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Above undated message substituted from Template:Dashboard.wikiedu.org assignment by PrimeBOT ( talk) 15:46, 16 January 2022 (UTC)
In the introduction, we read the following:
...the development of new algorithms (mathematical formulas) and statistics...
I am not a Computer scientist, but I think an algorithm is not a mathematical formula. Furthermore, I don't think one develops statistics, one applies statistcal methods or a theoretical scientist might develop new statistical theories. —Preceding unsigned comment added by 88.67.52.3 ( talk) 12:48, 23 January 2011 (UTC)
You spelled Gnome incorrectly —Preceding unsigned comment added by Henriettaminge ( talk • contribs)
Members of the Wikipedia:WikiProject Good articles are in the process of doing a re-review of current Good Article listings to ensure compliance with the standards of the Good Article Criteria. (Discussion of the changes and re-review can be found here). A significant change to the GA criteria is the mandatory use of some sort of in-line citation (In accordance to WP:CITE) to be used in order for an article to pass the verification and reference criteria. Currently this article does not include in-line citations. It is recommended that the article's editors take a look at the inclusion of in-line citations as well as how the article stacks up against the rest of the Good Article criteria. GA reviewers will give you at least a week's time from the date of this notice to work on the in-line citations before doing a full re-review and deciding if the article still merits being considered a Good Article or would need to be de-listed. If you have any questions, please don't hesitate to contact us on the Good Article project talk page or you may contact me personally. On behalf of the Good Articles Project, I want to thank you for all the time and effort that you have put into working on this article and improving the overall quality of the Wikipedia project. LuciferMorgan 02:20, 16 December 2006 (UTC)
I just realized that Whole Genome Shotgun Sequencing and sequence assembly is really considered an informatics solution to the sequencing problem compared to BAC for large sections of DNA. This might be an important accomplishment of bioinformatics to mention. 128.206.82.56 ( talk) 19:46, 23 April 2009 (UTC)done
Much of this discussion and page deals with trying to describe what bioinformatics is by either enumerating it's parts, or defining it in contrast to something else, like 'computational biology' (or trying to insist they are the same thing). The remainder of the page tends to be a battle between people adding thier favourite legitimate bioinformatics resources, tools, publications, centres, and others trying to trip them down (because of WP:NOT#DIRECTORY and spam)
I don't have an exact quote, or a reference as it was presented during a talk, but this very rough paraphrase might start us thinking about this page in a slightly different way.
-- Jethero 05:46, 23 February 2007 (UTC)
From this, I think we might be able to find a focus or thread through some of the content, and perhaps a way of identifying what have been core 'bioinformatics' breakthroughs, versus what are areas and fields and disciplines that simply make use of computers and computational methods and expertise, or focus on lists of people, books or software that call themselves 'bioinformatics'. (To be clear, I am not saying these things are not bioinformatics, in a broad sense)
To go along with this, I would propose that we:
Take a look at some of the other Natural Sciences pages for inspiration, or vote on the proposals above. -- Jethero 05:46, 23 February 2007 (UTC)
The LEAD is awful. The references are not in WP standard form. There is a huge internal and external link farm. There are too many redlinks. It includes too much unreadable text for the beginning reader. I suggest that an introductory article be made, called Introduction to bioinformatics, as was done at evolution, quantum mechanics, general relativity and other technical science articles.-- Filll 13:19, 26 July 2007 (UTC)
Please insert references that support the following claim: "The term bioinformatics was coined by Paulien Hogeweg in 1978 for the study of informatic processes in biotic systems". I was searching for them and I did not find any. —Preceding unsigned comment added by Daforerog ( talk • contribs) 14:28, 17 February 2009 (UTC)
This article is now at Good Article Review for possible delisting of its Good Article status. Concerns are listed at the good article review page. Please remember to assume good faith and improve the article to meet the Good Article criteria. - Malkinann 10:07, 26 July 2007 (UTC)
This article has been delisted per consensus at WP:GA/R. The discussion, now in archive, can be seen here. Once the article is brought up to standards, it may be renominated at WP:GAC. Regards, Lara ♥Love 15:19, 7 August 2007 (UTC)
Please give your opinion on the {{ External links}} cleanup tag that was just added. From my limited personal knowledge, the items that are now listed under 'major organizations' and 'major journals' do in fact appear to be major ones for this field. At the recent GA review, no-one complained that there were too many external links in the article. Comments? EdJohnston 21:24, 21 August 2007 (UTC)
I recently submitted Bio-IT World for inclusion as a major journal in the field of bioinformatics, and hope that the editors of this post consider its value as an industry resource. Bio-ITWorld ( talk) 17:56, 30 October 2008 (UTC)
I think "computational docking" and "protein structure prediction" belongs to "Modeling of biological systems". Should it be placed there? Biophys ( talk) 01:55, 3 July 2008 (UTC)
Bioinformatics is also here to put some light on catabolic and anabolic pathways which are usually coded in the genes. How about documenting it explicitly folks? -- 84.157.227.183 ( talk) 09:35, 25 July 2008 (UTC)
Recently, an editor added a link here to a List of bioinformatics companies. It seems perfectly reasonable to maintain such a list, but my fear is that it may accumulate spam, or to speak more delicately, it may attract 'less notable entries, added by company representatives.' Part of the problem is this preamble to the list:
The primary purpose of this list is to serve as a holding place for the identities of Bioinformatics companies, particularly those for which articles have not yet been created.
I have suggested over at Talk:List of bioinformatics companies that the list should *exclude* the companies that do not have articles. I'd welcome any comments on that article's talk page, either pro or con. EdJohnston ( talk) 15:35, 14 August 2008 (UTC)
I have removed the following:
This was placed under "Analysis of gene expression" and does not match that topic. Please see the section on "Genome annotation" and improve that if you think it needs additional information.
Also:
This appears to be an "introduction" - it reads like the introduction to a student essay. The article already has a lead, you might consider making an addition there but I don't see what this contributes. I don't think adding a list of databases is appropriate without a relevant reference since it is biased - it's just what one writer thinks is useful for his own research.
— Preceding unsigned comment added by Madeleine Price Ball ( talk • contribs) 06:11, 23 September 2009
I'm not sure, but does the description of Genome annotation appear once at the end of the sequence analysis section, and then in its own section? Seems like a repeat.-- 92.2.233.95 ( talk) 17:10, 4 February 2012 (UTC)
"Bioinformatics is the application of information technology to the field of molecular biology. "
We currently are applying information technology to the field of (bological) taxonomy, and will be including profile data. Perhaps this definition might be made broader?
Reference [1] "Bioinformatics Journal" seems a bit vague, as the page it directs to has none of the information cited in the Introduction. Anybody have any thoughts on this? gzur ( talk) 13:28, 22 September 2011 (UTC)
The start of the article has THREE lines of subject areas! I don't think this is necessary and it can (and is) summed up before it with "computer science." — Preceding unsigned comment added by 68.9.159.72 ( talk) 05:30, 29 October 2011 (UTC)
I propose to add the International Society for Computational Biology as an external link ( http://www.iscb.org/). I think that this is the major society for the field that organises one of the largest conferences. Please let me know if you think this is innappropriate. Alexbateman ( talk) 16:58, 29 February 2012 (UTC)
The Introduction section seems long, rambling and somewhat repetitive. It could probably be improved by splitting into subsections, such as "History", "Approaches to modeling", etc. -- Mark viking ( talk) 06:05, 3 February 2013 (UTC)
I suggest to reorganize this article by replacing the Major Research areas heading. Instead, I would group the existing sections into the following groups: (1) sequence analysis, (2) Gene and protein expression, (3) Regulation and networks, (4) Structural bioinformatics, i.e. using molecular structures, docking etc., (5) Text mining, (6) Image analysis, (7) Others (not sure if this is needed at this point but it may be later). All existing sections can be sorted into one of these groups. This will make navigation easier. If no one objects I will go ahead and reorganize things by mid February or so. Peteruetz ( talk) 20:09, 30 January 2014 (UTC)
A few things I noticed (this may turn into a longer list):
I think one thing that is badly needed is determining, obviously based on WP:RS, a clear and restrictive definition of what is and isn't part of bioinformatics, otherwise this article will continue to devolve into a series of "me too" sections. Samsara ( FA • FP) 09:31, 27 August 2014 (UTC)
I think these deserve to be mentioned somewhere. They were featured prominently at the last RECOMB conference. — Preceding unsigned comment added by Djh901 ( talk • contribs) 20:07, 24 July 2016 (UTC)
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This edit request by an editor with a conflict of interest has now been answered. |
Here I am writing to propose a change to this page that I believe to be appropriate and factual, but I am disclosing my COI, namely that I lead the development of BioCyc, and am paid to work on BioCyc by the institution that employs me (they have not directed me specifically to modify this page). Many peer-reviewed articles have been published about BioCyc, so I have no problem with peer-review of my Wikipedia contribution. The most recent article is: https://www.ncbi.nlm.nih.gov/pubmed/26527732. I also note that a Google search of "Metabolic Pathways" includes both KEGG and MetaCyc (one of the BioCyc databases) right after each other on the first page. You will note I have also made some other changes to the page to suggest additional databases that are among the most highly used databases in the bioinformatics field and not listing them is a great omission.
I'm proposing to add BioCyc as well as KEGG in the listing of metabolic pathway databases, as so. BioCyc and KEGG are both highly used databases in the field, as anyone in the field knows.
Used in Network Analysis: Metabolic Pathway Databases ( KEGG, BioCyc), Interaction Analysis Databases, Functional Networks
This is the
talk page for discussing improvements to the
Bioinformatics article. This is not a forum for general discussion of the article's subject. |
Article policies
|
Find medical sources: Source guidelines · PubMed · Cochrane · DOAJ · Gale · OpenMD · ScienceDirect · Springer · Trip · Wiley · TWL |
Archives: 1 |
Bioinformatics is a former featured article. Please see the links under Article milestones below for its original nomination page (for older articles, check the nomination archive) and why it was removed. | ||||||||||||||||||||||
This article appeared on Wikipedia's Main Page as Today's featured article on March 28, 2004. | ||||||||||||||||||||||
|
Rosalind (education) was nominated for deletion. The discussion was closed on 11 February 2013 with a consensus to merge. Its contents were merged into Bioinformatics. The original page is now a redirect to this page. For the contribution history and old versions of the redirected article, please see its history; for its talk page, see here. |
This
level-5 vital article is rated C-class on Wikipedia's
content assessment scale. It is of interest to the following WikiProjects: | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
|
Text and/or other creative content from this version of Bioinformatics was copied or moved into Life sciences with this edit. The former page's history now serves to provide attribution for that content in the latter page, and it must not be deleted as long as the latter page exists. |
Daily pageviews of this article
A graph should have been displayed here but
graphs are temporarily disabled. Until they are enabled again, visit the interactive graph at
pageviews.wmcloud.org |
A summary of this article appears in Computational biology. |
A summary of this article appears in DNA. |
The Wikimedia Foundation's Terms of Use require that editors disclose their "employer, client, and affiliation" with respect to any paid contribution; see WP:PAID. For advice about reviewing paid contributions, see WP:COIRESPONSE. |
This page has been cited as a
source by a notable professional or academic publication: Harvard Journal of Law & Technology |
This article is or was the subject of a Wiki Education Foundation-supported course assignment. Further details are available on the course page. Student editor(s): Heatherjanee.
Above undated message substituted from Template:Dashboard.wikiedu.org assignment by PrimeBOT ( talk) 15:46, 16 January 2022 (UTC)
In the introduction, we read the following:
...the development of new algorithms (mathematical formulas) and statistics...
I am not a Computer scientist, but I think an algorithm is not a mathematical formula. Furthermore, I don't think one develops statistics, one applies statistcal methods or a theoretical scientist might develop new statistical theories. —Preceding unsigned comment added by 88.67.52.3 ( talk) 12:48, 23 January 2011 (UTC)
You spelled Gnome incorrectly —Preceding unsigned comment added by Henriettaminge ( talk • contribs)
Members of the Wikipedia:WikiProject Good articles are in the process of doing a re-review of current Good Article listings to ensure compliance with the standards of the Good Article Criteria. (Discussion of the changes and re-review can be found here). A significant change to the GA criteria is the mandatory use of some sort of in-line citation (In accordance to WP:CITE) to be used in order for an article to pass the verification and reference criteria. Currently this article does not include in-line citations. It is recommended that the article's editors take a look at the inclusion of in-line citations as well as how the article stacks up against the rest of the Good Article criteria. GA reviewers will give you at least a week's time from the date of this notice to work on the in-line citations before doing a full re-review and deciding if the article still merits being considered a Good Article or would need to be de-listed. If you have any questions, please don't hesitate to contact us on the Good Article project talk page or you may contact me personally. On behalf of the Good Articles Project, I want to thank you for all the time and effort that you have put into working on this article and improving the overall quality of the Wikipedia project. LuciferMorgan 02:20, 16 December 2006 (UTC)
I just realized that Whole Genome Shotgun Sequencing and sequence assembly is really considered an informatics solution to the sequencing problem compared to BAC for large sections of DNA. This might be an important accomplishment of bioinformatics to mention. 128.206.82.56 ( talk) 19:46, 23 April 2009 (UTC)done
Much of this discussion and page deals with trying to describe what bioinformatics is by either enumerating it's parts, or defining it in contrast to something else, like 'computational biology' (or trying to insist they are the same thing). The remainder of the page tends to be a battle between people adding thier favourite legitimate bioinformatics resources, tools, publications, centres, and others trying to trip them down (because of WP:NOT#DIRECTORY and spam)
I don't have an exact quote, or a reference as it was presented during a talk, but this very rough paraphrase might start us thinking about this page in a slightly different way.
-- Jethero 05:46, 23 February 2007 (UTC)
From this, I think we might be able to find a focus or thread through some of the content, and perhaps a way of identifying what have been core 'bioinformatics' breakthroughs, versus what are areas and fields and disciplines that simply make use of computers and computational methods and expertise, or focus on lists of people, books or software that call themselves 'bioinformatics'. (To be clear, I am not saying these things are not bioinformatics, in a broad sense)
To go along with this, I would propose that we:
Take a look at some of the other Natural Sciences pages for inspiration, or vote on the proposals above. -- Jethero 05:46, 23 February 2007 (UTC)
The LEAD is awful. The references are not in WP standard form. There is a huge internal and external link farm. There are too many redlinks. It includes too much unreadable text for the beginning reader. I suggest that an introductory article be made, called Introduction to bioinformatics, as was done at evolution, quantum mechanics, general relativity and other technical science articles.-- Filll 13:19, 26 July 2007 (UTC)
Please insert references that support the following claim: "The term bioinformatics was coined by Paulien Hogeweg in 1978 for the study of informatic processes in biotic systems". I was searching for them and I did not find any. —Preceding unsigned comment added by Daforerog ( talk • contribs) 14:28, 17 February 2009 (UTC)
This article is now at Good Article Review for possible delisting of its Good Article status. Concerns are listed at the good article review page. Please remember to assume good faith and improve the article to meet the Good Article criteria. - Malkinann 10:07, 26 July 2007 (UTC)
This article has been delisted per consensus at WP:GA/R. The discussion, now in archive, can be seen here. Once the article is brought up to standards, it may be renominated at WP:GAC. Regards, Lara ♥Love 15:19, 7 August 2007 (UTC)
Please give your opinion on the {{ External links}} cleanup tag that was just added. From my limited personal knowledge, the items that are now listed under 'major organizations' and 'major journals' do in fact appear to be major ones for this field. At the recent GA review, no-one complained that there were too many external links in the article. Comments? EdJohnston 21:24, 21 August 2007 (UTC)
I recently submitted Bio-IT World for inclusion as a major journal in the field of bioinformatics, and hope that the editors of this post consider its value as an industry resource. Bio-ITWorld ( talk) 17:56, 30 October 2008 (UTC)
I think "computational docking" and "protein structure prediction" belongs to "Modeling of biological systems". Should it be placed there? Biophys ( talk) 01:55, 3 July 2008 (UTC)
Bioinformatics is also here to put some light on catabolic and anabolic pathways which are usually coded in the genes. How about documenting it explicitly folks? -- 84.157.227.183 ( talk) 09:35, 25 July 2008 (UTC)
Recently, an editor added a link here to a List of bioinformatics companies. It seems perfectly reasonable to maintain such a list, but my fear is that it may accumulate spam, or to speak more delicately, it may attract 'less notable entries, added by company representatives.' Part of the problem is this preamble to the list:
The primary purpose of this list is to serve as a holding place for the identities of Bioinformatics companies, particularly those for which articles have not yet been created.
I have suggested over at Talk:List of bioinformatics companies that the list should *exclude* the companies that do not have articles. I'd welcome any comments on that article's talk page, either pro or con. EdJohnston ( talk) 15:35, 14 August 2008 (UTC)
I have removed the following:
This was placed under "Analysis of gene expression" and does not match that topic. Please see the section on "Genome annotation" and improve that if you think it needs additional information.
Also:
This appears to be an "introduction" - it reads like the introduction to a student essay. The article already has a lead, you might consider making an addition there but I don't see what this contributes. I don't think adding a list of databases is appropriate without a relevant reference since it is biased - it's just what one writer thinks is useful for his own research.
— Preceding unsigned comment added by Madeleine Price Ball ( talk • contribs) 06:11, 23 September 2009
I'm not sure, but does the description of Genome annotation appear once at the end of the sequence analysis section, and then in its own section? Seems like a repeat.-- 92.2.233.95 ( talk) 17:10, 4 February 2012 (UTC)
"Bioinformatics is the application of information technology to the field of molecular biology. "
We currently are applying information technology to the field of (bological) taxonomy, and will be including profile data. Perhaps this definition might be made broader?
Reference [1] "Bioinformatics Journal" seems a bit vague, as the page it directs to has none of the information cited in the Introduction. Anybody have any thoughts on this? gzur ( talk) 13:28, 22 September 2011 (UTC)
The start of the article has THREE lines of subject areas! I don't think this is necessary and it can (and is) summed up before it with "computer science." — Preceding unsigned comment added by 68.9.159.72 ( talk) 05:30, 29 October 2011 (UTC)
I propose to add the International Society for Computational Biology as an external link ( http://www.iscb.org/). I think that this is the major society for the field that organises one of the largest conferences. Please let me know if you think this is innappropriate. Alexbateman ( talk) 16:58, 29 February 2012 (UTC)
The Introduction section seems long, rambling and somewhat repetitive. It could probably be improved by splitting into subsections, such as "History", "Approaches to modeling", etc. -- Mark viking ( talk) 06:05, 3 February 2013 (UTC)
I suggest to reorganize this article by replacing the Major Research areas heading. Instead, I would group the existing sections into the following groups: (1) sequence analysis, (2) Gene and protein expression, (3) Regulation and networks, (4) Structural bioinformatics, i.e. using molecular structures, docking etc., (5) Text mining, (6) Image analysis, (7) Others (not sure if this is needed at this point but it may be later). All existing sections can be sorted into one of these groups. This will make navigation easier. If no one objects I will go ahead and reorganize things by mid February or so. Peteruetz ( talk) 20:09, 30 January 2014 (UTC)
A few things I noticed (this may turn into a longer list):
I think one thing that is badly needed is determining, obviously based on WP:RS, a clear and restrictive definition of what is and isn't part of bioinformatics, otherwise this article will continue to devolve into a series of "me too" sections. Samsara ( FA • FP) 09:31, 27 August 2014 (UTC)
I think these deserve to be mentioned somewhere. They were featured prominently at the last RECOMB conference. — Preceding unsigned comment added by Djh901 ( talk • contribs) 20:07, 24 July 2016 (UTC)
Hello fellow Wikipedians,
I have just modified 2 external links on Bioinformatics. Please take a moment to review my edit. If you have any questions, or need the bot to ignore the links, or the page altogether, please visit this simple FaQ for additional information. I made the following changes:
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regular verification using the archive tool instructions below. Editors
have permission to delete these "External links modified" talk page sections if they want to de-clutter talk pages, but see the
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Cheers.— InternetArchiveBot ( Report bug) 22:54, 2 November 2016 (UTC)
This edit request by an editor with a conflict of interest has now been answered. |
Here I am writing to propose a change to this page that I believe to be appropriate and factual, but I am disclosing my COI, namely that I lead the development of BioCyc, and am paid to work on BioCyc by the institution that employs me (they have not directed me specifically to modify this page). Many peer-reviewed articles have been published about BioCyc, so I have no problem with peer-review of my Wikipedia contribution. The most recent article is: https://www.ncbi.nlm.nih.gov/pubmed/26527732. I also note that a Google search of "Metabolic Pathways" includes both KEGG and MetaCyc (one of the BioCyc databases) right after each other on the first page. You will note I have also made some other changes to the page to suggest additional databases that are among the most highly used databases in the bioinformatics field and not listing them is a great omission.
I'm proposing to add BioCyc as well as KEGG in the listing of metabolic pathway databases, as so. BioCyc and KEGG are both highly used databases in the field, as anyone in the field knows.
Used in Network Analysis: Metabolic Pathway Databases ( KEGG, BioCyc), Interaction Analysis Databases, Functional Networks