Talk:Bioinformatics

Introduction

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)

I think you are correct. Though I have seen the assignment operator confused a number of times with the equality symbol or logical syllogism etc. Maybe it should read "... the development of new algorithms which apply mathematical formulas and statistical models to ..."

Comedy?

You spelled Gnome incorrectly —Preceding unsigned comment added by Henriettaminge (talk • contribs)

• I don't know if you're trying to be serious, but the word is 'genome'. ju66l3r 06:35, 20 July 2006 (UTC)

GA Re-Review and In-line citations

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)

Whole Genome Shotgun Sequencing

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

• Yes. Whole Genome Shotgun (WGS) sequencing projects constitute the largest part (in terms of bp size) of GenBank. It is very much a bioinformatics approach and, as such, should be mentioned in this article. When I have some more time, I will add some information. --Thorwald (talk) 04:52, 24 April 2009 (UTC)
  • You might consider adding next generation sequencing information. Huge challenge at the moment.193.190.172.82 (talk) 17:39, 11 May 2009 (UTC)
    • I would prefer it be called "High throughput" rather than "next generation", "next generation" seems like a dated term. Will there be yet another generation. High throughput sequencing seems more meaningful, this term may be outgrown as well, but it may weather better than "next generation". —Preceding unsigned comment added by 128.206.82.56 (talk) 21:48, 28 July 2009 (UTC)

Insight from Michael Watterman and proposed changes

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.

Every major advancement in the field of Bioinformatics is a direct result of a new type of data being generated, from a real experiment, which is in a form or volume that we did not yet have the capability of understanding. Then there is a scramble to understand this new data. Once the new tools are available, there is only so far you can go with the existing data. Eventually, there is another new experiment done, and a new type of data emerges. -- MICHAEL WATERMAN, University of Southern California in a lecture at ISMB2006, Fortaleza

I don't know if I necessarily agree. I think the example above is shotgun sequencing, which was primarily a bioinformatic improvment on previous sequencing capabilities. Was it a bioinformatics break through or laboratory break through. I also doubt it was Michael Waterman who said that, since he was trained as a physicist. 128.206.82.56 (talk) 22:01, 16 July 2009 (UTC)done

-- 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:

• remove all current 'references' that are not used as inline citations (move them to a 'list of books' if we want). It's almost impossible to remain NPOV and exclude some books and papers and not others. -- Jethero 05:46, 23 February 2007 (UTC)

• remove all external links, move them to the 'list of bioinformatics research groups' or a similar page and have a policy of no external links (unless they are inline citations). They invite spam, and also legitimate additions that we don't have room for but can't eliminate without violating NPOV or upsetting a fan -- Jethero 05:46, 23 February 2007 (UTC)

• continue to remove all software references (move them to a list of bioinformatics software if we want). same arguments -- Jethero 05:46, 23 February 2007 (UTC)

• remove all but the slightest trace of the 'computational biology vs. bioinformatics' debate from the top. The intro paragraph is much too long, compared to other 'dispiplines of science' pages, and confusing for someone not familiar with either term. -- Jethero 05:46, 23 February 2007 (UTC)

• set up sections which encourage additions of names and dates in bioinformatics (famous bioinformaticians, watersheds, large projects in the past) -- Jethero 05:46, 23 February 2007 (UTC)

• the field develops rapidly, but we don't yet have the perspective to neutrally call paper/tool/discovery A more important that B, so we should focus on things that have been established as 'notable' in the past, say 5+ years, and get that right. This is another way to avoid the article reading like it should contain a list of tools and resources that are relevant today. (NCBI's GenBank, established in 19xx, was critical for xxxx rather that just a link) -- Jethero 05:46, 23 February 2007 (UTC)

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)

Suggestions

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 seems like a very good idea. —Preceding unsigned comment added by 204.134.43.129 (talk) 22:10, 22 April 2011 (UTC)

Good Article Review

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)

Editors can go to Wikipedia:Good article review#Bioinformatics to see what others have written, and to add their own comments. In that review, someone has already suggested making an introductory article. I can see us needing Introduction to general relativity because of the profundity of that topic, but Introduction to bioinformatics seems like overkill. Making the article better would eliminate the need for such an introduction. EdJohnston 15:58, 26 July 2007 (UTC)

If there was a firm committment to augment this article with much more explanatory material, this would obviate the need for an introductory article. This article is currently short enough that probably both advanced and introductory material could be accommodated in the same article.--Filll 16:00, 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)

Does the External Links section need cleanup?

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)

No, first and foremost this is self promotion and is therefore ethically wrong, second I have been working in bioinformatics for ten years now and I never heard of your journal, so I doubt it is a major journal in the field. Looking at the website, it doesn't look like a peer reviewed scientific publications journal, but more a sort of business advertising thingy irrelevant to Bioinformatics article. Blastwizard (talk) 09:58, 31 October 2008 (UTC)

Modeling

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)

I would agree since people in those fields in consuming bioinformatics generally make no pretense of contributing to algorithmic understanding of biological data. Specifically protein structure predictions usually are only concerned with a single molecule of significance and likewise with protein docking interfaces and the algorithms for these tasks seldom scale to large databases. 69.29.27.17 (talk) 02:09, 5 March 2009 (UTC)OK

Metabolic Pathways

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)

Spam concern about List of bioinformatics companies

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)

Out of place material

I have removed the following:

Gene finding typically refers to the area of computational biology that is concerned with algorithmically identifying stretches of sequence, usually genomic DNA, that are biologically functional. This especially includes protein-coding genes, but may also include other functional elements such as RNA genes and regulatory regions. Gene finding is one of the first and most important steps in understanding the genome of a species once it has been sequenced.

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:

Bioinformatics is the rapidly growing and developing field in computational science era. The major databases which are useful for life science research are NCBI, DDBJ, EMBL, TIGR, PDB, SWISS-PROT and TrEMBL. These databases are public databases, conduct research in computational biology, and develop software tools for analyzing genome and rpoteome data. With the rapidly emergence and vast development of this field, it has the bright perspectives in upcoming decades.[11]

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.

[the above was unsigned]

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)

Definition

"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?

I am not so sure.

What kind of profile data do you have? Bobthefish2 (talk) 05:25, 20 February 2011 (UTC)

Oh my bad.. it seems this post was made ages ago. Bobthefish2 (talk) 05:27, 20 February 2011 (UTC)

Vague reference

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)

Deleted it and the sentence it tagged, which was so broad as to be meaningless. I guess this talk page section serves as a record that Bioinformatics Journal might be a resource for expanding the article. --Danger (talk) 13:53, 22 September 2011 (UTC)

Start of Article

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)

Propose to add ISCB to external links

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)