Bioinformatics: Difference between revisions

Revision as of 12:00, 15 September 2024

Revision as of 18:44, 27 October 2024

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== History ==

The first definition of the term ''bioinformatics'' was coined by [[Paulien Hogeweg]] and [[Ben Hesper]] in 1970, to refer to the study of information processes in biotic systems.<ref>{{cite journal |last1=Ouzounis |first1=C. A. |last2=Valencia |first2=A. |date=2003 |title=Early bioinformatics: the birth of a discipline—a personal view |journal=Bioinformatics |volume=19 |issue=17 |pages=2176–2190 | pmid=14630646 | doi=10.1093/bioinformatics/btg309| doi-access=free}}</ref><ref name="Hogeweg2011">{{cite journal |vauthors=Hogeweg P |title=The Roots of Bioinformatics in Theoretical Biology |journal=PLOS Computational Biology |volume=7 |issue=3 |pages=e1002021 |date=2011 |pmid=21483479 |pmc=3068925 | doi=10.1371/journal.pcbi.1002021 | bibcode = 2011PLSCB...7E2021H | doi-access = free }}</ref><ref>{{Cite journal| vauthors = Hesper B, Hogeweg P |year=1970|title=BIO-INFORMATICA: een werkconcept |trans-title=BIO-INFORMATICS: a working concept |language=nl |journal=Het Kameleon|volume=1 |issue=6| pages=28–29}}</ref><ref>{{cite arXiv |vauthors=Hesper B, Hogeweg P |eprint=2111.11832v1 |title=Bio-informatics: a working concept. A translation of "Bio-informatica: een werkconcept" by B. Hesper and P. Hogeweg |date=2021 |class=q-bio.OT}}</ref><ref>{{cite journal |vauthors = Hogeweg P |title=Simulating the growth of cellular forms |journal=Simulation |volume=31 |issue=3 |pages=90–96 |year=1978 |doi=10.1177/003754977803100305 |s2cid=61206099 }}</ref> This definition placed bioinformatics as a field parallel to [[biochemistry]] (the study of chemical processes in biological systems).<ref name="Hogeweg2011" /> A recent article in a peer-reviewed journal provides an interesting brief history of bioinformatics <ref>{{Cite journal |last=Gauthier |first=Jeff |last2=Vincent |first2=Antony T. |last3=Charette |first3=Steve J. |last4=Derome |first4=Nicolas |date=2019-11-27 |title=A brief history of bioinformatics |url=https://pubmed.ncbi.nlm.nih.gov/30084940/ |journal=Briefings in Bioinformatics |volume=20 |issue=6 |pages=1981–1996 |doi=10.1093/bib/bby063 |issn=1477-4054 |pmid=30084940}}</ref>

Bioinformatics and computational biology involved the analysis of biological data, particularly DNA, RNA, and protein sequences. The field of bioinformatics experienced explosive growth starting in the mid-1990s, driven largely by the [[Human Genome Project]] and by rapid advances in DNA sequencing technology.{{cn|date=May 2024}}

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==Software and tools==

[[List of bioinformatics software|Software tools for bioinformatics]] include simple command-line tools, more complex graphical programs, and standalone web-services. They are made by [[bioinformatics companies]] or by public institutions. Every year, the scientific journal ''Nucleic Acids Research'' publish special issues on databases <ref>{{Cite journal |last=Rigden |first=Daniel J. |last2=Fernández |first2=Xosé M. |date=2024-01-05 |title=The 2024 Nucleic Acids Research database issue and the online molecular biology database collection |url=https://pubmed.ncbi.nlm.nih.gov/38035367/ |journal=Nucleic Acids Research |volume=52 |issue=D1 |pages=D1–D9 |doi=10.1093/nar/gkad1173 |issn=1362-4962 |pmid=38035367}}</ref> and on web servers <ref>{{Cite journal |last=Seelow |first=Dominik |date=2023-07-05 |title=Editorial: the 21st annual Nucleic Acids Research Web Server Issue 2023 |url=https://pubmed.ncbi.nlm.nih.gov/37309890/ |journal=Nucleic Acids Research |volume=51 |issue=W1 |pages=W1–W4 |doi=10.1093/nar/gkad517 |issn=1362-4962 |pmid=37309890}}</ref>.

===Open-source bioinformatics software===

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[[MOOC]] platforms also provide online certifications in bioinformatics and related disciplines, including [[Coursera]]'s Bioinformatics Specialization at the [[University of California, San Diego]], Genomic Data Science Specialization at [[Johns Hopkins University]], and [[EdX]]'s Data Analysis for Life Sciences XSeries at [[Harvard University]].

Several recent articles in international scientific journals have put forward several recommendations for the development of training activities in bioinformatics <ref>{{Cite journal |last=Jjingo |first=Daudi |last2=Mboowa |first2=Gerald |last3=Sserwadda |first3=Ivan |last4=Kakaire |first4=Robert |last5=Kiberu |first5=Davis |last6=Amujal |first6=Marion |last7=Galiwango |first7=Ronald |last8=Kateete |first8=David |last9=Joloba |first9=Moses |last10=Whalen |first10=Christopher C. |date=2022-01-17 |title=Bioinformatics mentorship in a resource limited setting |url=https://pubmed.ncbi.nlm.nih.gov/34591953/ |journal=Briefings in Bioinformatics |volume=23 |issue=1 |pages=bbab399 |doi=10.1093/bib/bbab399 |issn=1477-4054 |pmc=8769693 |pmid=34591953}}</ref> <ref>{{Cite journal |last=Via |first=Allegra |last2=Blicher |first2=Thomas |last3=Bongcam-Rudloff |first3=Erik |last4=Brazas |first4=Michelle D. |last5=Brooksbank |first5=Cath |last6=Budd |first6=Aidan |last7=De Las Rivas |first7=Javier |last8=Dreyer |first8=Jacqueline |last9=Fernandes |first9=Pedro L. |last10=van Gelder |first10=Celia |last11=Jacob |first11=Joachim |last12=Jimenez |first12=Rafael C. |last13=Loveland |first13=Jane |last14=Moran |first14=Federico |last15=Mulder |first15=Nicola |date=2013-09 |title=Best practices in bioinformatics training for life scientists |url=https://pubmed.ncbi.nlm.nih.gov/23803301/ |journal=Briefings in Bioinformatics |volume=14 |issue=5 |pages=528–537 |doi=10.1093/bib/bbt043 |issn=1477-4054 |pmc=3771230 |pmid=23803301}}</ref> <ref>{{Cite journal |last=Carvalho-Silva |first=Denise |last2=Garcia |first2=Leyla |last3=Morgan |first3=Sarah L. |last4=Brooksbank |first4=Cath |last5=Dunham |first5=Ian |date=2018-11 |title=Ten simple rules for delivering live distance training in bioinformatics across the globe using webinars |url=https://pubmed.ncbi.nlm.nih.gov/30439935/ |journal=PLoS computational biology |volume=14 |issue=11 |pages=e1006419 |doi=10.1371/journal.pcbi.1006419 |issn=1553-7358 |pmc=6237289 |pmid=30439935}}</ref> <ref>{{Cite journal |last=Greene |first=Anna C. |last2=Giffin |first2=Kristine A. |last3=Greene |first3=Casey S. |last4=Moore |first4=Jason H. |date=2016-01 |title=Adapting bioinformatics curricula for big data |url=https://pubmed.ncbi.nlm.nih.gov/25829469/ |journal=Briefings in Bioinformatics |volume=17 |issue=1 |pages=43–50 |doi=10.1093/bib/bbv018 |issn=1477-4054 |pmc=4719066 |pmid=25829469}}</ref> <ref>{{Cite journal |last=Via |first=Allegra |last2=De Las Rivas |first2=Javier |last3=Attwood |first3=Teresa K. |last4=Landsman |first4=David |last5=Brazas |first5=Michelle D. |last6=Leunissen |first6=Jack A. M. |last7=Tramontano |first7=Anna |last8=Schneider |first8=Maria Victoria |date=2011-10 |title=Ten simple rules for developing a short bioinformatics training course |url=https://pubmed.ncbi.nlm.nih.gov/22046119/ |journal=PLoS computational biology |volume=7 |issue=10 |pages=e1002245 |doi=10.1371/journal.pcbi.1002245 |issn=1553-7358 |pmc=3203054 |pmid=22046119}}</ref>.

==Conferences==