Talk:Bioinformatics/Archive 1

Answered Q&A
Q.How do you call the use of biology for tasks of computing? Biocomputing? -- Error

A.Biocomputing is another (albeit, loose) synonym for Computational Biology or Bioinformatics: see definition from http://www.dictionary.com:

I don't know of a single term used to describe this type of work in general. An example of what you refer to is DNA computing, or computing with DNA. Other commonly used phases include "biology inspired computing" or more broadly, "Nature-Inspired Computing".

--Jethero 07:57, 26 October 2005 (UTC)

mission / goal?
This page is, or should be:
 * a clear, concise definition of bioinformatics
 * a snapshot of major areas of study in bioinformatics
 * a review of major, mature projects
 * a history of bioinformatics (timeline, dates, key people, articles, publications)
 * a hub, connecting all of the sub- and sister-disciplines of bioinformatics, such as biomedical informatics, biomedical imaging, systems biology

This page is not, or should not be: These all already exist on the www, and can be found and linked to if required, or can be created as a separate wikipedia entry
 * a collection of links, which will quickly become unmaintainable and is easy to and tempting to vandalize
 * a collection of software or tools, which is easy to and tempting to vandalize
 * advertising for large/small/academic/commercial projects (of which we currently have some)
 * a debate about the definition of computational biology or bioinformatics
 * a collection of conferences
 * a collection of univeristy programs or courses

steering discussions
There are several suggestions made when this page was removed as a featured article, and these are the areas that we should improve:
 * it's relatively short
 * lacks of a history of informatics
 * lacks current and future developments
 * lacks names and information of people prominent in this field
 * lacks supporting votes (i.e. active members)
 * not effectively illustrated --FOo 02:19, 21 September 2005 (UTC)
 * The image of DNA is utterly generic and without relevance to bioinformatics --FOo 02:19, 21 September 2005 (UTC)
 * A simplified depiction of an alignment, or a screenshot of a bioinformatics program, or even simply some visual representation of a gene would be more worthwhile illustrations. --FOo 02:19, 21 September 2005 (UTC)
 * too many 'see alsos' scattered about willy-nilly, and the "related fields" section - Tuf-Kat 04:05, 21 September 2005 (UTC)
 * could use more citations - Tuf-Kat 04:05, 21 September 2005 (UTC)
 * has way too many external links - Tuf-Kat 04:05, 21 September 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 &#x274b; 03:25, 14 Feb 2005 (UTC)

External links problem
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.

People at 63.196.131.66 just added a massive number of external links to various types of courses on bioinformatics. I'm sure there is lots of these around nowadays and that it is relevant for the article, but this list was far too long. The list was also followed by an external link from which it was taken. This is why I removed the list and kept only the external link to the page that contains it. The list of external links to organizations and software projects will doubtlessly also keep growing. Just don't let this turn into an article of lists of links! Andkaha(talk) 06:30, September 13, 2005 (UTC)
 * Indeed, the list was copyvio anyway.  --Alan Au 08:18, 14 September 2005 (UTC)

Bioinformatics Timeline
Starting with, perhaps, the composition of DNA, base pairing, discovery of RNA structure, stem-loops, homology searching (physical, not computational) and the digital nature of DNA, Watson & Crick circa 1951, etc, can we put together some idea of the major watersheds leading to modern bioinformatics? From that we could probably show the branching of each of the disciplines and/or applications that are currently listed

here is a timeline of bioinformatics with some relevant primary sources Jethero 05:15, 22 February 2007 (UTC)
 * http://www.netsci.org/Science/Bioinform/feature06.html
 * http://www.geocities.com/bioinformaticsweb/his.html
 * http://www.ncbi.nlm.nih.gov/Education/BLASTinfo/milestones.html
 * http://ibi.zju.edu.cn/bioinplant/courses/bioin_history.htm
 * Early bioinformatics: the birth of a disciplne -- a personal view Christos A. Ouzounis and Alfonso Valencia. Bioinformatics. 2003, 19(17): 2176-2190

To Do / Task asignment

 * add more concrete history, dates, names
 * trim or move links which are subject to change and cannot be maintained

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 &#x274b; 03:25, 14 Feb 2005 (UTC)

add common themes in 'bioinformatics' areas of research
I propose a discussion / breakdown of the common themes which bring together many of the things which are considered 'Bioinformatics' applications or areas of research: for example I'll attempt to start one here:

Data-reduction and Visualization Seeing can often be equated with understanding, especialy in diagnostics or in interpretation of results. With the recent increased capacity for acquiring data in biology, the human observer can often not see the entire set of results which can be ''seen' by the instrument, so we employ computational techniques to reduce the data while maintaining some of the more important underlying meaning, and we present this data in a visually accessible format.

Integration Likewise, an observer can seldom see all the ancillary data that has been previously observed related to a new experiment. Bioinformatics approaches strive tie togher the relevant data

Computational Analysis?

RNA structure prediction
Why isn't there any discussion of the computational analysis of (non-coding) RNA in this article? In my opinion, RNA secondary structure prediction is one of the successes of bioinformatics. I see that there was a dispute between Bioinformin and Alan Au about RNA Bioinformatics, but surely no one objects to including text on RNA secondary structure prediction, or RNA structure prediction in general? Or do they? Blackcat100 03:06, 3 September 2006 (UTC)

Changes

 * 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.

Re: Section on Genome annotation. Although you could argue that Haemophilus was the first free-living organism to be completely sequenced (publsihed July 1995) it should be noted that significant amounts of sequence from other species were completed before (S.cerevisiae Chromosome III (1992), Chromosomes II, VIII & XI (1994), Chromosomes I & VI (1995) and 2.2 Mb of C.elegans (1994)). All of these projects had software systems for the annotation of genome sequence and therfore it is misleading to state that the system for the analysis of Haemophilus was 'first'. It would be better to keep this section general and encourage interested people to the 'Gene prediction' page. Affe 02:43, 16 February 2006 (UTC)

Removals

 * Bioinfo-Online News was removed by Bioinform. I'm not sure who put it up, but it does look like a site on the subject. No removal statement was included, so I'm asking for one. Was it biased? Did it not include anything other sites didn't? For reasons good or bad, they do need to be explained in edit summaries.


 * I don't think that every research group out there should be linked in this article. I can think of 4 or 5 more just at my grad school that could easily be added.  If we list every lab doing this, the list will grow out of hand quickly (hundreds of labs easily).  I propose removing individual research groups from the article.  Perhaps they can be listed elsewhere? Anyone Agree/Disagree? Spin2cool 01:07, 29 July 2006 (UTC)
 * absolutely agree Jethero 02:25, 31 October 2006 (UTC)

Education on bioinformatics
It would be a good idea to make links to universities and other places where this science is teached, cos it's different from plain biological schools and yet not so wide-spread. --GolerGkA 11:25, 25 January 2006 (UTC)


 * disagree it could be a topic for another article, with owners who felt like managing a 'course directory' rather than a informational article as this is. It could be linked from here.  However, it would be essential to maintain a WP:NPOV and to respect the WP:NOT and WP:NOT policies.
 * disagree. There is a link now to an open directory of bioninformatics research centers. Putting specific links in the article invites abuse and spam. -Cquan (talk, AMA Desk) 06:10, 26 April 2007 (UTC)

sequence analysis
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

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

gene annotation
This subsection has a reference to gene finding. Strictly, gene annotation and gene finding are two totally different things. Both are important in their own right and should be separated. --137.158.200.124 12:08, 11 July 2007 (UTC)
 * good point, however there will not be room in this article to cover genome annotation at that level of depth. Is there an article on gene annotation that you would like to create a link to?  Also, in this specific case I think we are talking about 'genome annotation', which is different from gene annotation. G enome annotation is specifically documenting the location of sequence features in a genome.  One major element of genome annotation is is essentially finding where the genes are situated.  If you can make that more clear in the section, please do. Or if you have links to other aspects of genome annotation, such as transcription factor binding site mapping, that would be good too. JetheroTalk 02:09, 12 July 2007 (UTC)

Doubts about Bioinformatics and Systems Biology
I feel a bit disturbed by the early mentioning of systems biology in this articel. Bioinformatics indeed has a large overlap with systems biology, but there are many, many parts in Bioinformatics that are not really parts of systems biology: protein and RNA folding are if at all at the very edge of SB (they rather intersect with computational chemistry and computational physics), as well as many drug discovery topics are not really SB. The list of non-SB bioinformatics topics can be extended arbitrarily -- just think of the large and diverse areas of phylogeny reconstruction or DNA computing.

For the above reasons, I propose to simply eliminate the systems biology sentence.

Any objections?
 * agree: From some viewpoints, systems biology is one component of application of computational biology. From other viewpoints, it can be considered an approach or a philosophy or a paradigm, and others might consider it a field unto it's own. In any case, I don't think it belongs as the second sentence. user:jethero

Official Definition(s) of Bioinformatics (and their reliable sources)
bio·in·for·mat·ics Pronunciation: "bI-O-"in-f&r-'ma-tiks Function: noun plural but singular in constr : the collection, classification, storage, and analysis of biochemical and biological information using computers especially as applied in molecular genetics and genomics —bio·in·for·mat·ic /-tik/ adjective Source: Merriam-Webster's Medical Dictionary, © 2002 Merriam-Webster, Inc. Jethero 02:41, 4 November 2005 (UTC)

bioinformatics The field of science concerning the application of computer science and information technology to biology; using computers to handle biological information, especially computational molecular biology. (2005-01-07) Source: The Free On-line Dictionary of Computing, © 1993-2005 Denis Howe Jethero 02:41, 4 November 2005 (UTC)

The terms bioinformatics and computational biology are often used interchangeably, although the former is, strictly speaking, a subset of the latter. Source: NCBI - http://www.ncbi.nlm.nih.gov/About/primer/bioinformatics.html Jethero 02:41, 4 November 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 &#x274b; (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: Computational Biology vs. Bioinformatics
Bioinformatics &rarr; 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 &#x274b; (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 &#x274b; (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 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 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 &#x274b; (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 &#x274b; (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 &#x274b; (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. &rarr;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 &#x274b; (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 &rarr; 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)
 * I think of bioinformatics as primarily concerned with sequence analysis and function prediction (genomics mainly, I guess) while computational biology is less concerned with deducing information from nature, while more concerned with predicting information about nature via simulations of biological processes. So I see a direction of information flow difference here. 128.175.205.36 10:09, 6 March 2006 (UTC)

Definition of Bioinformatics versus Computational Biology, continued
In the following I discuss some editing history of this page and try to justify my actions, weighing in on defining the distinction between bioinformatics and computational biology.

On March 17th, 2006, I contributed to the Wikipedia definitions of bioinformatics and computational biology by reversing "former" and "latter" in what came before to result in the following sentence, thereby more closely rephrasing the definitions from BISTI at NIH:

The terms bioinformatics and computational biology are often used interchangeably, although properly the former typically focuses on algorithm development and specific computational methods, while the latter focuses more on hypothesis testing and discovery in the biological domain.

I also added the distinction and phrases of "technique-driven research" and "hypothesis-driven research" in Although this distinction is used by National Institutes of Health in their working definitions of Bioinformatics and Computational Biology, it is clear that there is a tight coupling of developments and knowledge between the more hypothesis-driven research in computational biology and technique-driven research in bioinformatics.

On July 28th, the first sentence was changed anonymously to:

the former typically involves the manipulation of large biological databases, whilst the second includes model building and simulations.

I disagree with this change because I think that neither "manipulation of large biological databases" nor "model building and simulations" is sufficient to describe what either bioinformaticians or computational biologists do in practice respectively.

As a sampling of research activities of bioinformaticians and computational biologists, please see for example the program of The Nordic Bioinformatics meeting in 2006.

Below I describe what I believe is a consensual view of the definitions of these terms and their distinctions. I define the fields in terms of the training, competence, interests and activities of the people who practice them.

A computational biologist is a biologist, while a bioinformatician need not be a biologist. A biologist is someone who:


 * 1) is conversant -- to the level of an undergraduate biology degree -- with the fundamentals of the major biological subdisciplines of cell and molecular biology, organismal and developmental biology, physiology, and population biology including ecology, evolution, and systematics,
 * 2) can critically read the biological literature in their own and related fields of expertise or research, regardless of the technical mode of inquiry used,
 * 3) can converse with other biologists in their own and related fields of expertise and research.
 * 4) can recognize and interpret a biological result or discovery in their inquiries.
 * 5) relatively naive in the operation of a computer, but well versed in manuals of popular programs.
 * 6) can not critically read computer science literature.
 * 7) can not converse with computer scientists in a manner other than in a directive manner, ie "Please analyze this data or implement a program which calculates this equation."
 * 8) is generally unable to effectively design and manage large software development and database construction projects.

Computational biologists are biologists who conduct hypothesis-driven biological research on a computer. Their research can be published -- without collaboration or coauthorship by other biologists -- in biological journals that are not specialized for bioinformatics or computational biological research. Advances in computational biology need not involve technical advances in the areas of bioinformatics or statistics, but they often do. Rather, such advances usually involve the creative application, extension or synthesis of methods to test biological hypotheses or make discoveries that lead to new hypotheses in the biological domain.

In contrast, one can find today many practicing and accomplished bioinformaticians that have never formally trained in biology and would never call themselves biologists. Among their ranks include computer scientists, statisticians, mathematicians, and physicists. While bioinformaticians can and do carry out computational biological research in collaboration with biologists, they also conduct valuable and interesting research that nevertheless does not advance biological knowledge per se. For instance, bioinformaticians might concentrate on creating, improving and extending algorithms or solving mathematical, computer scientific, or physical problems that have been inspired by biological systems, or posed and reframed from the management and analysis of biological data. Again, such research need not have direct or obvious biological application nor immediately advance biological knowledge to be published and appreciated by the bioinformatics community.

Other examples of bioinformatics research are the creation of new methods for the visualization or mining of existing data to increase the value or utility of existing biological data. These methods become part of computational biological research only first when a biologist uses them to advance biological knowledge.

In a further example, an algorthmic improvement for more efficient estimation of a known statistical quantity of biological interest may be a valuable advance in bioinformatics but is not computational biology until it is applied.

Getting back to the article and the changes made: bioinformaticians do much more than manipulate large biological databases. They abstract the formal nature of biological data and discover and improve algorithms and representations for working with these data and kinds of data. Computational biologists need not be involved in simulation and model-building but rather use every and any available or imaginable technique of bioinformatics, statistics, simulation and model-building that they can muster in order to investigate and discover biological phenomena.

I believe that my views about these definitions lie close to those of other workers in our fields. With this in mind I will revert the sentence that was changed, not out of disrespect for the anonymous author, but to make this article more closely agree with what I believe to be the consensual perspective of working bioinformaticians and computational biologists who are my colleagues. I certainly welcome further discussion towards collaborative improvement of the article on this point. --David Ardell 04:52, 2 August 2006 (UTC)


 * To help alleviate this confusion, the NIH in July 2000 published an official Working Definition of Bioinformatics and Computational Biology:
 * "Preamble
 * Bioinformatics and computational biology are rooted in life sciences as well as computer and information sciences and technologies. Both of these interdisciplinary approaches draw from specific disciplines such as mathematics, physics, computer science and engineering, biology, and behavioral science.  Bioinformatics and computational biology each maintain close interactions with life sciences to realize their full potential. Bioinformatics applies principles of information sciences and technologies to make the vast, diverse, and complex life sciences data more understandable and useful. Computational biology uses mathematical and computational approaches to address theoretical and experimental questions in biology.  Although bioinformatics and computational biology are distinct, there is also significant overlap and activity at their interface.
 * Definition
 * The NIH Biomedical Information Science and Technology Initiative Consortium agreed on the following definitions of bioinformatics and computational biology recognizing that no definition could completely eliminate overlap with other activities or preclude variations in interpretation by different individuals and organizations.
 * Bioinformatics: Research, development, or application of computational tools and approaches for expanding the use of biological, medical, behavioral or health data, including those to acquire, store, organize, archive, analyze, or visualize such data.
 * Computational Biology: The development and application of data-analytical and theoretical methods, mathematical modeling and computational simulation techniques to the study of biological, behavioral, and social systems."
 * What I take home from those definitions is that (1) a distinguishing characteristic of bioinformatics is that it is concerned with data (generally large data sets or large volumes of data), whereas computational biology includes all uses of computers for biology; and (2) a distinguishing characteristic of computational biology is that it is a branch of biology (i.e its goals are to understand life) wheras bioinformatics includes mathematical and computational goals (such as understanding forms of structure in data sets). I would argue strongly that the two subjects deserve separate Wikipedia pages. Mglg 21:17, 28 August 2006 (UTC)

definition of bioinformatics versus computational biology, again
Bioinformatics has to do with database management and data mining with large data sets. Computational biology is largely about algorithm development for bioinformatic use. I quote my professor, Sorin Istrail:

"Although “Computational Biology” and “Bioinformatics” are often used interchangeably, we will refer to Bioinformatics as primarily being about applying computational genomics tools, with well-established biological relevance, in large-scale applications in molecular biology and medical laboratories. Computational Biology, in turn, is about building these powerful genomics tools. Although there is significant overlap, both areas are essential: Computational Biology is more about the science, while Bioinformatics is more about the technology and engineering. To use a metaphor, Bioinformatics is about expeditions on the sea shores to find precious metals, or at the bottom of the sea to find oil, while Computational Biology is about building metal detectors or oil detection systems." http://www.cs.brown.edu/courses/cs196-1/

An experimental biologist may collaborate with a bioinformatician to analyze her microarray data, while the computational biologist is concerned with designing algorithms for general biological problems, such as protein folding, or gene prediction. —The preceding unsigned comment was added by Rohan.maddamsetti (talk • contribs) 20:56, 1 April 2007 (UTC).


 * disagree - based on NIH definition. Our current paragraph might be able to use a rewrite, removing the compbio vs. bfx debate from the article, but just swapping the words doesn't make sense. It depends on the perspective you are coming from. CompBio students / practitioners may think of Bioinformaticians as 'applying their work', and visa versa, Bioinformatics students / practitioners think of Biologists and Computational Biologists 'using' their work to solve biological problems. We need a neutral perspective WP:NPOV. (a biochemist's perspective. Is biochemistry biology or chemistry? Perhaps neither.) JetheroTalk 21:20, 1 April 2007 (UTC)

VCU Bioinformatics and Bioengineering Summer Institute

 * I propose the addition of VCU's Bioinformatics and Bioengineering Summer Institute to the external links listing. The BBSI is hosted by Virginia Commonwealth University, is non-profit, and may spark the interests of students who are thinking of pursuing this evolving scientific field.Opertinicy 21:33, 6 June 2007 (UTC)
 * Thanks for enquiring about this on the Talk page. Wikipedia is not for promotion or advertising. I suggest that this Institute would not qualify as a 'Major organization' so it would not fit under that heading, and that is the only logical section. Unfortunately this article would expand without bound if we linked to every worthwhile activity. EdJohnston 01:48, 7 June 2007 (UTC)


 * I propose the addition of an online book available at http://www.bioinfbook.org/. —Preceding unsigned comment added by 132.210.240.52 (talk) 16:13, 15 April 2008 (UTC)

Open Directory Project Links

 * in line with External_links recommendation, I recommend we use DMOZ categories on this page for each of our high-spam sections to redirect the innocent 'spammers' that are truely trying to help list useful resources. (i.e. ) Jethero 20:48, 1 April 2007 (UTC)
 * Voting for this will be open for at least 1 month or 3 affirmative votes before i post the new links to appropriate sections Jethero 20:48, 1 April 2007 (UTC)
 * Voting for this will be open for at least 1 month or 3 affirmative votes before i post the new links to appropriate sections Jethero 20:48, 1 April 2007 (UTC)
 * Voting for this will be open for at least 1 month or 3 affirmative votes before i post the new links to appropriate sections Jethero 20:48, 1 April 2007 (UTC)
 * Voting for this will be open for at least 1 month or 3 affirmative votes before i post the new links to appropriate sections Jethero 20:48, 1 April 2007 (UTC)
 * Voting for this will be open for at least 1 month or 3 affirmative votes before i post the new links to appropriate sections Jethero 20:48, 1 April 2007 (UTC)
 * Voting for this will be open for at least 1 month or 3 affirmative votes before i post the new links to appropriate sections Jethero 20:48, 1 April 2007 (UTC)
 * Voting for this will be open for at least 1 month or 3 affirmative votes before i post the new links to appropriate sections Jethero 20:48, 1 April 2007 (UTC)
 * Voting for this will be open for at least 1 month or 3 affirmative votes before i post the new links to appropriate sections Jethero 20:48, 1 April 2007 (UTC)
 * Voting for this will be open for at least 1 month or 3 affirmative votes before i post the new links to appropriate sections Jethero 20:48, 1 April 2007 (UTC)
 * Voting for this will be open for at least 1 month or 3 affirmative votes before i post the new links to appropriate sections Jethero 20:48, 1 April 2007 (UTC)
 * Voting for this will be open for at least 1 month or 3 affirmative votes before i post the new links to appropriate sections Jethero 20:48, 1 April 2007 (UTC)
 * Voting for this will be open for at least 1 month or 3 affirmative votes before i post the new links to appropriate sections Jethero 20:48, 1 April 2007 (UTC)

Internal Links to Conferences
These internal links to bioinformatics related conferences were added by User:Kevin.cohen without any discussion (at least that I can see). Keep or no? -Cquan (talk, AMA Desk) 05:40, 26 April 2007 (UTC)
 * Conferences
 * Pacific Symposium on Biocomputing
 * keep for PSB as the article has some noteworthy information not immediately available on the conference website. PSB is a major conference for researchers in this field. If added, goes under 'see also', not 'external links' JetheroTalk 05:54, 26 April 2007 (UTC)


 * Intelligent Systems for Molecular Biology
 * remove for ISMB as the article is not noteworthy (for now). ISMB is a major conference for researchers in this field. If added, goes under 'see also', not 'external links' JetheroTalk 05:54, 26 April 2007 (UTC)

Internal Links
Programming language supporting Including: BioJava, BioPerl, BioPython and BioRuby etc. See Open Bioinformatics Foundation for details.
 * Personally, this looks like internal spam. No add. Cquan (after the beep...) 01:07, 24 July 2007 (UTC)

Removal of research lab links
I don't think that every research group out there should be linked in this article. If we list every lab doing bioinformatics work, the list will grow out of hand quickly (I'm guessing easily a thousand labs worldwide). I propose removing individual research groups from the article. Perhaps they can be listed elsewhere? Agree/Disagree? Spin2cool 01:07, 29 July 2006 (UTC)
 * Kind of Disagree, I wouldn't mind this section to be moved to a new article with a link from bioinformatics article, but the content is worth of wikipedia, providing some clean up. There are few dead links and pages linked to that do not contain much. In addition, there is a confusion between research groups who actually publish some work and/or develop some bioinformatics applications or servers and groups only providing technical support in bioinformatics for their institution but do not contribute per se to the field, the latter should not be linked here. The problem is that, many research groups often provide some level of bioinformatics support. Good luck to anyone who volunteers cleaning up. Blastwizard 08:26, 29 July 2006 (UTC)


 * Agree WP is not a directory. WP recommends using dmoz for external links instead Open Directory Project Jethero 20:38, 1 April 2007 (UTC)

Molecular Station Bioinformatics
Is there a reason Molecular Station Bioinformatics is being removed as link spam? The site is the biggest bioinformatics portal right now with over 800 links.

(link removed to foil search-engine optimization)
 * see User_talk:Alan_Au for my response --Alan Au 23:30, 17 February 2006 (UTC)

I believe there are wikipedia users that are against this site as they may be webmasters of competing sites. I will report you to the wikipedia authorities as myself and others have been posting relevant, informative information and some links some of which include Molecular Station. I contributed RNA Bioinformatics information which was deleted by the user Alan Au on the basis of the fact that it is not accepted by the general scientific community. He "looked this up" on PubMed (meaning he has no idea about bioinformatics - as everyone knows about RNA bioinformatics). He searched for "RNA Bioinformatics" on PubMed (I am posting this to "optimize" PubMed). A search for "Protein Bioinformatics" yields 6 hits, of which even any summer student in science would know is relevant to hundreds of thousands of scientific articles. Wikipedia sadly is not an informative source due to the actions of a small group of individuals which have a power trip editing others contributions. For all we know a new user could be a Professor, whereas the user Alan Au could be a high school student, which seems the case as he never even knew RNA Bioinformatics existed. A few relevant RNA bioinformatics sources which prove the degree of "acceptance by the scientific community": RNA Bioinformatics Presentation RNA World RNA World

RNA biocomputing and bioinformatics is relevant to the study of RNA, Viruses, Translational Regulation and Splicing.: RNA Folding and Secondary Structure prediction(example M-fold), RNAi prediction and siRNA design, rRNA/tRNA gene prediction, RNA domain analysis. -- Bioinformin
 * Please see User_talk:Bioinformin for my response. --Alan Au 04:57, 5 March 2006 (UTC)

Removed external link to bioinformatics.net
I'm a newcomer to this page, but I saw it flagged at WP:WPSPAM, courtesy of the tag. The only link that looked at all dubious was bioinformatics.net, so I removed it, and the cleanup-spam tag as well. The front page of bioinformatics.net does look like a link farm, though it's conceivable someone might find it useful. That site is a redirect to bioinformatics.vg, a domain belonging to the Virgin Islands, the well-known hub of bioinformatics research. There is no reference to bioinformatics.net in the present article. If there is a reason to keep the link, please discuss here. EdJohnston 22:52, 29 December 2006 (UTC)

Links moved from article

 * 1)  http: //www.ensembl.org Ensembl Genome Browser
 * 2)  http: //genome.ucsc.edu UCSC Bioinformatics Site
 * 3)  http: //www.genome.gov/10005107#10 ENCODE project

Directories &amp; portals
I removed this section from the article, since it seems like an invitation to add linkspam. However, I've copied it here for the moment, on the off chance enough people want to put it back into the article. --Alan Au 08:24, 4 February 2006 (UTC)
 * http: //www.bioinformatics.ca/ Bioinformatics.ca: a portal to bioinformatics activities in Canada
 * http: //www.bioinformatics.vg/ Bioinformatics.net: software tools directory
 * http: //www.colorbasepair.com/ ColorBasePair.com: a bioinformatics portal
 * http: //www.genefinding.org/ GeneFinding.Org: directory of gene finding systems and related tools

Moved comments from 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)

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)

genetic algorithms
Than genetic algorithms is the opposite of computational evolutionary biology seems a little bit odd to me, as the genetic algorithm was merly inspired by (schoolbook) biology, and have very little to do wiyh biology except for the name (and the fact that it often occures in the bioinformatics literature for solving difficult problems, probably partly because of the name), since it in fact has nothing to do with biology.

bioinformatics VS computational biology
The terms bioinformatics and computational biology are often used interchangeably, although the latter typically focuses on algorithm development and specific computational methods.

Shouldn't that be the former rather than the latter??? &mdash;The preceding unsigned comment was added by 136.206.1.17 (talk &bull; contribs) 17:13, 19 September 2005.
 * I personally consider latter to be correct, as algorithm development is typically considered the core of computational biology. --Alan Au 19:57, 21 September 2005 (UTC)