User talk:Vramasub

Hi Vramasub, and Please excuse this intrusion as you have been around a bit already but if no one has said it before: Welcome to Wikipedia!

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WikiProject Computational Biology

Hi,

Thanks for signing up to WikiProject Computational Biology. There is a growing list of tasks that you can help out with if you have a few free moments. See the discussion page. Alexbateman (talk) 09:16, 9 June 2011 (UTC)

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Zinc Finger Edits

I agree that the organization of the Zinc Finger wikipedia article had some issues, but I do not agree that simply moving most of the "Engineered Zinc Finger Arrays" section to the Zinc Finger Chimeras article improved things. It is generally a good idea to discuss such a drastic change on the relevant talk page prior to actually executing the change since many people have likely put in a substantial amount of time writing the existing article. You removed almost 90% of the references and about half of the text. In addition, the "Zinc finger chimera" article is not really the appropriate place to move all information regarding engineered zinc finger constructs. This section included information about altering the DNA binding specificity of zinc finger arrays whether or not they were fused to a second protein domain to create a zinc finger chimera.

If you really feel that the extra information on engineered zinc finger constructs and applications of such constructs makes the zinc finger article difficult to navigate for the average reader, then I would suggest replacing the references you removed that deal with the biochemistry of naturally occurring zinc finger arrays, writing a better summary of the zinc finger engineering field and its applications, and then creating a new article dedicated to engineering zinc finger arrays to alter their specificity that includes all relevant detailed information and references from both the previous zinc finger article and the zinc finger chimera article. Of course, this will involve more work than simply cutting and pasting text or the end result will be unorganized and difficult to read. I'm happy to discuss further on the relevant talk pages. ScienceGeekling (talk) 02:43, 13 June 2012 (UTC)

I'd certainly be happy to talk, after I posted the suggestion to merge I barely saw any discussion on the topic so I figured that nobody was really paying attention. I certainly plan to do more with the page in the next couple of weeks, I simply didn't have the time to at the moment. I think that the zinc finger page itself should only be talking about what the zinc finger structure itself. Like you said, adding more information about the biochemistry would be good. I disagree that the engineered arrays should have their own page, however, since by themselves they don't serve any function. The reason such engineered arrays are useful is because they can be combined with other functional domains, so I would think it makes more sense to make that a subsection in the zinc finger chimera page. It certainly needs to be rewritten, though, and my wholesale copy-paste was more of a stopgap than anything else. What are your thoughts? Vramasub (talk) 03:57, 13 June 2012 (UTC)

zinc fingers as a class of proteins were studied long before the structure was known so limiting the zinc finger article to only information related to the structure as you propose doesn't make sense. The fact that you can alter the specificity of this class of proteins is incredibly relevant to numerous areas of scientific research and biotechnology. Much of the early work with engineered zinc fingers just studied their binding and specificity rather than using them as chimeras with fused functional domains. And many zinc finger chimeras use the non-engineered DNA binding domain of Zif268/Egr1 so zinc finger chimera and engineered zinc finger arrays are not equivalent.ScienceGeekling (talk) 17:09, 13 June 2012 (UTC)

I'm glad that you have the time to improve the article and you have already made some good edits to the introduction. But another reason I objected to moving the majority of the references to the zinc finger chimeras article is that I've never actually heard anyone use the term "zinc finger chimera". The page view statistics for this article are correspondingly low. But you don't have to take my word for it- google the phrases "zinc finger" and "zinc finger chimera" and compare the number of hits. Additional support for including information on engineered zinc fingers and their application in the main article can be found in the fact that hits for the phrase "zinc finger nuclease" (these generally use engineered zinc fingers) are almost half as numerous as hits for the far more general phrase "zinc finger". So visitors to wikipedia are quite likely to be searching for information about engineered zinc finger nucleases when they find their way to this article. If you feel the current article is unbalanced then I'd suggest balancing it out by adding more information rather than removing relevant information.ScienceGeekling (talk) 15:08, 14 June 2012 (UTC)

Mostly agree with your points. I personally have only heard the zinc finger chimera term used very sparsely, so I certainly understand that a lot of the information might be better placed on the main zinc finger page. While zinc finger chimera and engineered zinc finger arrays are not equivalent, however, I don't think discussing the latter without alluding to the former makes much sense because research into altering binding specificity only serves a purpose in the context of such chimeras. Zinc finger nucleases are definitely the most prolific example of such chimeras, so it does make sense to have information about them in the main page. The main problem I had with the page was that the methods related information was too detailed for a general page on zinc fingers in my opinion. I think a good way to organize the main article would be to have the introduction, history and classes sections as they are. Underneath that I think there should be a section on engineered zinc fingers in general with subsections, one explaining that specificity can be engineered and then one each for the possible uses, of which the two main ones are for constructing nucleases and transcription factors. However, I think a lot of the information on methodology should go into a separate article, or at least should be moved underneath a more gentle introduction to the topic itself.

Also, I think we should come to some sort of consensus on how to deal with the articles Zinc finger, Zinc finger chimera, Zinc finger transcription factor, and Zinc finger nuclease before any more editing. Let me know what you think about organizing the information in general, I think that should help with the rest. Sorry if I'm a little slow at responding for the next few days, I'm busy traveling around with questionable internet connections until Sunday.

Experiments that alter the specificity of zinc fingers also provide information on the behavior of natural zinc finger proteins with unknown specificities and allow us to better understand protein-DNA interactions in general. One purpose of such research is to target desired DNA sequences- but this is not the only purpose. But I agree with most of your other points. How about changing the "Engineered zinc finger proteins" section to "Applications", write a brief intro explaining that zinc fingers can be re-targeted, have a short paragraph on each major application (with links to the relevant full articles), and end with a streamlined version of the methods to do the engineering? This way no one has to wade through detail they might not be interested in to get to what they find interesting, but the detail is still there if they do happen to be interested. ScienceGeekling (talk) 15:10, 15 June 2012 (UTC)

That sounds good to me, that was pretty close to how I did it initially, which you objected to because of the wholesale moving of a lot of the information. Where do you think these details should go? In other words, what other full articles should we have on the subject? I think the zinc finger nuclease and zinc finger transcription factor are necessary, but in view of what we've said here the information on zinc finger chimeras might be better moved into a streamlined section in the main zinc finger article. In that case, what other full articles need to be added?

Hopefully we don't need any new articles. If we turn the engineered zinc finger section into an applications section that starts with an intro and covers zinc finger nucleases and zinc finger transcription factors and then move the engineering details to the end of the section, I'm sure I can shrink the zinc finger engineering methods down to a single paragraph and still retain the most critical references. I'll give this a shot sometime this weekend. If you beat me to it, please move the details to the end of the article and I'll streamline and update the details when I get a chance. At this point we probably need to try some edits and see how it goes. ScienceGeekling (talk) 06:12, 22 June 2012 (UTC)

I just updated the applications section as we discussed. It would probably make sense to move further discussion to the talk page for this article. ScienceGeekling (talk) 15:26, 25 June 2012 (UTC)

ISCB Wikipedia Competition 2013

Dear Vramasub,

I thought that you would be interested to know that the International Society for Computational Biology was running its Wikipedia competition again this year. You can find out more at the URL below:

http://en.wiki.x.io/wiki/Wikipedia:WikiProject_Computational_Biology/ISCB_competition_announcement_2013

To enter you must be a student or post-doctoral trainee. I would also be grateful if you could also let your colleagues know about the competition as we would like to get even more great entries this year :-)

Best wishes. Alexbateman (talk) 14:45, 22 August 2013 (UTC)

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