UTC)
Hi Boghog,
Thanks for fleshing out SPRED3 and SPRED1.
I am particularly interested in NF1 and NF1-like syndromes and the mutations leading to them. Genes related to this are Neurofibromin 1, SPRED1, SPRED2, SPRED3, SPRY1, SPRY2, SPRY3 and SPRY4. Neurofibromin 1 has had thousands of distinct observed mutations of various types.
I am not a professional in this area. I am trying to understand the condition for personal reasons. I have noticed that there seems to be a split among professionals working in the area:
With respect to NF1-related genes, I would like to make publicly available on Wikipedia the known mutations to the extent that they are in public domain. Do you support the idea of having more systematic inclusion of detailed observed gene mutation data on Wikipedia, and if so, what is the best way to go about it?
Thanks, Erxnmedia ( talk) 14:01, 7 June 2011 (UTC)
Hi Boghog,
That's great, I didn't known OMIM, and those pages drill right down to the nucleotide sequence for mutations which is great.
I have been working in general on Neurofibromatosis-related pages. This condition occurs about 1:3500 births and has many complications but is relatively unknown outside of those affected and the relatively small group of people that do research on it. Researchers on Neurofibroma are divided into mouse-model in-vitro cure researchers who are PhDs in biology and MDs doing human trials of specific drugs. Because there are thousands of possible mutations to Neurofibromin 1, the outcome of the disease is highly variable, and involves many of the body's systems. One of the main drivers of NF research is the Children's Tumor Foundation (CTF).
Because of the multiplicity of negative outcomes I was hoping that there would be a gene therapy cure. I communicated with a couple of leaders in the field regarding gene therapy specifically, and I got these responses. The first is David Muir, who said "research dollars are being channeled by those 'in the know' into drug therapy trials for NF1. The nature of the NF1 gene makes gene therapy insurmountably challenging at this time." He recommended asking the question to his colleague Peggy Wallace who is on the Board of Directors and is a long-time scientific advisor of the CTF. She said that
With regard to your gene therapy questions, the idea of just replacing or fixing the gene is appealing, but not currently feasible. However, there are some approaches being developed, aimed at trying to coax the gene to function despite its mutation (e.g. a drug that helps cells skip stop mutations, and therapies aimed at correcting splicing abnormalities). These don't actually fix the gene itself, so would need to be long-term therapies (a potential roadblock for some therapies). These are already under consideration in NF (we're testing one of the skip/stop drugs here, in a mouse model). No such therapies are FDA-approved for any condition yet, but some are in clinical trials in other conditions. These would be aimed more specifically at an individual's own mutation (I suspect there are probably over 1000 independent NF1 mutations known by now, but there's not an up-to-date database at the moment). I don't know the mutation distribution for SPRED1. NF1 mutations are of all different types. I'm not sure what you mean by taxonomy, but you can break down the mutations generally into deletions, insertions, and nucleotide substitutions; the effect of each depends on the size/location of that change. I believe that about 20-30% are stop mutations, 30-50% cause splicing errors, and the others are insertions/deletions/missense mutations. One issue with the splicing repair approach might be difficulty getting the therapy delivered to the Schwann cells due to the blood/nerve barrier; drugs that are small enough can probably get there. Also it will be hard to get therapies FDA approved which carry any kind of health risk, especially in a person who is pre-symptomatic (as in prevention) since there's no predicting what complications an individual will have (if any) and so you can't give a risk/benefit analysis. That will be a problem for systemic, long-term therapies. It will likely be easier to get approval for targeted therapies that are of relatively short duration (e.g. the photodynamic therapy work that Dr. Muir is testing on the tumors in mouse models). We also don't know if a therapy to short-cut a mutation (as mentioned above) will work in a symptom which has already progressed beyond being dependent just on loss of neurofibromin. So those are some of the considerations. The Children's Tumor Foundation is leading the charge in trying to take the best ideas to preclinical testing and then actual clinical trials, leveraging federal dollars. Some of the clinical trials have already tried some of the drugs you mention below, but to the best of my knowledge, there have been no treatments with uniformly good response.
I have edited the following pages related to NF, and suggested a WikiProject or Medicine Task Force for this area specifically, but it was considered to be too specialized:
Thanks, Erxnmedia ( talk) 19:08, 7 June 2011 (UTC)
Hi Boghog,
The practice in the medical industry seems to be to publish descriptions of individual clinically significant observed mutations in articles, but not to publish say the sequences of every one of a body of patients who have various mutations of a given gene. These sequences are published but in closed-access commercial database projects.
The achievable goal may be to scrape published articles for descriptions of particular mutation sites and their clinical significance. For example SPRED1 mutation list.
If you can design a bot which does a good job at this then I would apply it to every gene cataloged in Wikipedia in a batch. I would also add/merge all of the articles in User:Cboursnell/Sandbox which seem to be the result of this kind of bot, see my interaction with Alexbateman who has created this batch in sandbox and gave permission to publish all but hasn't published them himself: User talk:Cboursnell#EVH domain, EVH1 domain, Sprouty domain.
For what I am interested in, I have worked on Ena/Vasp homology proteins, EVH1 domain, SPR domain, SPRED1, SPRED2, SPRED3, SPRY1, SPRY2, SPRY3 and SPRY4.
Thanks, Erxnmedia ( talk) 03:29, 9 June 2011 (UTC)
Hi Boghog
I see we are getting duplication of material between the thymosin beta4 page and the part of the beta thymosins entry dealing with beta4. I added the Riley heart studies there earlier today, where there was already context about tissue regenerative activities and a generally fuller account of beta 4. I'm not sure what ought to be done about such a duplicatiion, but presumably at least some more "See Also" links? Jgedwards ( talk) 22:44, 9 June 2011 (UTC)
Looks good, thanks. Presume there will always be duplication where articles about gene families as well as individual human genes. I see the publicity re heart repair caused a notable spike in hits to the thymosin pages. I'm still hoping to get onto the closely related WH2 domains - would be good for Pfam also to have that.
I'd welcome advice on another matter: I've made significant progress with phylogeny of beta thymosins. For example there's a very interesting exception to the restriction to multicellular animals - a beta thymosin in a choanoflagellate, an organism believed to be at the margin of multicellularity. Question is whether for Wikipedia, this has to be in peer reviewed journal paper, or whether one can directly cite the openly available evidence of a sequence database entry. Jgedwards ( talk) 11:28, 10 June 2011 (UTC)
Boghog - thanks for this. Clearly a rigorous attitude to citation is the way to ensure reliability. Given that beta thymosin sequences are so strongly conserved, I reckon the unicellular exception I mentioned possibly counts as obvious to "routine comparison". You can just tblastn the human b4 sequence or any of the many others, against Monosiga genomic and there are also two transcripts. So I'll probably add it - if anyone (including yourself) maintains this is synthesis then I won't argue and they can of course delete it. I see there is a good article about choanoflagellates, relation to animals etc which mentions the Monosiga genome.
I hadn't caught up with WH2 - well done with that. It reads well. Presumably it should shortly appear as default annotation in Pfam. There's a view that thymosins are essentially WH2 domains - based on partial sequence similarity and fold when bound to actin. It's controversial and I've summarised as neutrally as I could in the beta thymosins article. Jgedwards ( talk) 22:20, 10 June 2011 (UTC)
A deletion discussion has just been created at Category talk:Unclassified Chemical Structures, which may involve one or more orphaned chemical structures, that has you user name in the upload history. Please feel free to add your comments. Ronhjones (Talk) 22:48, 10 June 2011 (UTC)
Hi boghog
I just noticed your WH2 links SCAR1 to SETX. These are completely unrelated proteins which unfortunately at some stage have acquired a coincidentally common synonym. The WH2-containing SCAR1 WASP family .proteins are named after a screen in Dictyostelium - something like Suppressor of Cyclic AMP Receptor. SETX is a considerably larger protein, probably a helicase, and doesn't contain WH2, as you can see by posting it into Pfam. I'd suggest killing the link. Jgedwards ( talk) 00:37, 11 June 2011 (UTC)
Hi Boghog
Would appreciate your response to discussion on Beta thymosins discussion page Jgedwards ( talk) 08:22, 13 June 2011 (UTC)
[2]. Biophys ( talk) 16:31, 17 June 2011 (UTC)
Thanks for the info about the gene pages. I was unaware that there was a style guide for the gene articles. I'll try and get all those articles put right by the end of the weekend. I did leave a couple thoughts here. -- Kerowyn Leave a note 06:35, 24 June 2011 (UTC)
Thanks for the cleanup on GPRC6A! — Preceding unsigned comment added by Gryderart ( talk • contribs) 20:07, 29 June 2011 (UTC)
You should really get the admin bits. Would be happy to nominate you if interested. Doc James ( talk · contribs · email) 09:42, 6 June 2011 (UTC)
Are we able to move the sandbox version that you have created to the main version? It seems to work well. Wish to start adding "clinical data" to more articles. -- Doc James ( talk · contribs · email) 05:07, 17 May 2011 (UTC)
Sorry to be a pain but wondering if their has been any movement on creating a bot? My abilities in this realm are poor. Might be a good idea to learn though. Doc James ( talk · contribs · email) 22:13, 16 June 2011 (UTC)
After having removed the `[sic]`s from [[ the code sample on Fast inverse square root, I had a look through the edit history. From what I gather you added them as a measure to preserve the comments from vandalism claims—as sensible as that is, that's not what they're for.
88.9.243.28 ( talk) 08:36, 22 July 2011 (UTC)
A chance to use " hobgoblin"? No. I understand the value of consistency; and it's not foolish consistency we're talking here, right?
Well, I'm a generalist wandered as per often into specialized territory. If you'd just reverted the format and level of detail on the authors' names, I maybe'd have let it go. But you also went for the journal-name link.
On the authors' names, I'll ask you a question: Is there anything lost by straying beyond the prescribed form in an instance? There's no possibility of confusion. I gave more information, so any specialized reader, or a general reader who knew nothing of Vancouver style, could understand the way I'd expanded the names. The question may become, Why did I do it? I was interested in the last name of one of the authors. That's it. I found for instance that s/he was on the Edit. Board of that BJU Int.. So I upgraded that article, too, and linked this one to it. Does it add anything, to have the additional information and the links to make it easily available to the maybe casually interested? (I did appreciate your "good faith" nod; and I think I'm granting the same to you; I've seen you're producing lots of (specialized) articles for Wikipedia. ... I ... like ... that they're here. ... I don't like to feel they're ... "off limits," though.) To me, what I did does seem to add something. You use consistency and a query to remove what I deemed worthwhile additional information. You seem to be trying to keep the shield of specialization drawn around a subject. To that I'd just start to close by asking of you, Why?
You may well counter that my solitary edit of this one article's and one journal's information unfairly and inexplicably makes that information stand out from "the rest." It's a reasonable counter. I'm currently just beginning to ponder the Wiki back-and-forth over different citation templates. Not directly related, I know, .... But just the way you didn't even think to link to "Vancouver style," just sort of waved it in front of us .... Well .... Whatever.
Well, I guess I am (sneaking up to and now finally) saying that your bid for consistency is sort of foolish. No disrespect intended. I stumbled in. I found the author listing confusing, as to whose last names went with which initials. I've learned now. But I also left a clearer alternative. I don't need to challenge the whole Vancouver protocol of 30+ years standing. I just like to know, and to communicate ... to others of my ilk, that there are alternatives. No big deal, no big boat-rock. Do you really need to enforce, rather than just observe, that discipline, that protocol? Respectfully yours, Swliv ( talk) 14:01, 12 July 2011 (UTC)
Even though it's been quiet on-wiki, the Wikipedia Ambassador Program has been busy over the last few months getting ready for the next term. We're heading toward over 80 classes in the US, across all disciplines. You'll see courses start popping up here, and this time we want to match one or more Online Ambassadors to each class based on interest or expertise in the subject matter. If you see a class that you're interested, please contact the professor and/or me; the sooner the Ambassadors and professors get in communication, the better things go. Look for more in the coming weeks about next term.
In the meantime, with a little help I've identified all the articles students did significant work on in the last term. Many of the articles have never been assessed, or have ratings that are out of date from before the students improved them. Please help assess them! Pick a class, or just a few articles, and give them a rating (and add a relevant WikiProject banner if there isn't one), and then update the list of articles.
Once we have updated assessments for all these articles, we can get a better idea of how quality varied from course to course, and which approaches to running Wikipedia assignments and managing courses are most effective.
-- Sage Ross - Online Facilitator, Wikimedia Foundation ( talk) 17:22, 27 July 2011 (UTC)
Those fields that you are adding by (bog)bot are probably numbers that are verifiable correct, aren't they? If so, it would be good if CheMoBot would follow them and tag them if someone would change them ...
My questions hence:
With that list/such lists I could upgrade my script, and update the index also for these fields (pff .. then I have to upgrade that script again, but that is due anyway, as there are other tasks approaching, and I have another list ready to be incorporated as well). -- Dirk Beetstra T C 22:19, 31 July 2011 (UTC)
P.S. One of the problematic ones is still the KEGG, I have a list InChI <-> KEGG (directly from KEGG) but unfortunately that is InChI, and not StdInChI .. the former is too variable to verify (different tastes). Do you by any chance know a better list? -- Dirk Beetstra T C 22:19, 31 July 2011 (UTC)
But you source all data from drugbank by searching for the INN, or from the drugbank identifier? -- Dirk Beetstra T C 23:05, 31 July 2011 (UTC)
{{PAGENAME}}
) as the title, so actually that one is obsolete. Though, maybe it was before that patch of the Wikimedia software came through, that the 'pagename' would say 'P-Toluenesulfonic acid' instead of 'p-Toluenesulfonic acid', and hence we used a name-parameter to override the pagename. Now obsolete, maybe should be parsed out.By the way, thanks! Because of your sorting I found a bug in User:CheMoBot (now resolved) - of course the last parameter ends before the closing double curly brackets. -- Dirk Beetstra T C 23:07, 31 July 2011 (UTC)
We might want to consider to write something so that the StdInChI and StdInChIKey are rendered into the final result of the page with a drugbox (not necessarily display, it is ugly) - then they get Google indexed, and you can find the article by looking for the StdInChI, some thing that some people do look for. Note that the value for InChI get stored without the 'InChI=' in front of it (to avoid the ugly 'InChI = InChI=<value>', which probably will get removed by some in some cases as 'duplicate, so probably wrong' etc.), so that needs to be added to the rendering. -- Dirk Beetstra T C 17:05, 1 August 2011 (UTC)
This field in the box is not working see Lisinopril for example. Doc James ( talk · contribs · email) 20:20, 1 August 2011 (UTC)
Have been going over the bot edits.
Wondering if we could set it to add lines of text even if they are not used? For example in the edit to amitriptyline it would be nice for it to add "|trade name=" even if it does not fill it in. [10] Doc James ( talk · contribs · email) 03:19, 16 August 2011 (UTC)
Hello! If you're planning to be an active Online Ambassador for the upcoming academic term, now is the time to join one or more pods. (A pod consists of the instructor, the Campus Ambassadors, and the Online Ambassadors for single class.) The Memorandum of Understanding (MOU) explains the expectations for being part of a pod as an Online Ambassador. (The MOU for pods in Canada is essentially the same.) In short, the role of Online Ambassadors this term consists of:
This replaces the 1-on-1 mentoring role for Online Ambassadors that we had in previous terms; rather than being responsible for individual students (some of whom don't want or help or are unresponsive), Online Ambassadors will be there to help whichever students in their class(es) ask for help.
You can browse the upcoming courses here: United States; Canada. More are being added as new pods become active and create their course pages.
Once you've found a class that you want to work with—especially if you some interest or expertise in the topic area—you should sign the MOU listing for that class and get in touch with the instructor. We're hoping to have at least two Online Ambassadors per pod, and more for the larger classes.
If you're up for supporting any kind of class and would like me to assign you to a pod in need of more Online Ambassadors, just let me know.
-- Sage Ross - Online Facilitator, Wikimedia Foundation ( talk) 16:31, 19 August 2011 (UTC)
PS: There are still a lot of student articles from the last term that haven't been rated. Please rate a few and update the list!
Was wondering if we should provide verification (ie a ref) for the drug categories. People are not to use Wikipedia for prescribing but this would add a bit of safety and allay potential fears. For example was looking at lisinopril which was given a D however the drug.com ref says it is a C in the first trimester and D in the second and third. What we had before could cause excess fear. [11]. Does the FDA have a site that lists all the preg catergories for all the meds? Doc James ( talk · contribs · email) 01:03, 23 August 2011 (UTC)
Hi, I'm fairly new to editing protein articles, so perhaps you could clarify something for me? What's the rationale behind the Further Reading sections on most protein/gene articles like the one you added here. Some of the papers in that one were only vaguely related to the subject. I assume these sections are auto-generated but I'm not convinced they are necessarily useful. A more select list might be less confusing for some readers. Do you use a bot to generate the lists? Thanks. -- Pontificalibus ( talk) 21:28, 30 August 2011 (UTC)
Hi Boghog, I saw your new section and I think it's well-written. One additional thing that'd be helpful is to include an example chart of concentration vs. time with arrows pointing to the phase where passive diffusion dominates and the phase where elimination dominates (By the way, do you mean elimination as in "excretion" or elimination as in "metabolism" + "excretion"? Some pharmacologists use the term "elimination" in the same way as "excretion"). -- Bobthefish2 ( talk) 18:13, 26 August 2011 (UTC)
AAAAAAAAAAAAAAHHHHHHHHHHHHHHHH?????? What on Earth did you do to the Polymyxin B article??????? I reverted your edit as the article was entirely unusable due to formatting errors - if you were adding legit information, please consult faqs and edit using proper format - PLEASE USE THE SANDBOX IF YOU AREN'T FAMILIAR WITH EDITING WIKIPEDIA ARTICLES.
If you are merely playing with or learning about editing bots, please stop as you have corrupted an article on a highly important subject. Bots are inherently dependent upon humans and humans make mistakes. Please don't assist those who seek to discredit Wikipedia. — Preceding unsigned comment added by 99.99.78.137 ( talk) 08:15, 1 September 2011 (UTC)
I'm sorry, I didn't mean to revert your reference-reformatting edit (about 20 minutes ago) to UBQLN1. I was just editing at the same time you were.
I think you since got your edits back in, which do improve the article.
Thanks,
H.Tamahagane 20:24, 1 September 2011 (UTC)
Hi there! It looks like BogBot dropped a critical "</nowiki>" off the end of the IUPAC name field of the {{ Drugbox}}. Diff here - Alison ❤ 19:02, 3 September 2011 (UTC)
Yes it is working for me... Could I run the bot from where I am? Doc James ( talk · contribs · email) 22:05, 3 September 2011 (UTC)
Hi Boghog. I just wanted to let you know that I have marked the image File:Tryptophan biosynthesis.png on Commons with the "disputed chem" tag because there appears to be an error in the third structure - there is an extra carbon between the sugar and the anthranilate group. Can you please have a look and fix it? Or I can create a new image, if necessary. -- Ed ( Edgar181) 11:45, 11 September 2011 (UTC)
Hey Bog(b/h)o(g/t)! Can you examine this edit. You are there deleting info and breaking the page with moving comment marks. Subsequently, CheMoBot has a problem with the page, but I am not sure if that is due to the edit by the bot, or if I have a mistake in my coding as well. I'll keep an eye on this one, may debug CheMoBot as well on that page if it persists still. Thanks! -- Dirk Beetstra T C 10:39, 15 September 2011 (UTC)
Hi! I've just noticed that BogBot places the synonyms parameter in the Chemical data section, [14] not in the Identifiers section where it is displayed (and where I think it belongs). Not a big thing, but I thought you might want to know. Cheers, ἀνυπόδητος ( talk) 12:15, 19 September 2011 (UTC)
<ref>
tags on this page without content in them (see the
help page).Hi Boghog. I am in the process of getting the Rfambot to convert the pages with the old rfam box to the new Infobox rfam. I will also be getting the bot to update and maintain some of the Rfam relevant fields in the infobox rfam. It would be useful to us if there was a field in the template for Rfam release version - so we can keep track of updates as some of the fields in the template do vary from release to release. The 'Rfam release' field need not be displayed in the box, infact its is probably better if is not. Unfortunately, none of us here at Rfam seems seem to know how to add a field that is not actually displayed. Can you help with this? I think in the old rfambox I just added the release information to the box in the page and it was never actually part of the template. I presume there is a nicer way of doing this? thanks Jennifer_Rfm ( talk) 10:49, 14 September 2011 (UTC)
Hey Boghog, on a related note, I've been playing around with the template in the sandbox trying to make it accept and display multiple GO/SO terms in a single field (i.e. without resorting to displaying GO1:, GO2: etc.) but my basic knowledge of template syntax is not up to the task. From reading the help on meta it looks like I either need nested #ifs or a #switch, but I'm quite unfamiliar with template wikimarkup so I was helping you could help me out or point me in the right direction? Any help or advice would be much appreciated! Jebus989 ✰ 15:18, 15 September 2011 (UTC)
Hello, Ambassadors!
I wanted to give you one last update on where we are this term, before my role as Online Facilitator wraps up at the end of this week. Already, there are over 800 students in U.S. classes who have signed up on course pages this term. About 40 classes are active, and we're expecting that many more again once all the classes are up and running.
On a personal note, it's been a huge honor to work with so many great Wikipedians over the last 15 months. Thanks so much to everyone who jumped in and decided to give the ambassador concept a try, and double thanks those of you who were involved early on. Your ideas and insights and enthusiasm have been the foundation of the program, and they will be the keys the future of the program.
Still waiting to get involved with a class this term, or ready to take on more? We have seven classes that are already active and need OA support, and eleven more that have course pages started but don't have active students yet. Please consider joining one or more of these pods!
Active courses that really need Online Ambassadors:
Courses that may be active soon that need Online Ambassadors:
-- Sage Ross - Online Facilitator, Wikimedia Foundation ( talk) 23:11, 27 September 2011 (UTC)
So is your new ChemDrug template ready to roll out or are you still fixing bugs? I might have to find a new page to write so I can test it out :-) Meodipt ( talk) 02:26, 29 September 2011 (UTC)
As a layman (and newcomer to this), I think the public would benefit from an explanation of what it means for a generic to fall within the 85-125% range. The FDA's AB designation of approved generics within that range begs the question: If a brand name drug has several generic versions, is it worthwhile trying to identify the particular generic version closest to 100%? If not, why is it that different formulations may have varying side effects on the same patient? But if so, consumers may be disappointed to find that the underlying studies are not publically available from the FDA except possibly through a Freedom of Information Act request (which takes months and is expensive). Garsbh ( talk) 18:33, 27 September 2011 (UTC)
Boghog, What do you think of the current state of the article on Macrophage migration inhibitory_factor ? I undid changes that basically weaken every statement into something along the lines of "it has been suggested that maybe.." despite these statements being backed up by cited literature. The other editor than undid my revisions. I fear getting into an edit war. How do you suggest I proceed? Thanks Benjamin Good ( talk) 22:07, 3 October 2011 (UTC)
Thanks for help, that looks better now. 70.137.128.110 ( talk) 08:09, 9 October 2011 (UTC)
I believe the entry for pyrithyldione may have the same problem, citing the wrong patent. I know these substances are obsolete, but it should be right if its an encyclopedia. A search brings up an entry for "presidon", but this seems to be a substance without the double bond. (the 3,3-diethyl- 2,4-dioxo-tetrahydro-pyridine) so there seems to be both variations (w/wo double bond) have been around as sedatives. The drugbank and the like entries are notoriously unreliable, meanwhile they cite the Wikipedia, good grief. And then we cite them, and so forth. Have already found such a bug earlier, where simply the DB entries were bogus. I better do not see a doctor, if I still know whats good for me... :) (: what does IGOR the humpback alway say to Dr. Frankenstein, in the lab, "Yesss master", but not with me! :)
70.137.128.110 (
talk)
10:12, 9 October 2011 (UTC)
http://www.ncbi.nlm.nih.gov/pubmed?term=presidon&itool=QuerySuggestion
brings up several hits which seem to be the same substance, but from 1949. Can you confirm? Unfortunately no text/abstracts available except one fulltext fragment about agranulocytosis, found by doi. Too old this stuff. 70.137.128.110 ( talk) 11:01, 9 October 2011 (UTC)
ok the above tetrahydropyridine is with a double bond, I miscounted. So presidon is the right hit. remains to be found why we have a synthesis for the 6-substituted substance instead of methyprylone here, and why the book is off target there, also with the piperidine. 70.137.128.110 ( talk) 11:12, 9 October 2011 (UTC)
Thank you for fixing that. The pyrithyldione is an intermediary of methyprylone, can you make a grafic for that too? How do you make these, what do you use as a tool? (Igor curious, master) 70.137.140.56 ( talk) 20:50, 9 October 2011 (UTC)
Can you please take a look at the synthesis, it shows the wrong substance. (not the same shown in stucture picture of chem box, but the 6-methyl derivative) 70.137.128.110 ( talk) 08:29, 9 October 2011 (UTC)
I wonder why they call the intermediate a piperidinedione with that double bond, in the book source.
The 6-substitution, I believe they got it from here
http://www.google.com/patents?id=2wxWAAAAEBAJ&printsec=abstract&zoom=4#v=onepage&q&f=false
this patent by the same guys from Roche describes a synthesis of a 6-substituted similar substance, not a 5-substituted substance.
Thank you for fixing that. The pyrithyldione is an intermediary, can you make a grafic for that too? How do you make these, what do you use as a tool? 70.137.140.56 ( talk) 20:50, 9 October 2011 (UTC)
Is the patent text above wrong? It descibes a 6-substituted example. 70.137.140.56 ( talk) 20:50, 9 October 2011 (UTC)
Do I see this correctly, that the 5-position is attacked with formaldehyde, and not the 6-position, because of keto-enol tautomerism? (Igor curious) 70.137.131.247 ( talk) 08:31, 11 October 2011 (UTC)
Thank you. I believe I have understood. 70.137.143.37 ( talk) 06:47, 13 October 2011 (UTC)
BogBot seems to have messed up the IUPAC name of Fusidic acid. Please investigate. I've restored the name by now. — Pt (T) 03:31, 13 October 2011 (UTC)
Hi Boghog! We're thinking of trying to increase the usage of the {{ SWL}} template on Gene Wiki articles and recently introduced a proposal at the Village Pump explaining our motivation and soliciting community feedback. Would you be interested in checking it out and seeing what you think? The proposal is here: Expanding the use of the SWL template. We've used a general example for the Village Pump but you can imagine the utility for human gene articles as well.
Thanks, Pleiotrope ( talk) 23:47, 18 October 2011 (UTC)
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Delivered by MessageDeliveryBot on behalf of Wiki Media Foundation at 11:49, 25 October 2011 (UTC).
Hello Boghog. It would appear the molecular mass for 4-Acetoxy-DET is off by 1 g/mol. Instead of 273.36 g/mol it should real 274.36 g/mol according to both PubChem and my own calculations.
(new msg as of 21:45) andy4789 ★ · (talk? contribs?) 21:45, 9 November 2011 (UTC)
Hi, this message is to let you know about disambiguation links you've recently created. A link to a disambiguation page is almost always unintended, since a disambiguation page is merely a list of "Did you mean..." article titles. For more information, see the FAQ or drop a line at the DPL WikiProject.
Any suggestions for improving this automated tool are welcome. Thanks, DPL bot ( talk) 13:05, 16 November 2011 (UTC)
[16] -- Anthonyhcole ( talk) 10:14, 20 November 2011 (UTC)
Thank you for reverting my section blanking on Tryptophan. I was not aware that it (turkey=tryptophan=drowsiness) is a widely held misbelief. I do however think the section should be shortened. Carstensen ( talk) 01:17, 23 November 2011 (UTC)
Good song! With regard to my retirement... There is an external hate speech web site with personal information that links to my wikipedia account. These guys are currently active, which is hardly a coincidence. I would not really pay attention, but this is not just a couple of jerks. For example, someone came to the College of Engineering in a city where I work and made a couple of edits pretending to be me [17]. That was done to prevent my return to the subject area related to Russia (I was topic banned). So, I would rather quit. Thank you very much for help and collaboration! You are doing great work here. Biophys ( talk) 23:36, 7 November 2011 (UTC)
Hey Bog taking another look at the drug class box. Have applied it on the statin page. Wondering if we can hide the fields with nothing in them? -- Doc James ( talk · contribs · email) 07:57, 25 November 2011 (UTC)
Hi. I did some really heavy stuff with Pymol engine lately. I tried to get similar images like yours but those colors and groups are so confusing. Is there any way you could help me with those? I admire your images on wikipedia sites... I have no idea how to get similar results. Hopefully, if you find some time to help me, please contact me and I will describe my issues.
Thanks in advance and once again, great stuff! Big thanks from all Wikipedia society! — Preceding unsigned comment added by Konieckropka ( talk • contribs) 22:57, 20 November 2011 (UTC)
It would be difficult to recreate File:3CNA_Concanavalin_A.png graphic using only the PyMol Gui since each of the monomers in this structure is individually colored. Below is the script that I used to create this figure. Please note that you must have the pdb filed named 3CNA_tetramer.pdb in the same directory as the script. The pdb file containing the tetramer was the taken from the PDB: 3CNA site, "download files/biological assembly". The standard 3CNA PDB file contains only the monomer. I hope this helps. Boghog ( talk) 06:20, 28 November 2011 (UTC)
##
set auto_zoom, off
cmd.bg_color(color="white")
set antialias = 1
# set stick_radius = 0.20
set cartoon_tube_radius = 0.40
set cartoon_smooth_loop = 0
set cartoon_sampling = 25
set spec_power = 200
set spec_refl = 1.5
set cartoon_transparency = 0.0
set cartoon_flat_sheets = 0
set cartoon_smooth_loops = 0
set dash_width = 3
set dash_gap = 0.25
set dash_radius = 0.2
set dash_length = 0.2
set dash_round_ends = on
set depth_cue = 0
set ray_trace_fog = 0
set sphere_scale = 1
cmd.load("3CNA_tetramer.pdb","complex")
cmd.hide("everything", "complex")
set_view (\
0.125021607, -0.992153525, 0.000000000,\
0.992153525, 0.125021785, 0.000000000,\
0.000000000, 0.000000000, 1.000000000,\
0.000000000, 0.000000000, -192.770080566,\
-0.000003815, -0.000015259, 0.000000000,\
149.219680786, 236.320480347, 0.000000000 )
cmd.select("backbone", "complex & name c+o+n+na")
cmd.disable("backbone")
cmd.select("sidechains", "complex & ! backbone ")
cmd.disable("sidechains")
#cmd.select("metals", "elem cu+zn")
#cmd.disable("metals")
cmd.show("spheres", "elem ca")
cmd.show("spheres", "elem mn")
# util.chainbow("complex")
cmd.color("red", "chain A")
cmd.color("magenta", "chain B")
cmd.color("green", "chain C")
cmd.color("cyan", "chain D")
cmd.color("gold", "elem ca")
cmd.color("grey90", "elem mn")
#cmd.color("yellow", "ligand & elem s")
#cmd.color("red", "ligand & elem o")
#cmd.color("blue", "ligand & elem n")
#cmd.color("organge", "ligand & elem p")
#cmd.color("grey90", "ligand & elem c")
set cartoon_fancy_helices, on
set cartoon_smooth_loops, on
#set cartoon_side_chain_helper, on
cmd.show("cartoon")
cmd.ray("1440","1080")
cmd.png("3CNA.png")
One or more of the files that you uploaded or altered has been listed at Wikipedia:Files for deletion. Please see the discussion to see why this is (you may have to search for the title of the image to find its entry), if you are interested in it/them not being deleted. Thank you.
Delivered by MessageDeliveryBot on behalf of MGA73 ( talk) at 17:42, 28 November 2011 (UTC).
Hi Boghog, thanks for the excellent reaction diagram.
Shouldn't the last step's product be called 1,3,7-trimethylxanthine and not 1,3,7-tiimethylxanthine?
http://en.wikipedia.org/?title=File:Caffeine_biosynthesis.tif&page=1
Hi. My group and I have been editting the TBR1 page in wikipedia for our Neuroscience class. We noticed that you had edited it severaal times and would appreciate any advice you have on how to make it better. We are trying to make it a Good Article according to Wikipedia standards. Thanks.
JaimeeDavis ( talk) 21:01, 3 December 2011 (UTC)
Hello Boghog,
I am working with
JaimeeDavis to edit the
TBR1 page. We recently took all of your advice as well as that of our peers and edited the page. We changed a lot of the structure around, reworded some things, added more information, and added a picture of the protein. Overall, I think it is well organized, thorough, and covers a broad spectrum. We nominated this page as a
Good Article. Seeing that you seem to be an expert on the topic, if you find the time we would really appreciate a review of our nomination. You have been such a great help. Thank you.
Grant.vandervoort ( talk) 00:59, 6 December 2011 (UTC)
This is your last warning. The next time you remove or blank page content or templates from Wikipedia, as you did at Macrophage migration inhibitory factor, you may be blocked from editing without further notice. — Preceding unsigned comment added by Elias Jack ( talk • contribs) 17:01, 6 December 2011 (UTC)
Hi. When you recently edited IL1RL1, you added links pointing to the disambiguation pages Stratification and Mortality ( check to confirm | fix with Dab solver). Such links are almost always unintended, since a disambiguation page is merely a list of "Did you mean..." article titles. Read the FAQ • Join us at the DPL WikiProject.
It's OK to remove this message. Also, to stop receiving these messages, follow these opt-out instructions. Thanks, DPL bot ( talk) 10:17, 20 December 2011 (UTC)
Template:PD-USGov-NCBI-PubChem has been nominated for deletion. You are invited to comment on the discussion at the template's entry on the Templates for discussion page. Sfan00 IMG ( talk) 10:01, 24 December 2011 (UTC)
I was thinking this one was better as it contains inline refs http://www.drugs.com/npp/vitamin-d.html Doc James ( talk · contribs · email) 20:37, 29 December 2011 (UTC)
Excellent diagram! I just noticed its inclusion. Great work. -- Rmrfstar ( talk)
This is an archive of past discussions. Do not edit the contents of this page. If you wish to start a new discussion or revive an old one, please do so on the current talk page. |
Archive 1 | ← | Archive 3 | Archive 4 | Archive 5 | Archive 6 | Archive 7 | → | Archive 10 |
>Why are you leaving me personal messages on my talk page about a CfD? If your comment is related to the CfD keep the discussion there.
[email protected] (
talk)
20:42, 11 January 2011 (UTC)
See also this comment which I left on Protonk's talk page. Richwales ( talk · contribs) 17:27, 16 January 2011 (UTC)
Hi Boghog, could you please have a look at my AfD and comment (either way)? It has just been re-listed the 2nd time. thanks, MichaK ( talk) 08:19, 24 January 2011 (UTC)
Template:IUPHAR ligand has been nominated for deletion. You are invited to comment on the discussion at the template's entry on the Templates for discussion page. — This, that, and the other (talk) 09:46, 25 January 2011 (UTC)
Hi! Thanks for signing the Online Ambassador interest list. We're gearing up for the next term right now, and the Wikipedia Ambassador Program will be supporting considerably more courses, with considerably more student activity... possibly upwards of 500 students who will need mentors.
If you're still interested, I encourage you to take a look at the Online Ambassador guidelines; the "mentorship process" describes roughly what will be expected of mentors in the coming term. If that's something you want to do, please apply!
You can find instructions for applying at WP:ONLINE. The main things we're looking for in Online Ambassadors are friendliness, regular activity (since mentorship is a commitment that spans several months), and the ability to give detailed, substantive feedback on articles (both short new articles, and longer, more mature ones). If you have any questions, please let me know.
I hope to hear from you soon.-- Sage Ross - Online Facilitator, Wikimedia Foundation ( talk) 20:29, 3 January 2011 (UTC)
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Delivered by EdwardsBot ( talk) 00:31, 29 January 2011 (UTC)
Hi! I've noticed that you fixed my links to Pubmed articles, making them standard and nice-looking. Could you please help me to understand, what is the best way to do it? Is it some kind of a special add-on program? I'll reference Pubmed in the future for sure, and I'd like to it properly =) Khakhalin ( talk) 18:22, 27 January 2011 (UTC)
The WikiProject Barnstar | ||
For your open, friendly, and helpful response to the comments at Wikipedia talk:WikiProject Molecular and Cellular Biology#Squint_talk, and for your subsequent diligent efforts to resolve the concerns presented by the user. People like you make WikiProjects a delight to work with, and help us focus on solving the problem, rather than assigning the blame. WhatamIdoing ( talk) 22:20, 10 February 2011 (UTC) |
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Delivered by EdwardsBot ( talk) 18:21, 11 February 2011 (UTC)
Thank you so much for what you're doing on Pain, and for your calm, constructive rationality. -- Anthonyhcole ( talk) 11:01, 13 February 2011 (UTC)
A) I just did that edit I'd mentioned - turned out to be many - cleaned it right up - 'Beta clamp: sandbox:", and B) is there an elucidation [for me] of 'Boghog'? Many thanks! ~ Betaclamp ( talk) 08:03, 15 February 2011 (UTC)
Hi Boghog!
If you're still interested in being a mentor this term, please add your profile to Wikipedia:Online Ambassadors/Mentors. If you have any questions about the ambassador role or what you're interested in doing as an Online Ambassador (whether mentoring, pitching in in other ways, or something else), please let me know.-- Sage Ross - Online Facilitator, Wikimedia Foundation ( talk) 17:36, 14 February 2011 (UTC)
This message is going out to all of the Online Ambassadors who are, or will be, serving as mentors this term.
Hi there! This is just a friendly reminder to check in on what your mentees are doing. If they've started making edits, take a look and help them out or do some example fixes for them, if they need it. And if they are doing good, let them know it!
If you aren't mentoring anyone yet, it looks like you will be soon; at least one large class is asking us to assign mentors for them, and students in a number of others haven't yet gotten to asking ambassadors to be their mentors, but may soon. -- Sage Ross - Online Facilitator, Wikimedia Foundation ( talk) 20:05, 21 February 2011 (UTC)
You prolly already are aware of this algorithm flaw, but in case not, I thought I'd mention that the Further Reading lists I see on many science pages many times contain publications that do not provide meaningful information with the wiki page.
For instance, on the STARD8 page, one reference is the DNA sequence of chromosome X. Well, true, STARD8 is there, but this does not increase any understanding of the protein. Moreover, an existing reference on the page already cites its localization to that chromosome.
STARD13 has a Further Reading article (Strausberg RL, Feingold EA, Grouse LH, et al. (2003)) that is entirely about a new way to generate cDNAs vs actually having anything to do with STARD13.
Is the Further Reading usually added for readers to supplement Stub class articles which either no one has fleshed out yet or there is still too little scientific info on? Skingski ( talk) 21:49, 21 February 2011 (UTC)
Hey Boghog. One of the classes working with the Wikipedia Ambassador Program, Jonathan Obar's Media and Telecommunication Policy, is working in small groups and would like us to assign a mentor to each group (rather than having students request the mentors they'd like, as other classes are doing).
I invite you to sign on as the mentor for one or more groups, especially if any of the topics catch your interest. To sign up, go to the course page and add yourself as "Mentor: you" in the section for that group. They students and/or professor or campus ambassadors should be cleaning things up soon to list all the usernames for each group and add a few more groups. Once you know who the students are in the group, you can leave them each a quick introduction to let them know you'll be mentoring their group.
Thanks!-- Sage Ross - Online Facilitator, Wikimedia Foundation ( talk) 19:07, 22 February 2011 (UTC)
Hi Boghog. Just a quick reply to the question in your edit summary. I put the image under hidden text as at the time it was a redlink, but the uploader expressed concern over the deletion. So, no I personally have no reason to doubt User talk:Spitfire ch. By the way (as I see you are a mentor and have been around for a while) would you be able to keep an eye on the file. I offered to help, but my experience, especially around images is low. I am guessing an email would clear it up?
Nevermind, I see you have it under control. AIRcorn (talk) 10:18, 27 February 2011 (UTC)
Thank you for the excellent job you've done on converting Pain to vcite. (It looks like you've finished.) I really appreciate it. You found a resolution to a conflict and worked diligently to implement it. You're gold. -- Anthonyhcole ( talk) 18:21, 27 February 2011 (UTC)
Please take a look at this project page and see if you can be a mentor to one of the many Areas of Study. If you can, please put your name in the "Online Mentor" area of the Area of Study of your choice and then contact the students you will be working with. As the Coordinating Online Ambassador for this project, please let me know if I can be of assistance. Take Care... Neutralhomer • Talk • 04:31, 3 March 2011 (UTC)
Dear Boghog, Thanks for your many contributions to the gene wiki articles! I set up a twitter feed that summarizes edits to the gene wiki pages and am curious what you think of it? Is it useful to you? I'm very much open to suggestions for alterations if you have any ideas. See twitter/GeneWikiPulse . Thanks again for making so many great contributions! Benjamin Good ( talk) 23:46, 1 March 2011 (UTC)
That is what I think: [1]. I will be back in a week and would be happy to discuss this in more detail. Thanks, Hodja Nasreddin ( talk) 23:28, 4 March 2011 (UTC)
Howdy, Online Ambassador!
This is a quick message to all the ambassadors about marking and tracking which articles students are working on. For the classes working with the ambassador program, please look over any articles being worked on by students (in particular, any ones you are mentoring, but others who don't have mentors as well) and do these things:
And of course, don't forget to check in on the students, give them constructive feedback, praise them for positive contributions, award them {{ The WikiPen}} if they are doing excellent work, and so on. And if you haven't done so, make sure any students you are mentoring are listed on your mentor profile.
Thanks! -- Sage Ross - Online Facilitator, Wikimedia Foundation ( talk) 18:10, 15 March 2011 (UTC)
Rubredoxin—NAD(P)(+) reductase has one more set of parentheses than Ferredoxin—NADP(+) reductase. Could you check if one is an error? (Also NADPH—hemoprotein reductase, NADPH—cytochrome-c2 reductase.) — kwami ( talk) 06:59, 21 March 2011 (UTC)
Long-chain-fatty-acyl—CoA synthetase: acyl or acid? Synonyms?
Methylenetetrahydrofolate—tRNA-(uracil-5-)-methyltransferase: should that last hyphen be there?
Glucose—1-phosphate uridylyltransferase may have been an error: no em dash?
Nother merge at ubiquinol-cytochrome-c reductase, plus ones at galactose—1-phosphate uridylyltransferase & lecithin—cholesterol acyltransferase where I just guessed at the em dash.
Okay, in all the remaining links (which are 134, down from 200+), it's the last hyphen before the last space that's the em dash. A bot could do that. Though some are redirects, and I don't know about the names they redirect to.
[Okay, now the only hyphen.] — kwami ( talk) 07:18, 21 March 2011 (UTC)
Sure thing. All moves (from that sandbox) finished.
I see you merged 2',3'-cyclic-nucleotide 3'-phosphodiesterase to the form w the capital Cyclic. Yet the box is still l.c. Shouldn't it have been the other way around? (If it's just a problem of the page histories, I can shuffle them around.)
BTW, I have not copy edited the articles to match their new titles. — kwami ( talk) 08:25, 21 March 2011 (UTC)
plastoquinol-plastocyanin reductase rd's to plastocyanin, but plastoquinol—plastocyanin reductase rd's to cytochrome b6f complex.
Boggy, please look at Template talk:Chromosomal abnormalities - I'm not sure whether it needs expansion by another example of abnormality. Cheers, -- CopperKettle 21:29, 25 March 2011 (UTC)
Hi Boghog! I'm trying to find mentors for each of the groups in the Energy Economics and Policy course. Would you be willing to mentor this group? If so, please sign up on the course page and introduce yourself to the students in the group. If not, let me know so I can find someone else. Thanks!-- Sage Ross - Online Facilitator, Wikimedia Foundation ( talk) 14:43, 28 March 2011 (UTC)
Thanks for taking the time in correcting my errors in the reference formatting, I didn't realize that that I added a reference that was already there. 7mike5000 ( talk) 17:45, 29 March 2011 (UTC)
I'm speechless. ~ Betaclamp ( talk) 05:32, 5 April 2011 (UTC)
Hi Boghog
I am working on producing a Wiki page on Mercury Regulation for an Environmental Economics and Policy course at Indiana University and I was wondering if you would like to be my mentor. Thanks!
Ejking311 ( talk) 18:34, 27 February 2011 (UTC)Ejking311 (Lizzie)
Ejking311 ( talk) 03:55, 7 March 2011 (UTC)Ejking311
Hi Boghog. I've been thinking about changing my outline to reflect different categories of Mercury Regulation (ie - Direct Effects (use and release) and Indirect Effects (Environmental Standards)). I like this new approach but I'm worried that it may not be easy for a reader to get to laws such as the "Mercury Export Ban Act of 2008". Do you think I should try to work with this new outline or stay with the old one that focuses more on the individual regulations as opposed to grouping them? My page reflects some of these changes but I haven't deleted anything so I apologize if it is hard to read currently. Also, I've found some wonderful pdfs of tables on the web and I'd love to use them but I seem to recall that it can kind of be an ordeal to upload pictures on wikipedia. Do you think I could just redo the table in wikipedia and cite the source? Let me know what you think about this as well. As always, thanks for your help! Ejking311 ( talk) 22:47, 5 April 2011 (UTC)ejking311
Good work so far on DHSA. Please add appropriate categories to the article. I added two templates to the talk page. WP:ARS member -- DThomsen8 ( talk) 17:15, 10 April 2011 (UTC)
I noticed that you like to strip URLs in references if a DOI is supplied. I agree there can be justification for that but you shouldn't be so quick to do it automatically. In the particular reference I supplied, the URL points to a full text, open-access journal. It is easier for a wikipedia reader to simply click on the link and be taken to the article than to make extra effort to search for the article by DOI... which in most instances leads to articles that are behind subscription paywalls. Not everyone is in a university with a massive e-journal subscription list, so as a result they become conditioned to NOT doing further searching. Moreover, DOIs frequently lead to publishers' sites that only post the *abstract* of an article, instead of the full text... and many people are turned off by this, further leading to a disincentive for searching DOIs.
In this wikipedia article, some of the DOIs lead to open-access journal articles, but some don't (e.g., the Annu Rev Genetics reference). The reference I supplied has a URL for a full-text article that's not hidden behind a paywall, and it's a primary review article that covers the entire content of this wikipedia article in better detail, so I think you'd agree that it's best with the URL back in.
If you like to clean things up by stripping away URLs (which can change) in favor of DOIs (which are not supposed to change), I see the rationale. But consider modifying your practice so you don't do it automatically. While the DOI in this reference does in fact lead to the full-text, open-access article, again, that is atypical and I assure you that many people (e.g., at home, in public libraries, in high schools) don't bother with DOIs because they've been repeatedly burned by links to things behind paywalls, so they will appreciate a direct URL link to the article.
Whatever you decide to do in the future, I suggest you leave this reference alone (with URL intact) for the reasons stated. That said, I realized I made a typo in the URL... adding a period and digit... the correct URL (which you can confirm yourself) is: http://genomebiology.com/2002/3/10/reviews/3013
Lapabc ( talk) 15:33, 11 April 2011 (UTC)
Hey Boghog. You seem to be very good with these templates. Wondering if you could combine {{Infobox drug}}, {{Drugbox}}, and {{Chembox}}? Thanks. Doc James ( talk · contribs · email) 23:35, 14 April 2011 (UTC)
Howdy Boghog,
I'm working on a new version of the Protein Box Bot for Gene Wiki articles. As I understand it from
Andrew, the old version of the bot hasn't been running in some time, and as pages are edited, the PBB controls and templates are generally removed (makes sense).
I imagine that the new bot's role would be more suited to updating small details easily pulled from existing databases, like EC numbers and homologene IDs, so that higher-contributing editors (like you) can spend more time editing the text of the articles and less time on the minutiae. I've read some discussions relating to the bot's updating of the summary text on various talk pages, so I think the new version will be restricted updating the sidebar GNF_Protein_box template and the information it contains (and, of course, subject to any control flags). In any case, I was hoping to get your input as I went forward. Is there anything you would want to ensure for this version particularly, or any behaviors to include?
Pleiotrope (
talk)
00:30, 7 April 2011 (UTC)
{{
nobots}}
flag, something I saw requested on the ideas page. We're having a code review on Monday, but in the meantime I thought I'd just run through the current workflow of the bot and see what you think. (I won't be updating any other templates besides the one on my sandbox for a while)
Hi Boghog, thanks for the assistance on the section I altered yesterday. Please let me know if there is anything else you think I can do to improve that section. Thanks! Aventre3 ( talk) 13:07, 22 April 2011 (UTC)
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Delivered by EdwardsBot ( talk) 16:31, 22 April 2011 (UTC)
This is an automated message from VWBot. I have performed a search with the contents of KIAA0895, and it appears to be very similar to another Wikipedia page: KIAA0895L. It is possible that you have accidentally duplicated contents, or made an error while creating the page— you might want to look at the pages and see if that is the case. If you are intentionally trying to rename an article, please see Help:Moving a page for instructions on how to do this without copying and pasting. If you are trying to move or copy content from one article to a different one, please see Wikipedia:Copying within Wikipedia and be sure you have acknowledged the duplication of material in an edit summary to preserve attribution history.
It is possible that the bot is confused and found similarity where none actually exists. If that is the case, you can remove the tag from the article. VWBot ( talk) 05:18, 25 April 2011 (UTC)
Greetings, Boghog. I've noticed that Swmmr1928 ( talk · contribs) has been having difficulties at Moonlighting protein, seemingly due to a lack of familiarity with Wikipedia norms and conventions. I wonder if I could trouble you to help accommodate their alterations in a revised form, or if that is not in the article's interest, explain to them in a bit more depth why? They seem a little frustrated with the situation at present, and could use some help from us ambassadors. Regards, Skomorokh 17:03, 28 April 2011 (UTC)
April 30, 2011
Hi Boghog. Thanks for your comments. I re-read what are to be included in Wikipedia. Wikipedia is not the place for New Discoveries. Thanks VRodrig110 ( talk) 17:28, 30 April 2011 (UTC)
Hi Boghog. Thanks for reformatting my reference on the Arginine vasopressin page; I didn't realize that I had cited the earlier EPub. With regards to the reference that was originally present there, I removed it simply because the newer reference was more current and was unequivocal about the effect of AngII on AVP secretion. I don't want to make a big deal out of it, but I don't see the point of including the older reference as well. Please let me know what your thoughts on this are. Thanks, Techfiend ( talk) 06:31, 2 May 2011 (UTC)
Hi Boghog/Archive 5,
Your work as an Online Ambassador is making a big contribution to Wikipedia. Right now, we're trying to measure just how much student work improves the quality of Wikipedia. If you'd like contribute to this research and get a firsthand look at the quality improvement that is happening through the project, please sign up to assess articles. Assessment is happening now, just use the quantitative metric and start assessing! Your help would be hugely appreciated!
Thank you, ARoth (Public Policy Initiative) ( talk) 17:10, 6 May 2011 (UTC)
Thankyou for your Great Edits!
I think according to this, we still need an In-text attribution for the table in this section.
I added the align right tags to the tables in the Moonlighting protein article per these requests. However, the requests are from inexperienced users and maybe that is why you reverted the edit/did not discuss. Do you agree that the tables disrupt the flow when they are aligned in the center?
Also, can you explain why most proteins are not enzymes? Do you have numbers to back your claim? I am a bit confused after searching. Swmmr1928 talk 23:51, 4 May 2011 (UTC)
Is there anything wrong with quoting from a journal article's abstract? Swmmr1928 talk 01:59, 13 May 2011 (UTC)
Thank you for your friendly form letter of welcome to WikiProject_Molecular_and_Cellular_Biology.
I noticed a protein-box-bot template on another protein, and tried adding one on the same pattern to KLF14. It doesn't work, unsurprisingly. Is the bot still active, and if so how do I get it to give me a box? -- Dan Wylie-Sears 2 ( talk) 23:00, 17 May 2011 (UTC)
Hi! This is the last call for signing on for a Wikipedia Ambassador hooded sweatshirt (in case you missed the earlier message in one of the program newsletters about it). If you would like one, please email me with your name, mailing address, and (US) sweatshirt size. We have a limited number left, so it will be first-come, first-served. (If more than one size would work for you, note that as well.)
Cheers, Sage Ross - Online Facilitator, Wikimedia Foundation ( talk) 19:40, 19 May 2011 (UTC)
Hi Ambassador,
We are at a pivotal point in the development of the Wikipedia Ambassador Program. Your feedback will help shape the program and role of Ambassadors in the future. Please take this 10 minute survey to help inform and improve the Wikipedia Ambassadors.
WMF will de-identify results and make them available to you. According to KwikSurveys' privacy policy: "Data and email addresses will not be sold, rented, leased or disclosed to 3rd parties." This link takes you to the online survey: http://kwiksurveys.com?u=WPAmbassador_talk
Feel free to contact me with any questions or comments, Thank You!
Amy Roth (Research Analyst, Public Policy Initiative) ( talk) 20:36, 24 May 2011 (UTC)
Is no merge of these two articles necessary?
Swmmr1928 talk 01:13, 28 May 2011 (UTC)
Wondering if you could implement a number of improvements to this infobox as suggested here Template_talk:Interventions_infobox I just cannot get it to work. Doc James ( talk · contribs · email) 23:45, 1 June 2011 (UTC)
I have recently created the above infobox which I have used here at Complete blood count. Still not working perfectly. Wondering if you could help fix a few things mentioned here Template_talk:Diagnostic_infobox#Things_that_need_fixing? Doc James ( talk · contribs · email) 09:24, 3 June 2011 (UTC)
Are we able to move forwards with the changes to the drugbox? I have no strong feelings about transclusion but it would be nice to get the clinical data added. Doc James ( talk · contribs · email) 09:30, 3 June 2011 (UTC)
The Medicine Barnstar | ||
For the incredible work you have done on the medical templates. Doc James ( talk · contribs · email) 09:18, 4 June 2011 (UTC) |
Hey Boghog Have brought your changes to the drugbox live. I think I have it set up correct but wondering if you could double check. Will work on updating the top 20 most common prescriptions with the new info. Doc James ( talk · contribs · email) 07:14, 6 June 2011 (UTC)
Hi Boghog,
Thanks for fleshing out SPRED3 and SPRED1.
I am particularly interested in NF1 and NF1-like syndromes and the mutations leading to them. Genes related to this are Neurofibromin 1, SPRED1, SPRED2, SPRED3, SPRY1, SPRY2, SPRY3 and SPRY4. Neurofibromin 1 has had thousands of distinct observed mutations of various types.
I am not a professional in this area. I am trying to understand the condition for personal reasons. I have noticed that there seems to be a split among professionals working in the area:
With respect to NF1-related genes, I would like to make publicly available on Wikipedia the known mutations to the extent that they are in public domain. Do you support the idea of having more systematic inclusion of detailed observed gene mutation data on Wikipedia, and if so, what is the best way to go about it?
Thanks, Erxnmedia ( talk) 14:01, 7 June 2011 (UTC)
Hi Boghog,
That's great, I didn't known OMIM, and those pages drill right down to the nucleotide sequence for mutations which is great.
I have been working in general on Neurofibromatosis-related pages. This condition occurs about 1:3500 births and has many complications but is relatively unknown outside of those affected and the relatively small group of people that do research on it. Researchers on Neurofibroma are divided into mouse-model in-vitro cure researchers who are PhDs in biology and MDs doing human trials of specific drugs. Because there are thousands of possible mutations to Neurofibromin 1, the outcome of the disease is highly variable, and involves many of the body's systems. One of the main drivers of NF research is the Children's Tumor Foundation (CTF).
Because of the multiplicity of negative outcomes I was hoping that there would be a gene therapy cure. I communicated with a couple of leaders in the field regarding gene therapy specifically, and I got these responses. The first is David Muir, who said "research dollars are being channeled by those 'in the know' into drug therapy trials for NF1. The nature of the NF1 gene makes gene therapy insurmountably challenging at this time." He recommended asking the question to his colleague Peggy Wallace who is on the Board of Directors and is a long-time scientific advisor of the CTF. She said that
With regard to your gene therapy questions, the idea of just replacing or fixing the gene is appealing, but not currently feasible. However, there are some approaches being developed, aimed at trying to coax the gene to function despite its mutation (e.g. a drug that helps cells skip stop mutations, and therapies aimed at correcting splicing abnormalities). These don't actually fix the gene itself, so would need to be long-term therapies (a potential roadblock for some therapies). These are already under consideration in NF (we're testing one of the skip/stop drugs here, in a mouse model). No such therapies are FDA-approved for any condition yet, but some are in clinical trials in other conditions. These would be aimed more specifically at an individual's own mutation (I suspect there are probably over 1000 independent NF1 mutations known by now, but there's not an up-to-date database at the moment). I don't know the mutation distribution for SPRED1. NF1 mutations are of all different types. I'm not sure what you mean by taxonomy, but you can break down the mutations generally into deletions, insertions, and nucleotide substitutions; the effect of each depends on the size/location of that change. I believe that about 20-30% are stop mutations, 30-50% cause splicing errors, and the others are insertions/deletions/missense mutations. One issue with the splicing repair approach might be difficulty getting the therapy delivered to the Schwann cells due to the blood/nerve barrier; drugs that are small enough can probably get there. Also it will be hard to get therapies FDA approved which carry any kind of health risk, especially in a person who is pre-symptomatic (as in prevention) since there's no predicting what complications an individual will have (if any) and so you can't give a risk/benefit analysis. That will be a problem for systemic, long-term therapies. It will likely be easier to get approval for targeted therapies that are of relatively short duration (e.g. the photodynamic therapy work that Dr. Muir is testing on the tumors in mouse models). We also don't know if a therapy to short-cut a mutation (as mentioned above) will work in a symptom which has already progressed beyond being dependent just on loss of neurofibromin. So those are some of the considerations. The Children's Tumor Foundation is leading the charge in trying to take the best ideas to preclinical testing and then actual clinical trials, leveraging federal dollars. Some of the clinical trials have already tried some of the drugs you mention below, but to the best of my knowledge, there have been no treatments with uniformly good response.
I have edited the following pages related to NF, and suggested a WikiProject or Medicine Task Force for this area specifically, but it was considered to be too specialized:
Thanks, Erxnmedia ( talk) 19:08, 7 June 2011 (UTC)
Hi Boghog,
The practice in the medical industry seems to be to publish descriptions of individual clinically significant observed mutations in articles, but not to publish say the sequences of every one of a body of patients who have various mutations of a given gene. These sequences are published but in closed-access commercial database projects.
The achievable goal may be to scrape published articles for descriptions of particular mutation sites and their clinical significance. For example SPRED1 mutation list.
If you can design a bot which does a good job at this then I would apply it to every gene cataloged in Wikipedia in a batch. I would also add/merge all of the articles in User:Cboursnell/Sandbox which seem to be the result of this kind of bot, see my interaction with Alexbateman who has created this batch in sandbox and gave permission to publish all but hasn't published them himself: User talk:Cboursnell#EVH domain, EVH1 domain, Sprouty domain.
For what I am interested in, I have worked on Ena/Vasp homology proteins, EVH1 domain, SPR domain, SPRED1, SPRED2, SPRED3, SPRY1, SPRY2, SPRY3 and SPRY4.
Thanks, Erxnmedia ( talk) 03:29, 9 June 2011 (UTC)
Hi Boghog
I see we are getting duplication of material between the thymosin beta4 page and the part of the beta thymosins entry dealing with beta4. I added the Riley heart studies there earlier today, where there was already context about tissue regenerative activities and a generally fuller account of beta 4. I'm not sure what ought to be done about such a duplicatiion, but presumably at least some more "See Also" links? Jgedwards ( talk) 22:44, 9 June 2011 (UTC)
Looks good, thanks. Presume there will always be duplication where articles about gene families as well as individual human genes. I see the publicity re heart repair caused a notable spike in hits to the thymosin pages. I'm still hoping to get onto the closely related WH2 domains - would be good for Pfam also to have that.
I'd welcome advice on another matter: I've made significant progress with phylogeny of beta thymosins. For example there's a very interesting exception to the restriction to multicellular animals - a beta thymosin in a choanoflagellate, an organism believed to be at the margin of multicellularity. Question is whether for Wikipedia, this has to be in peer reviewed journal paper, or whether one can directly cite the openly available evidence of a sequence database entry. Jgedwards ( talk) 11:28, 10 June 2011 (UTC)
Boghog - thanks for this. Clearly a rigorous attitude to citation is the way to ensure reliability. Given that beta thymosin sequences are so strongly conserved, I reckon the unicellular exception I mentioned possibly counts as obvious to "routine comparison". You can just tblastn the human b4 sequence or any of the many others, against Monosiga genomic and there are also two transcripts. So I'll probably add it - if anyone (including yourself) maintains this is synthesis then I won't argue and they can of course delete it. I see there is a good article about choanoflagellates, relation to animals etc which mentions the Monosiga genome.
I hadn't caught up with WH2 - well done with that. It reads well. Presumably it should shortly appear as default annotation in Pfam. There's a view that thymosins are essentially WH2 domains - based on partial sequence similarity and fold when bound to actin. It's controversial and I've summarised as neutrally as I could in the beta thymosins article. Jgedwards ( talk) 22:20, 10 June 2011 (UTC)
A deletion discussion has just been created at Category talk:Unclassified Chemical Structures, which may involve one or more orphaned chemical structures, that has you user name in the upload history. Please feel free to add your comments. Ronhjones (Talk) 22:48, 10 June 2011 (UTC)
Hi boghog
I just noticed your WH2 links SCAR1 to SETX. These are completely unrelated proteins which unfortunately at some stage have acquired a coincidentally common synonym. The WH2-containing SCAR1 WASP family .proteins are named after a screen in Dictyostelium - something like Suppressor of Cyclic AMP Receptor. SETX is a considerably larger protein, probably a helicase, and doesn't contain WH2, as you can see by posting it into Pfam. I'd suggest killing the link. Jgedwards ( talk) 00:37, 11 June 2011 (UTC)
Hi Boghog
Would appreciate your response to discussion on Beta thymosins discussion page Jgedwards ( talk) 08:22, 13 June 2011 (UTC)
[2]. Biophys ( talk) 16:31, 17 June 2011 (UTC)
Thanks for the info about the gene pages. I was unaware that there was a style guide for the gene articles. I'll try and get all those articles put right by the end of the weekend. I did leave a couple thoughts here. -- Kerowyn Leave a note 06:35, 24 June 2011 (UTC)
Thanks for the cleanup on GPRC6A! — Preceding unsigned comment added by Gryderart ( talk • contribs) 20:07, 29 June 2011 (UTC)
You should really get the admin bits. Would be happy to nominate you if interested. Doc James ( talk · contribs · email) 09:42, 6 June 2011 (UTC)
Are we able to move the sandbox version that you have created to the main version? It seems to work well. Wish to start adding "clinical data" to more articles. -- Doc James ( talk · contribs · email) 05:07, 17 May 2011 (UTC)
Sorry to be a pain but wondering if their has been any movement on creating a bot? My abilities in this realm are poor. Might be a good idea to learn though. Doc James ( talk · contribs · email) 22:13, 16 June 2011 (UTC)
After having removed the `[sic]`s from [[ the code sample on Fast inverse square root, I had a look through the edit history. From what I gather you added them as a measure to preserve the comments from vandalism claims—as sensible as that is, that's not what they're for.
88.9.243.28 ( talk) 08:36, 22 July 2011 (UTC)
A chance to use " hobgoblin"? No. I understand the value of consistency; and it's not foolish consistency we're talking here, right?
Well, I'm a generalist wandered as per often into specialized territory. If you'd just reverted the format and level of detail on the authors' names, I maybe'd have let it go. But you also went for the journal-name link.
On the authors' names, I'll ask you a question: Is there anything lost by straying beyond the prescribed form in an instance? There's no possibility of confusion. I gave more information, so any specialized reader, or a general reader who knew nothing of Vancouver style, could understand the way I'd expanded the names. The question may become, Why did I do it? I was interested in the last name of one of the authors. That's it. I found for instance that s/he was on the Edit. Board of that BJU Int.. So I upgraded that article, too, and linked this one to it. Does it add anything, to have the additional information and the links to make it easily available to the maybe casually interested? (I did appreciate your "good faith" nod; and I think I'm granting the same to you; I've seen you're producing lots of (specialized) articles for Wikipedia. ... I ... like ... that they're here. ... I don't like to feel they're ... "off limits," though.) To me, what I did does seem to add something. You use consistency and a query to remove what I deemed worthwhile additional information. You seem to be trying to keep the shield of specialization drawn around a subject. To that I'd just start to close by asking of you, Why?
You may well counter that my solitary edit of this one article's and one journal's information unfairly and inexplicably makes that information stand out from "the rest." It's a reasonable counter. I'm currently just beginning to ponder the Wiki back-and-forth over different citation templates. Not directly related, I know, .... But just the way you didn't even think to link to "Vancouver style," just sort of waved it in front of us .... Well .... Whatever.
Well, I guess I am (sneaking up to and now finally) saying that your bid for consistency is sort of foolish. No disrespect intended. I stumbled in. I found the author listing confusing, as to whose last names went with which initials. I've learned now. But I also left a clearer alternative. I don't need to challenge the whole Vancouver protocol of 30+ years standing. I just like to know, and to communicate ... to others of my ilk, that there are alternatives. No big deal, no big boat-rock. Do you really need to enforce, rather than just observe, that discipline, that protocol? Respectfully yours, Swliv ( talk) 14:01, 12 July 2011 (UTC)
Even though it's been quiet on-wiki, the Wikipedia Ambassador Program has been busy over the last few months getting ready for the next term. We're heading toward over 80 classes in the US, across all disciplines. You'll see courses start popping up here, and this time we want to match one or more Online Ambassadors to each class based on interest or expertise in the subject matter. If you see a class that you're interested, please contact the professor and/or me; the sooner the Ambassadors and professors get in communication, the better things go. Look for more in the coming weeks about next term.
In the meantime, with a little help I've identified all the articles students did significant work on in the last term. Many of the articles have never been assessed, or have ratings that are out of date from before the students improved them. Please help assess them! Pick a class, or just a few articles, and give them a rating (and add a relevant WikiProject banner if there isn't one), and then update the list of articles.
Once we have updated assessments for all these articles, we can get a better idea of how quality varied from course to course, and which approaches to running Wikipedia assignments and managing courses are most effective.
-- Sage Ross - Online Facilitator, Wikimedia Foundation ( talk) 17:22, 27 July 2011 (UTC)
Those fields that you are adding by (bog)bot are probably numbers that are verifiable correct, aren't they? If so, it would be good if CheMoBot would follow them and tag them if someone would change them ...
My questions hence:
With that list/such lists I could upgrade my script, and update the index also for these fields (pff .. then I have to upgrade that script again, but that is due anyway, as there are other tasks approaching, and I have another list ready to be incorporated as well). -- Dirk Beetstra T C 22:19, 31 July 2011 (UTC)
P.S. One of the problematic ones is still the KEGG, I have a list InChI <-> KEGG (directly from KEGG) but unfortunately that is InChI, and not StdInChI .. the former is too variable to verify (different tastes). Do you by any chance know a better list? -- Dirk Beetstra T C 22:19, 31 July 2011 (UTC)
But you source all data from drugbank by searching for the INN, or from the drugbank identifier? -- Dirk Beetstra T C 23:05, 31 July 2011 (UTC)
{{PAGENAME}}
) as the title, so actually that one is obsolete. Though, maybe it was before that patch of the Wikimedia software came through, that the 'pagename' would say 'P-Toluenesulfonic acid' instead of 'p-Toluenesulfonic acid', and hence we used a name-parameter to override the pagename. Now obsolete, maybe should be parsed out.By the way, thanks! Because of your sorting I found a bug in User:CheMoBot (now resolved) - of course the last parameter ends before the closing double curly brackets. -- Dirk Beetstra T C 23:07, 31 July 2011 (UTC)
We might want to consider to write something so that the StdInChI and StdInChIKey are rendered into the final result of the page with a drugbox (not necessarily display, it is ugly) - then they get Google indexed, and you can find the article by looking for the StdInChI, some thing that some people do look for. Note that the value for InChI get stored without the 'InChI=' in front of it (to avoid the ugly 'InChI = InChI=<value>', which probably will get removed by some in some cases as 'duplicate, so probably wrong' etc.), so that needs to be added to the rendering. -- Dirk Beetstra T C 17:05, 1 August 2011 (UTC)
This field in the box is not working see Lisinopril for example. Doc James ( talk · contribs · email) 20:20, 1 August 2011 (UTC)
Have been going over the bot edits.
Wondering if we could set it to add lines of text even if they are not used? For example in the edit to amitriptyline it would be nice for it to add "|trade name=" even if it does not fill it in. [10] Doc James ( talk · contribs · email) 03:19, 16 August 2011 (UTC)
Hello! If you're planning to be an active Online Ambassador for the upcoming academic term, now is the time to join one or more pods. (A pod consists of the instructor, the Campus Ambassadors, and the Online Ambassadors for single class.) The Memorandum of Understanding (MOU) explains the expectations for being part of a pod as an Online Ambassador. (The MOU for pods in Canada is essentially the same.) In short, the role of Online Ambassadors this term consists of:
This replaces the 1-on-1 mentoring role for Online Ambassadors that we had in previous terms; rather than being responsible for individual students (some of whom don't want or help or are unresponsive), Online Ambassadors will be there to help whichever students in their class(es) ask for help.
You can browse the upcoming courses here: United States; Canada. More are being added as new pods become active and create their course pages.
Once you've found a class that you want to work with—especially if you some interest or expertise in the topic area—you should sign the MOU listing for that class and get in touch with the instructor. We're hoping to have at least two Online Ambassadors per pod, and more for the larger classes.
If you're up for supporting any kind of class and would like me to assign you to a pod in need of more Online Ambassadors, just let me know.
-- Sage Ross - Online Facilitator, Wikimedia Foundation ( talk) 16:31, 19 August 2011 (UTC)
PS: There are still a lot of student articles from the last term that haven't been rated. Please rate a few and update the list!
Was wondering if we should provide verification (ie a ref) for the drug categories. People are not to use Wikipedia for prescribing but this would add a bit of safety and allay potential fears. For example was looking at lisinopril which was given a D however the drug.com ref says it is a C in the first trimester and D in the second and third. What we had before could cause excess fear. [11]. Does the FDA have a site that lists all the preg catergories for all the meds? Doc James ( talk · contribs · email) 01:03, 23 August 2011 (UTC)
Hi, I'm fairly new to editing protein articles, so perhaps you could clarify something for me? What's the rationale behind the Further Reading sections on most protein/gene articles like the one you added here. Some of the papers in that one were only vaguely related to the subject. I assume these sections are auto-generated but I'm not convinced they are necessarily useful. A more select list might be less confusing for some readers. Do you use a bot to generate the lists? Thanks. -- Pontificalibus ( talk) 21:28, 30 August 2011 (UTC)
Hi Boghog, I saw your new section and I think it's well-written. One additional thing that'd be helpful is to include an example chart of concentration vs. time with arrows pointing to the phase where passive diffusion dominates and the phase where elimination dominates (By the way, do you mean elimination as in "excretion" or elimination as in "metabolism" + "excretion"? Some pharmacologists use the term "elimination" in the same way as "excretion"). -- Bobthefish2 ( talk) 18:13, 26 August 2011 (UTC)
AAAAAAAAAAAAAAHHHHHHHHHHHHHHHH?????? What on Earth did you do to the Polymyxin B article??????? I reverted your edit as the article was entirely unusable due to formatting errors - if you were adding legit information, please consult faqs and edit using proper format - PLEASE USE THE SANDBOX IF YOU AREN'T FAMILIAR WITH EDITING WIKIPEDIA ARTICLES.
If you are merely playing with or learning about editing bots, please stop as you have corrupted an article on a highly important subject. Bots are inherently dependent upon humans and humans make mistakes. Please don't assist those who seek to discredit Wikipedia. — Preceding unsigned comment added by 99.99.78.137 ( talk) 08:15, 1 September 2011 (UTC)
I'm sorry, I didn't mean to revert your reference-reformatting edit (about 20 minutes ago) to UBQLN1. I was just editing at the same time you were.
I think you since got your edits back in, which do improve the article.
Thanks,
H.Tamahagane 20:24, 1 September 2011 (UTC)
Hi there! It looks like BogBot dropped a critical "</nowiki>" off the end of the IUPAC name field of the {{ Drugbox}}. Diff here - Alison ❤ 19:02, 3 September 2011 (UTC)
Yes it is working for me... Could I run the bot from where I am? Doc James ( talk · contribs · email) 22:05, 3 September 2011 (UTC)
Hi Boghog. I just wanted to let you know that I have marked the image File:Tryptophan biosynthesis.png on Commons with the "disputed chem" tag because there appears to be an error in the third structure - there is an extra carbon between the sugar and the anthranilate group. Can you please have a look and fix it? Or I can create a new image, if necessary. -- Ed ( Edgar181) 11:45, 11 September 2011 (UTC)
Hey Bog(b/h)o(g/t)! Can you examine this edit. You are there deleting info and breaking the page with moving comment marks. Subsequently, CheMoBot has a problem with the page, but I am not sure if that is due to the edit by the bot, or if I have a mistake in my coding as well. I'll keep an eye on this one, may debug CheMoBot as well on that page if it persists still. Thanks! -- Dirk Beetstra T C 10:39, 15 September 2011 (UTC)
Hi! I've just noticed that BogBot places the synonyms parameter in the Chemical data section, [14] not in the Identifiers section where it is displayed (and where I think it belongs). Not a big thing, but I thought you might want to know. Cheers, ἀνυπόδητος ( talk) 12:15, 19 September 2011 (UTC)
<ref>
tags on this page without content in them (see the
help page).Hi Boghog. I am in the process of getting the Rfambot to convert the pages with the old rfam box to the new Infobox rfam. I will also be getting the bot to update and maintain some of the Rfam relevant fields in the infobox rfam. It would be useful to us if there was a field in the template for Rfam release version - so we can keep track of updates as some of the fields in the template do vary from release to release. The 'Rfam release' field need not be displayed in the box, infact its is probably better if is not. Unfortunately, none of us here at Rfam seems seem to know how to add a field that is not actually displayed. Can you help with this? I think in the old rfambox I just added the release information to the box in the page and it was never actually part of the template. I presume there is a nicer way of doing this? thanks Jennifer_Rfm ( talk) 10:49, 14 September 2011 (UTC)
Hey Boghog, on a related note, I've been playing around with the template in the sandbox trying to make it accept and display multiple GO/SO terms in a single field (i.e. without resorting to displaying GO1:, GO2: etc.) but my basic knowledge of template syntax is not up to the task. From reading the help on meta it looks like I either need nested #ifs or a #switch, but I'm quite unfamiliar with template wikimarkup so I was helping you could help me out or point me in the right direction? Any help or advice would be much appreciated! Jebus989 ✰ 15:18, 15 September 2011 (UTC)
Hello, Ambassadors!
I wanted to give you one last update on where we are this term, before my role as Online Facilitator wraps up at the end of this week. Already, there are over 800 students in U.S. classes who have signed up on course pages this term. About 40 classes are active, and we're expecting that many more again once all the classes are up and running.
On a personal note, it's been a huge honor to work with so many great Wikipedians over the last 15 months. Thanks so much to everyone who jumped in and decided to give the ambassador concept a try, and double thanks those of you who were involved early on. Your ideas and insights and enthusiasm have been the foundation of the program, and they will be the keys the future of the program.
Still waiting to get involved with a class this term, or ready to take on more? We have seven classes that are already active and need OA support, and eleven more that have course pages started but don't have active students yet. Please consider joining one or more of these pods!
Active courses that really need Online Ambassadors:
Courses that may be active soon that need Online Ambassadors:
-- Sage Ross - Online Facilitator, Wikimedia Foundation ( talk) 23:11, 27 September 2011 (UTC)
So is your new ChemDrug template ready to roll out or are you still fixing bugs? I might have to find a new page to write so I can test it out :-) Meodipt ( talk) 02:26, 29 September 2011 (UTC)
As a layman (and newcomer to this), I think the public would benefit from an explanation of what it means for a generic to fall within the 85-125% range. The FDA's AB designation of approved generics within that range begs the question: If a brand name drug has several generic versions, is it worthwhile trying to identify the particular generic version closest to 100%? If not, why is it that different formulations may have varying side effects on the same patient? But if so, consumers may be disappointed to find that the underlying studies are not publically available from the FDA except possibly through a Freedom of Information Act request (which takes months and is expensive). Garsbh ( talk) 18:33, 27 September 2011 (UTC)
Boghog, What do you think of the current state of the article on Macrophage migration inhibitory_factor ? I undid changes that basically weaken every statement into something along the lines of "it has been suggested that maybe.." despite these statements being backed up by cited literature. The other editor than undid my revisions. I fear getting into an edit war. How do you suggest I proceed? Thanks Benjamin Good ( talk) 22:07, 3 October 2011 (UTC)
Thanks for help, that looks better now. 70.137.128.110 ( talk) 08:09, 9 October 2011 (UTC)
I believe the entry for pyrithyldione may have the same problem, citing the wrong patent. I know these substances are obsolete, but it should be right if its an encyclopedia. A search brings up an entry for "presidon", but this seems to be a substance without the double bond. (the 3,3-diethyl- 2,4-dioxo-tetrahydro-pyridine) so there seems to be both variations (w/wo double bond) have been around as sedatives. The drugbank and the like entries are notoriously unreliable, meanwhile they cite the Wikipedia, good grief. And then we cite them, and so forth. Have already found such a bug earlier, where simply the DB entries were bogus. I better do not see a doctor, if I still know whats good for me... :) (: what does IGOR the humpback alway say to Dr. Frankenstein, in the lab, "Yesss master", but not with me! :)
70.137.128.110 (
talk)
10:12, 9 October 2011 (UTC)
http://www.ncbi.nlm.nih.gov/pubmed?term=presidon&itool=QuerySuggestion
brings up several hits which seem to be the same substance, but from 1949. Can you confirm? Unfortunately no text/abstracts available except one fulltext fragment about agranulocytosis, found by doi. Too old this stuff. 70.137.128.110 ( talk) 11:01, 9 October 2011 (UTC)
ok the above tetrahydropyridine is with a double bond, I miscounted. So presidon is the right hit. remains to be found why we have a synthesis for the 6-substituted substance instead of methyprylone here, and why the book is off target there, also with the piperidine. 70.137.128.110 ( talk) 11:12, 9 October 2011 (UTC)
Thank you for fixing that. The pyrithyldione is an intermediary of methyprylone, can you make a grafic for that too? How do you make these, what do you use as a tool? (Igor curious, master) 70.137.140.56 ( talk) 20:50, 9 October 2011 (UTC)
Can you please take a look at the synthesis, it shows the wrong substance. (not the same shown in stucture picture of chem box, but the 6-methyl derivative) 70.137.128.110 ( talk) 08:29, 9 October 2011 (UTC)
I wonder why they call the intermediate a piperidinedione with that double bond, in the book source.
The 6-substitution, I believe they got it from here
http://www.google.com/patents?id=2wxWAAAAEBAJ&printsec=abstract&zoom=4#v=onepage&q&f=false
this patent by the same guys from Roche describes a synthesis of a 6-substituted similar substance, not a 5-substituted substance.
Thank you for fixing that. The pyrithyldione is an intermediary, can you make a grafic for that too? How do you make these, what do you use as a tool? 70.137.140.56 ( talk) 20:50, 9 October 2011 (UTC)
Is the patent text above wrong? It descibes a 6-substituted example. 70.137.140.56 ( talk) 20:50, 9 October 2011 (UTC)
Do I see this correctly, that the 5-position is attacked with formaldehyde, and not the 6-position, because of keto-enol tautomerism? (Igor curious) 70.137.131.247 ( talk) 08:31, 11 October 2011 (UTC)
Thank you. I believe I have understood. 70.137.143.37 ( talk) 06:47, 13 October 2011 (UTC)
BogBot seems to have messed up the IUPAC name of Fusidic acid. Please investigate. I've restored the name by now. — Pt (T) 03:31, 13 October 2011 (UTC)
Hi Boghog! We're thinking of trying to increase the usage of the {{ SWL}} template on Gene Wiki articles and recently introduced a proposal at the Village Pump explaining our motivation and soliciting community feedback. Would you be interested in checking it out and seeing what you think? The proposal is here: Expanding the use of the SWL template. We've used a general example for the Village Pump but you can imagine the utility for human gene articles as well.
Thanks, Pleiotrope ( talk) 23:47, 18 October 2011 (UTC)
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Delivered by MessageDeliveryBot on behalf of Wiki Media Foundation at 11:49, 25 October 2011 (UTC).
Hello Boghog. It would appear the molecular mass for 4-Acetoxy-DET is off by 1 g/mol. Instead of 273.36 g/mol it should real 274.36 g/mol according to both PubChem and my own calculations.
(new msg as of 21:45) andy4789 ★ · (talk? contribs?) 21:45, 9 November 2011 (UTC)
Hi, this message is to let you know about disambiguation links you've recently created. A link to a disambiguation page is almost always unintended, since a disambiguation page is merely a list of "Did you mean..." article titles. For more information, see the FAQ or drop a line at the DPL WikiProject.
Any suggestions for improving this automated tool are welcome. Thanks, DPL bot ( talk) 13:05, 16 November 2011 (UTC)
[16] -- Anthonyhcole ( talk) 10:14, 20 November 2011 (UTC)
Thank you for reverting my section blanking on Tryptophan. I was not aware that it (turkey=tryptophan=drowsiness) is a widely held misbelief. I do however think the section should be shortened. Carstensen ( talk) 01:17, 23 November 2011 (UTC)
Good song! With regard to my retirement... There is an external hate speech web site with personal information that links to my wikipedia account. These guys are currently active, which is hardly a coincidence. I would not really pay attention, but this is not just a couple of jerks. For example, someone came to the College of Engineering in a city where I work and made a couple of edits pretending to be me [17]. That was done to prevent my return to the subject area related to Russia (I was topic banned). So, I would rather quit. Thank you very much for help and collaboration! You are doing great work here. Biophys ( talk) 23:36, 7 November 2011 (UTC)
Hey Bog taking another look at the drug class box. Have applied it on the statin page. Wondering if we can hide the fields with nothing in them? -- Doc James ( talk · contribs · email) 07:57, 25 November 2011 (UTC)
Hi. I did some really heavy stuff with Pymol engine lately. I tried to get similar images like yours but those colors and groups are so confusing. Is there any way you could help me with those? I admire your images on wikipedia sites... I have no idea how to get similar results. Hopefully, if you find some time to help me, please contact me and I will describe my issues.
Thanks in advance and once again, great stuff! Big thanks from all Wikipedia society! — Preceding unsigned comment added by Konieckropka ( talk • contribs) 22:57, 20 November 2011 (UTC)
It would be difficult to recreate File:3CNA_Concanavalin_A.png graphic using only the PyMol Gui since each of the monomers in this structure is individually colored. Below is the script that I used to create this figure. Please note that you must have the pdb filed named 3CNA_tetramer.pdb in the same directory as the script. The pdb file containing the tetramer was the taken from the PDB: 3CNA site, "download files/biological assembly". The standard 3CNA PDB file contains only the monomer. I hope this helps. Boghog ( talk) 06:20, 28 November 2011 (UTC)
##
set auto_zoom, off
cmd.bg_color(color="white")
set antialias = 1
# set stick_radius = 0.20
set cartoon_tube_radius = 0.40
set cartoon_smooth_loop = 0
set cartoon_sampling = 25
set spec_power = 200
set spec_refl = 1.5
set cartoon_transparency = 0.0
set cartoon_flat_sheets = 0
set cartoon_smooth_loops = 0
set dash_width = 3
set dash_gap = 0.25
set dash_radius = 0.2
set dash_length = 0.2
set dash_round_ends = on
set depth_cue = 0
set ray_trace_fog = 0
set sphere_scale = 1
cmd.load("3CNA_tetramer.pdb","complex")
cmd.hide("everything", "complex")
set_view (\
0.125021607, -0.992153525, 0.000000000,\
0.992153525, 0.125021785, 0.000000000,\
0.000000000, 0.000000000, 1.000000000,\
0.000000000, 0.000000000, -192.770080566,\
-0.000003815, -0.000015259, 0.000000000,\
149.219680786, 236.320480347, 0.000000000 )
cmd.select("backbone", "complex & name c+o+n+na")
cmd.disable("backbone")
cmd.select("sidechains", "complex & ! backbone ")
cmd.disable("sidechains")
#cmd.select("metals", "elem cu+zn")
#cmd.disable("metals")
cmd.show("spheres", "elem ca")
cmd.show("spheres", "elem mn")
# util.chainbow("complex")
cmd.color("red", "chain A")
cmd.color("magenta", "chain B")
cmd.color("green", "chain C")
cmd.color("cyan", "chain D")
cmd.color("gold", "elem ca")
cmd.color("grey90", "elem mn")
#cmd.color("yellow", "ligand & elem s")
#cmd.color("red", "ligand & elem o")
#cmd.color("blue", "ligand & elem n")
#cmd.color("organge", "ligand & elem p")
#cmd.color("grey90", "ligand & elem c")
set cartoon_fancy_helices, on
set cartoon_smooth_loops, on
#set cartoon_side_chain_helper, on
cmd.show("cartoon")
cmd.ray("1440","1080")
cmd.png("3CNA.png")
One or more of the files that you uploaded or altered has been listed at Wikipedia:Files for deletion. Please see the discussion to see why this is (you may have to search for the title of the image to find its entry), if you are interested in it/them not being deleted. Thank you.
Delivered by MessageDeliveryBot on behalf of MGA73 ( talk) at 17:42, 28 November 2011 (UTC).
Hi Boghog, thanks for the excellent reaction diagram.
Shouldn't the last step's product be called 1,3,7-trimethylxanthine and not 1,3,7-tiimethylxanthine?
http://en.wikipedia.org/?title=File:Caffeine_biosynthesis.tif&page=1
Hi. My group and I have been editting the TBR1 page in wikipedia for our Neuroscience class. We noticed that you had edited it severaal times and would appreciate any advice you have on how to make it better. We are trying to make it a Good Article according to Wikipedia standards. Thanks.
JaimeeDavis ( talk) 21:01, 3 December 2011 (UTC)
Hello Boghog,
I am working with
JaimeeDavis to edit the
TBR1 page. We recently took all of your advice as well as that of our peers and edited the page. We changed a lot of the structure around, reworded some things, added more information, and added a picture of the protein. Overall, I think it is well organized, thorough, and covers a broad spectrum. We nominated this page as a
Good Article. Seeing that you seem to be an expert on the topic, if you find the time we would really appreciate a review of our nomination. You have been such a great help. Thank you.
Grant.vandervoort ( talk) 00:59, 6 December 2011 (UTC)
This is your last warning. The next time you remove or blank page content or templates from Wikipedia, as you did at Macrophage migration inhibitory factor, you may be blocked from editing without further notice. — Preceding unsigned comment added by Elias Jack ( talk • contribs) 17:01, 6 December 2011 (UTC)
Hi. When you recently edited IL1RL1, you added links pointing to the disambiguation pages Stratification and Mortality ( check to confirm | fix with Dab solver). Such links are almost always unintended, since a disambiguation page is merely a list of "Did you mean..." article titles. Read the FAQ • Join us at the DPL WikiProject.
It's OK to remove this message. Also, to stop receiving these messages, follow these opt-out instructions. Thanks, DPL bot ( talk) 10:17, 20 December 2011 (UTC)
Template:PD-USGov-NCBI-PubChem has been nominated for deletion. You are invited to comment on the discussion at the template's entry on the Templates for discussion page. Sfan00 IMG ( talk) 10:01, 24 December 2011 (UTC)
I was thinking this one was better as it contains inline refs http://www.drugs.com/npp/vitamin-d.html Doc James ( talk · contribs · email) 20:37, 29 December 2011 (UTC)
Excellent diagram! I just noticed its inclusion. Great work. -- Rmrfstar ( talk)