Talk:Bioinformatics

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I'm not sure if this is the right place for this but I suggest that a new topic is created - 'sequence analysis', under which sequence alignment etc. would then fall. The reason for this is that any discussion of Hidden Markov Models, motifs and profile based methods would then fit in easily.

Any objections?

-MockAE

Sure, go ahead : sequence analysis ;-) --Magnus Manske 18:57 Jan 15, 2003 (UTC)

I'm a newbie, so hope I dont screw this up -- This is addressed to Magnus. The page you link to above, sequence analysis says DNA sequence analysis is the determination of the nucleotide sequence of DNA. That sounds a little different from my idea of the usage -- sequencing is the term used to determine the sequence of nucleotides, whereas sequence analysis in the context of DNA/bioinformatics is the computational analysis of predetermined sequence to extract information from it. --Venkatr_n

Edit: Just noticed that you're a biologist by profession too, no preaching intended above.

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How do you call the use of biology for tasks of computing? Biocomputing? -- Error

Contents

1 links to common programs? 2 Moved comments from Wikipedia:Cleanup 3 Feature article on Image processing for diagnostics and biomedical research 4 Pending links cleanup 5 First Sequenced Genome 6 Bioinformatics and CompBio 7 Page move discussion

links to common programs?

Why aren't some of the more common tools and databases mentioned here? BioPERL is great but most bioinformatics primers at least mention BLAST and NCBI in passing.

Moved comments from Wikipedia:Cleanup

• Bioinformatics - Poor organization, relatively unfundamental information presented early on. Focus on sequence similarity too narrow, bioinformatics is a broad field 155.91.19.73 00:45, 14 Dec 2004 (UTC)
  • This is already a featured article, moving your comments to Talk:Bioinformatics rather than cleanup because it is clearly not an obvious cleanup candidate because the page is properly wikified etc. --Lexor|Talk 13:50, Dec 16, 2004 (UTC)

Feature article on Image processing for diagnostics and biomedical research

I was wondering about the ideal place to start a feature article (or something like that) on bioinformatics principles as applied to processing of image data for use in diagnostics and proteomics and even natural biology. I am aware of some researchers who have scripted a small program to identify species of ants in a given frame and IDing it.

Probably a link could be provided in the main page of 'Bioinformatics' followed a stub about this topic.

Suggestions are welcome

Nattu

Er, you might just call the article 'Image processing for diagnostics and biomedical research' and link it from Medical imaging and Bioinformatics. Of course, since WP has a Medical imaging article, you probably should make the distinction between the new article and that one clear. jdb ❋ 03:25, 14 Feb 2005 (UTC)

Pending links cleanup

Wikipedia is not a repository of links, but this page will have a tendancy to grow in that direction, given the sheer number of bioinformatics-related stuff on the web. We should be particularly vigilant about pruning less-important links from the article and moving them to more specalized articles, if merited. jdb ❋ 03:25, 14 Feb 2005 (UTC)

First Sequenced Genome

The article seems to suggest that the Epstein-Barr virus was the first sequenced genome in 1984, I was under the influence that Frederick Sanger first sequenced the Phi-X174 Phage as the first sequenced genome in 1977 according to http://dorakmt.tripod.com/genetics/notes01.html ? -Adenosine- 02:34, Feb 23, 2005 (UTC)

I want to know what happened in 1984 with the Epstein-Barr virus that warrented the this claim that it was the first sequenced genome? Frederick Sanger's achievments in 1977 should not go unnoticed. -Adenosine- 07:46, Mar 8, 2005 (UTC)

Bioinformatics and CompBio

On the page move discussion I raised the question of whether there was a distinction per se between the terms Bioinformatics and computational biology. Even if there's only contextual differences (one journal, country, institution, or interlocuter vs. another), it might be worth noting in the article. Is there anything in bioinf that's notably held not to be in compbio? If so, what, and in what contexts? And vice versa, is there anything in compbio that's not in bioinf? In what contexts is either term preferred over the other? Alai 05:28, 4 Mar 2005 (UTC)

The NCBI has a discussion of this: see http://www.ncbi.nlm.nih.gov/About/primer/bioinformatics.html, scroll down to "What is Bioinformatics?" jdb ❋ (talk) 01:53, 5 Mar 2005 (UTC)

My reading of the above listed NCBI definition suggests that the sentence "The terms bioinformatics and computational biology are often used interchangeably, although the former is, strictly speaking, a subset of the latter." may no longer be accurate. I believe the two to be overlapping rather than one inclusive of the other. Specifically, my experience indicates that bioinformatics has grown to encompass sociotechnical issues (e.g. usability) not normally covered by traditional computation biology. Alan Au 04:09, 28 Apr 2005 (UTC)

Page move discussion

Bioinformatics → Computational biology

The article titled "bioinformatics" is now much broader than just bioinformatics (as it discusses protein structure prediction, computer simulation of bio systems, etc.) We should reverse the redirects, so Bioinformatics redirs to Computational biology, and Computational biology has the content now at Bioinformatics. -- jdb ❋ (talk) 18:14, 27 Feb 2005 (UTC)

• Oppose I see no discussion of the logic of such a change on the talk page, or any objection to content beyond the scope of the term "bioinformatics", which AFAIK explicitly includes all of the above, and is the more usual term, as I've encountered them. Alai 22:47, 27 Feb 2005 (UTC)

There's no discussion of the logic of the change on the talk page because (a) the request to move was added all of four hours ago, and (b) the "move requested" banner says that the discussion will take place here, not there. I admit that bioinformatics is a loosely-defined term (due to its novelty and lots and lots of hype), but the root of the word is informatics, a field into which some things in the article obviously fall (biodatabases, for instance), and some things less obviously fall (physics-based protein structure prediction, for instance). In a complete Wikipedia, the Bioinformatics article would discuss a subset of the comp. bio. article. jdb ❋ (talk) 02:46, 28 Feb 2005 (UTC)

Sure, you're not obligated to discuss it there first, but if there was any feeling that the title was a poor fit to the subject, surely it would have come up already, in the course of editting the page, one way or the other? Y'know, someone saying "stop, you fools, that's not bioinformatics!" (or less melodramatically, but you get the idea). Yes, bioinformatics is the informatics of biological systems; how is that any different from computational biology? I've never heard a bioinformatics talk on biodatabases, but I've been to several (so described) on protein sequencing and structure. I still don't follow the distinction you're getting at, and it's not one I've ever heard a bioinformaticist/computational biologist make. Alai 06:26, 28 Feb 2005 (UTC)

It's not at all uncommon in the literature. Bioinformatics (http://www3.oup.co.uk/jnls/list/bioinformatics/scope/) says it's concerned with "new developments in genome bioinformatics and computational biology", indicating both that there is a distinction and that the fields are close enough to be covered in the same journal. Likewise, Journal of Computational Biology (http://www.liebertpub.com/publication.aspx?pub_id=31) says that it includes (among other things) "new tools for computational biology" and "relational and object-oriented database technology for bioinformatics". That there is overlap between the fields is undeniable, but that shouldn't stop us from picking the more general term. As to why no-one mentioned it before, I suppose that most people simply don't care. jdb ❋ (talk) 15:27, 28 Feb 2005 (UTC)

I don't see that these demonstrate anything less than a 100% overlap, and certainly not that either term is more general than the other. The very title of the first journal is an assertion that Bioinformatics includes the full generality of the scope of the article. Possibly this is a matter of transatlantic usage: certainly the use of (unqualified) informatics to mean computing science is more common right of the Atlantic than to the left. If bioinformatics were to carry the same sense that "Medical informatics" does (i.e. medical information science) than I'd agree with you, but that's not the case, certainly as far as how it's used around here. Alai 19:48, 28 Feb 2005 (UTC)

Hm; you may be right. jdb ❋ (talk) 00:15, 1 Mar 2005 (UTC)

• Oppose It is good as it is. Suitable references can be made to Computational Biology and refining its definition. Morever, the public perception for the word Bioinformatics is greater than for computational biology. One wouldnt want to see the user redirected to a new location when he wants to know something about Bioinformatics (which has enough to talk different things than Computational biology).Nattu
  • Er, we redirect people all the time from specific terms to general ones when we only have articles for the latter. I suppose the correct way to do this would simply be to write a cbio article, move the appropriate parts of bioinformatics there, and link back and forth. jdb ❋ (talk) 15:27, 28 Feb 2005 (UTC)
    • But it's not a more general term. The second remedy here seems to me to be worse; this is not two distinct topics, this is a single topic with two names, both of which are fully covered in the present article; and for which there's already a redirect, so there's no possibility of anyone 'missing' the article. Alai 19:48, 28 Feb 2005 (UTC)
• Strongly oppose. Bioinformatics and Computational Biology are distinct but overlapping disciplines ... speaking from the standpoint of being an "Informatics Scientist" who practices "bioinformatics" and occupying an office directly adjacent to another "Informatics Scientist" who, we both agree, is a "computational biologist". Please do not add to the confusion by mixing these terms for convenience sake. Courtland 00:22, 2005 Mar 3 (UTC)
• Oppose These are subtly distinct fields and should retain (or eventually acquire) separate pages. Bioinformatics does include proteomics, alignment, and genome studies, so I'm not sure where that argument comes from. --Aranae 02:10, Mar 4, 2005 (UTC)
• Violently oppose. This is a very, very awful idea. Bioinfomatics is far more common, and they aren't even truely synonomous. →Raul654 02:28, Mar 4, 2005 (UTC)
• Oppose, as well. They're (slightly) different. Penwhale 02:31, 4 Mar 2005 (UTC)
  • Can the last three editors expand on what exactly the subtle/slight difference/non-overlap is? Is this something that the current article could address better? Alai 03:38, 4 Mar 2005 (UTC)

I second that request. WP would benefit very much from explanations of both terms with citations from some authority, whether they're synonymous or not. jdb ❋ (talk) 04:00, 4 Mar 2005 (UTC)

It's the fact that, because I am a mathematics person, I find that there's a slight difference between Bioinfo and Comp. Bio. I looked at it from a point of view, that Computational Bio should only be a small portion of Bioinfo. Put it this way, in a way, Bioinfo is a broader term than Comp. Bio. Penwhale 05:17, 4 Mar 2005 (UTC)

Not moved - violet/riga (t) 20:49, 4 Mar 2005 (UTC)

• Oppose As a supplementary point of interest, I would note that the National Library of Medicine redirects from Computational biology → Bioinformatics. See: http://www.nlm.nih.gov/tsd/acquisitions/cdm/CDMBookIOM.html (scroll down to Computational biology) Alan Au 04:20, 28 Apr 2005 (UTC)