User talk:Boghog2

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[edit] Great idea of "Transcription factor glossary" template

I just wanted to say I thought that was a novel idea and I hope it catches on in the other scientific wikipages that can be a little über-technical. Rhetth (talk) 23:32, 14 February 2008 (UTC)

Thanks Rhetth. I should point out that I had a lot of help from User:Forluvoft on the template and accompanying article. Boghog2 (talk) 11:59, 16 February 2008 (UTC)

[edit] REST

Hi! I noticed you added RE1-Silencing Transcription factor to REST, turning it into a disambiguation page. But Rest already seems to be an established disambiguation page for that word, including for acronyms and abbreviations, so I took the initiative of moving RE1-Silencing Transcription factor there (Representational State Transfer, which REST had previously redirected to, was already listed there), and changing REST to point to Rest rather than Representational State Transfer. I hope you don't mind! Best wishes, Duncan MacKenzie (talk) 19:27, 18 February 2008 (UTC).

Opps! My bad. I didn't notice the alternative lower case disambiguation page. Thanks for taking the initiative and fixing it. Cheers. Boghog2 (talk) 21:19, 18 February 2008 (UTC)

[edit] GSOC ideas

Hi Boghog, care to chime in on ideas for Google Summer of Code 2008 (see also the talk page there for context)? Originally I thought I'd only list PBB improvements, but it might also make sense to broaden it to any bio-related computer-assisted projects. Perhaps something relating to the protein-boxes you've been working so hard on? Ideas on this or any other topic are welcome... Cheers, AndrewGNF (talk) 17:53, 26 February 2008 (UTC)

Great idea Andrew! The interactive protein 3D graphics as you have already listed would also be at the top of my list. Navagation tools to quickly link to related protein pages would be second, although I am not quite sure how or even if one should try to implement that with some sort of bot. Navboxes are great with a few dozen entries, but with all the newly created PBB pages, we now have protein families with hundreds of individual WP articles and the Navboxes are becoming unwieldy (drill down Ajax anyone?). So tools for creation and maintenance of these links would be useful. I need to give this some more thought. Cheers. Boghog2 (talk) 21:36, 26 February 2008 (UTC)

[edit] Estrogen

... excellent work on the references! Thanks for doing that - it's way better - Alison ❤ 06:09, 5 March 2008 (UTC)

My pleasure. The citations in the estrogen article were very relevant but needed to be cleaned up a bit. However I should not take all the credit. The citation reformatting was very easy to do with the help of User:Diberri's Wikipedia template filling tool. Cheers. Boghog2 (talk) 12:52, 9 March 2008 (UTC)

[edit] 3D

Hi.
Nice formulae! I would appreciate it, if someone could add essential 3D structures. Some time ago someone explained the whole procedure and it seems to be very easy. The gratis online service CORINA, developed by the german professor Gasteiger, stands out for user-friendliness, speed and an amazing conformational accuracy. One must admit that the provided conformation may have the appearance characteristic of crystal structures, and in a context of receptor-ligand binding this may be a weakpoint that has to be weighed in each single case. I could cross-check the drawings with an old hyperchem version.
My idea and my advice is to make SAR principles directly comprehensable, instead of huddling together an inflation of poor 3D drawings, from which the layman can't grasp any interrelationship. This requires a basic knowledge of the pharmacophore by the drawer or at least a reviewer, and is expressed by an accurate alignment of structures overlapping the entries. I am willing to assist here and to give further explanations. —Preceding unsigned comment added by 87.183.95.239 (talk) 15:59, 13 March 2008 (UTC)

Likewise, thanks for your great contributions to the dopamine receptor articles. I can certainly produce 3D images of ligands, but deciding on the most appropriate conformation to use (i.e., the bound conformation) is not so straight forward. Certainly pharmacophore modeling of the ligands and/or homology modeling of the receptor followed by docking could be used, but this is somewhat inappropriate as Wikipedia has a no original research policy. However if you know of any good published studies on dopamine receptor pharmacophores, please let me know. Finally, if you haven't seen this yet, please check out User:Diberri's Wikipedia template filling tool. Given a PubMedID, one can quickly produced a full citation that can be copy and pasted into a Wikipedia article. Cheers. Boghog2 (talk) 08:17, 14 March 2008 (UTC)

Thanks for your reply.
wp hates high-quality and loves trash structures. To thoroughly elucidate the provenience, the flow of genesis of structures would be the crucial point, and to sufficiently explain (in the text) minor deficiencies, that may possibly reside. Interestingly, I myself was doing research in that lab (at that time with those fellows!) where the D5 ligand was synthesized. But, seemingly, I can't help here. 87.183.104.5 (talk) —Preceding comment was added at 23:12, 14 March 2008 (UTC)

[edit] Hoodwinked!

Good catch... slightly embarrassed...  ;) AndrewGNF (talk) 17:07, 7 April 2008 (UTC)

No problem. Looks like April Fools day struck a few days late. The spoof was actually quite cleaver so I can easily see how one could miss it. Referring to Lund as an anatomical region of a certain organ was for me a dead give away. ;-) Cheers. Boghog2 (talk) 17:38, 7 April 2008 (UTC)

[edit] FPR

Hi Boghog2, Thanks for the corrections on the FPR receptor page. The page is still under development but I have a constant problem with it. After each editing there is a mess on it due to the table on the right. I have tried to fuse the three tables but I could not make it. Could you help me please? (I am working on 'Chemotaxis' related pages, but FPR-receptor page is the first where I have constant problems...) Thank for your help in advance. Best regrds from Kohlasz (talk) 04:08, 10 April 2008 (UTC)

Hi Kohlasz. Great job on expanding the FPR article. Your figures are both beautiful and informative. Concerning the protein boxes, I don't believe there is a way of fusing the tables together without some major editing to the Template:Protein itself. Having both figures and schematic diagrams within the same article often cuases problems with overlap, text being squeezed into narrow columns, etc. Another problem is that the layout sometimes differs depending on which web browser is being used. I just moved the figures in the article in an attempt to minimize these problems. Does this look any better? The layout is still not perfect, but I hope it is an improvement. Cheers. Boghog2 (talk) 05:47, 10 April 2008 (UTC)


[edit] Ro15-4513

Hi Boghog2. I agree this page could do with a rewrite but there are other factors you have not considered. See talk page for details.Meodipt (talk) 09:02, 13 April 2008 (UTC)

[edit] Protein/gene stubs

I appreciate they're often about both, to some degree or another, but my category analysis identified that they were primarily categorised by (and thus, implicitly, as) genes, so that's why I proposed splitting them on that basis. (To which there seemed to be fairly general agreement.) Looking at a number of the article texts seemed to bear that out, but I realize there's bound to be exceptions. Would it be sufficient to clarify the scope of the stub types so as to expressly include "proteins by chromosome number"? If that's not a useful split for the articles, then they'll have to be "unsorted" back into the proteins in the short term, and sooner or later re-sorted on some other basis, to deal with the stub category size issue. I'd need to know more about what articles are affected before I could comment sensibly on the feasibility of doing so. My bot's not currently sorting these (it was a one-off run), so any chances back should be "stable" for the foreseeable future. Alai (talk) 14:45, 27 May 2008 (UTC)

Thanks for your reply. There has been a lot of discussion concerning whether the topic of these articles is about the gene or the protein (see for example here and here). The general consensus is that the topic is about both. A further complication is that the number of these pages deal with families of gene/proteins (e.g., Retinoid_X_receptor) in which the respective genes reside on different chromosomes. In addition, the protein boxes on many of these pages list the mouse ortholog which resides on a mouse chromosome most often with a different number. Categorizing by "proteins by chromosome number" doesn't really solve the problem. One could split protein stubs by function (e.g., enzymes, structural, transcription factors, etc.) but this would probably cause other problems (e.g., many proteins have more than one function). So I am not sure what the best solution would be. Perhaps this question should be posted on the MCB discussion page. Cheers. Boghog2 (talk) 06:42, 28 May 2008 (UTC)

[edit] Rollback

Hi there Boghog, I noticed your recent reversion of vandalism on Immune system and thought you might like access to the rollback feature. You may not have to use it much, but it greatly simplifies the reverting process, and I'm confident you wouldn't use it inappropriately. Just follow the above link for information on how to use it, or let me know if you have any doubts. Best, Fvasconcellos (t·c) 19:48, 5 June 2008 (UTC)

Thanks Fvasconcellos. I have occasionally run across a set of consecutive vandalism edits by a single editor that I wanted to revert and the roll back feature makes this much easier. I have read the rollback instructions and I promise to use this feature carefully. Cheers. Boghog2 (talk) 08:10, 6 June 2008 (UTC)

[edit] Tryptophan Biosynthesis

Your tryptophan biosynthesis image has a minor error -- the I-3-GP molecule looks like a phosphonate instead of a phosphate; needs one of those carbons to be an oxygen!Takometer (talk) 21:01, 7 June 2008 (UTC)

Thanks for pointing out the error. You have sharp eyes! The figure is now fixed. Cheers Boghog2 (talk) 22:43, 7 June 2008 (UTC)