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 |
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:
1.the application of biological models or processes in structuring computer programs or programming; the emulation of biological processes or environments in computer programming |
2.the application of computing in researching biological topics; the statistical analysis of biological data |
3.Source: Webster's New Millennium™ Dictionary of English, Preview Edition (v 0.9.6)Copyright © 2003-2005 Lexico Publishing Group, LLC |
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)
This page is, or should be:
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
There are several suggestions made when this page was removed as a featured article, and these are the areas that we should improve:
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)
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)
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)
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
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?
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)
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)
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)
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)
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)
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?
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 <application> 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)
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)
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)
Not moved - violet/riga (t) 20:49, 4 Mar 2005 (UTC)
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:
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)
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).
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)
Programming language supporting Including: BioJava, BioPerl, BioPython and BioRuby etc. See Open Bioinformatics Foundation for details.
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)
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)
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
I'm a newcomer to this page, but I saw it flagged at WP:WPSPAM, courtesy of the {{Cleanup-spam}} 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)
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)
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)
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.
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??? —The preceding unsigned comment was added by 136.206.1.17 ( talk • contribs) 17:13, 19 September 2005.
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 |
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:
1.the application of biological models or processes in structuring computer programs or programming; the emulation of biological processes or environments in computer programming |
2.the application of computing in researching biological topics; the statistical analysis of biological data |
3.Source: Webster's New Millennium™ Dictionary of English, Preview Edition (v 0.9.6)Copyright © 2003-2005 Lexico Publishing Group, LLC |
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)
This page is, or should be:
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
There are several suggestions made when this page was removed as a featured article, and these are the areas that we should improve:
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)
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)
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)
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
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?
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)
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)
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)
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)
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)
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?
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 <application> 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)
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)
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)
Not moved - violet/riga (t) 20:49, 4 Mar 2005 (UTC)
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:
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)
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).
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)
Programming language supporting Including: BioJava, BioPerl, BioPython and BioRuby etc. See Open Bioinformatics Foundation for details.
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)
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)
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
I'm a newcomer to this page, but I saw it flagged at WP:WPSPAM, courtesy of the {{Cleanup-spam}} 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)
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)
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)
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.
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??? —The preceding unsigned comment was added by 136.206.1.17 ( talk • contribs) 17:13, 19 September 2005.