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<p>The terms <em>bioinformatics</em> and <em>computational biology</em> are often used interchangeably. However <em>bioinformatics</em> more properly refers to the creation and advancement of algorithms, computational and statistical techniques, and theory to solve formal and practical problems inspired from the management and analysis of biological data. <em>Computational biology,</em> on the other hand, refers to hypothesis-driven investigation of a specific biological problem using computers, carried out with experimental or simulated data, with the primary goal of discovery and the advancement of biological knowledge. Put more simply, bioinformatics is concerned with the information while computational biology is concerned with the hypotheses. A similar distinction is made by National Institutes of Health in their working definitions of Bioinformatics and Computational Biology, where it is further emphasized 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.</p>
<p>A common thread in projects in bioinformatics and computational biology is the use of mathematical tools to extract useful information from data produced by high-throughput biological techniques such as genome sequencing. A representative problem in bioinformatics is the assembly of high-quality genome sequences from fragmentary "shotgun" DNA sequencing. Other common problems include the study of gene regulation using data from microarrays or mass spectrometry.</p>
<p> </p>
<h2p><span class="mw-headline"><font size="5">Major research areas</font></span></h2p>
<p> </p>
<h3><span class="mw-headline">Sequence analysis</span></h3>
<p>Evolutionary biology is the study of the origin and descent of species, as well as their change over time. Informatics has assisted evolutionary biologists in several key ways; it has enabled researchers to:</p>
<ul>
<li>trace the evolution of a large number of organisms by measuring changes in their DNA, rather than through physical taxonomy or physiological observations alone, </li> <li>more recently, compare entire genomes, which permits the study of more complex evolutionary events, such as gene duplication, lateral gene transfer, and the prediction of bacterial speciation factors, </li> <li>build complex computational models of populations to predict the outcome of the system over time </li> <li>track and share information on an increasingly large number of species and organisms </li>
</ul>
<p>Future work endeavours to reconstruct the now more complex tree of life.</p>
<p>Computational technologies are used to accelerate or fully automate the processing, quantification and analysis of large amounts of high-information-content biomedical imagery. Modern image analysis systems augment an observer's ability to make measurements from a large or complex set of images, by improving accuracy, objectivity, or speed. A fully developed analysis system may completely replace the observer. Although these systems are not unique to biomedical imagery, biomedical imaging is becoming more important for both diagnostics and research. Some examples are:</p>
<ul>
<li>high-throughput and high-fidelity quantification and sub-cellular localization (high-content screening, cytohistopathology) </li> <li>morphometrics </li> <li>clinical image analysis and visualization </li> <li>determining the real-time air-flow patterns in breathing lungs of living animals </li> <li>quantifying occlusion size in real-time imagery from the development of and recovery during arterial injury </li> <li>making behavioral observations from extended video recordings of laboratory animals </li> <li>infrared measurements for metabolic activity determination </li>
</ul>
<p> </p>
<h2p><span class="mw-headline"><font size="5">Software tools</font></span></h2p>
<p>First generation bioinformatics tools consisted of applications, usually with a text-based interface, which performed a specific task well. The computational biology tool best-known among biologists is probably BLAST, an algorithm for searching large databases of protein or DNA sequences. The NCBI provides a popular web-based implementation that searches their massive sequence databases. Also fairly early on, due to the amassing of sequence and annotation data, keyword search engines which were able to resolve gene and protein synonyms were important. Computer scripting languages such as Perl (thanks to its regular expressions handling facilities) and Python are often used to interface with biological databases and parse output from bioinformatics programs written in languages such as C or C++. Communities of bioinformatics programmers have set up free open source bioinformatics projects to develop and distribute the tools and modules they produce.</p>
<p>As the data sources expanded and diversified, both in content and geography, bioinformatic meta search engines, such as Sequence profiling tools, emerged to help find relevant information from several databases. These meta search engines might index data from a local server or even from a panel of third party services.</p>
<p>More recently, SOAP-based interfaces have been developed for a wide variety of bioinformatics applications allowing an application running on one computer in one part of the world to use algorithms, data and computing resources on servers in other parts of the world. A large availability of these SOAP-based bioinformatics web services, along with the open source bioinformatics collections, lead to the next generation of bioinformatics tools: the integrated bioinformatics platform. These tools range from a collection of standalone tools with a common data format under a single, slick standalone or web-based interface, to integrative and extensible bioinformatics workflow development environments.</p>
<p> </p>
<h2p><span class="mw-headline"><font size="5">See also</font></span></h2p>
<h3><span class="mw-headline">Related topics</span></h3>
<p>
<td valign="top">
<ul>
<li>Biocybernetics </li> <li>Bioinformatics companies </li> <li>Biologically-inspired computing </li> <li>Biomedical informatics </li> <li>Computational biology </li> <li>Computational biomodeling </li> <li>Computational genomics </li> <li>Dot plot (bioinformatics) </li>
</ul>
</td>
<td valign="top">
<ul>
<li>Metabolic network modelling </li> <li>Molecular modelling </li> <li>Morphometrics </li> <li>Natural computation </li> <li>Pharmaceutical company </li> <li>Protein-protein interaction prediction </li> <li>List of numerical analysis software </li>
</ul>
</td>
<td valign="top">
<ul>
<li>Applied mathematics </li> <li>Artificial intelligence </li> <li>Biology </li> <li>Cheminformatics </li> <li>Computational biology </li>
</ul>
</td>
<td valign="top">
<ul>
<li>Computational science </li> <li>Computer science </li> <li>Cybernetics </li> <li>Informatics </li> <li>Mathematical biology </li>
</ul>
</td>
<td valign="top">
<ul>
<li>Neuroinformatics </li> <li>Scientific computing </li> <li>Statistics </li> <li>Systems biology </li> <li>Theoretical biology </li>
</ul>
</td>
</p>
<p> </p>
<h2p><span class="mw-headline"><font size="5">References</font></span></h2p>
<ul>
<li>Aluru, Srinivas, ed. <em>Handbook of Computational Molecular Biology</em>. Chapman & Hall/Crc, 2006. <a class="internal" href="http://en.wikipedia.org/w/index.php?title=Special:Booksources&isbn=1584884061"><font color="#0066cc">ISBN 1584884061</font></a> (Chapman & Hall/Crc Computer and Information Science Series) </li> <li>Baldi, P and Brunak, S, <em>Bioinformatics: The Machine Learning Approach</em>, 2nd edition. MIT Press, 2001. <a class="internal" href="http://en.wikipedia.org/w/index.php?title=Special:Booksources&isbn=026202506X"><font color="#0066cc">ISBN 0-262-02506-X</font></a> </li> <li>Barnes, M.R. and Gray, I.C., eds., <em>Bioinformatics for Geneticists</em>, first edition. Wiley, 2003. <a class="internal" href="http://en.wikipedia.org/w/index.php?title=Special:Booksources&isbn=0470843942"><font color="#0066cc">ISBN 0-470-84394-2</font></a> </li> <li>Baxevanis, A.D. and Ouellette, B.F.F., eds., <em>Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins</em>, third edition. Wiley, 2005. <a class="internal" href="http://en.wikipedia.org/w/index.php?title=Special:Booksources&isbn=0471478784"><font color="#0066cc">ISBN 0-471-47878-4</font></a> </li> <li>Baxevanis, A.D., Petsko, G.A., Stein, L.D., and Stormo, G.D., eds., <em>Current Protocols in Bioinformatics</em>. Wiley, 2007. <a class="internal" href="http://en.wikipedia.org/w/index.php?title=Special:Booksources&isbn=0471250937"><font color="#0066cc">ISBN 0-471-25093-7</font></a> </li> <li>Claverie, J.M. and C. Notredame, <em>Bioinformatics for Dummies</em>. Wiley, 2003. <a class="internal" href="http://en.wikipedia.org/w/index.php?title=Special:Booksources&isbn=0764516965"><font color="#0066cc">ISBN 0-7645-1696-5</font></a> </li> <li>Cristianini, N. and Hahn, M. <a class="external text" title="http://www.computational-genomics.net/" rel="nofollow" href="http://www.computational-genomics.net/"><em><font color="#0066cc">Introduction to Computational Genomics</font></em></a>, Cambridge University Press, 2006. (<a class="internal" href="http://en.wikipedia.org/w/index.php?title=Special:Booksources&isbn=9780521671910"><font color="#0066cc">ISBN 9780521671910</font></a> | <a class="internal" href="http://en.wikipedia.org/w/index.php?title=Special:Booksources&isbn=0521671914"><font color="#0066cc">ISBN 0521671914</font></a>) </li> <li>Durbin, R., S. Eddy, A. Krogh and G. Mitchison, <em>Biological sequence analysis</em>. Cambridge University Press, 1998. <a class="internal" href="http://en.wikipedia.org/w/index.php?title=Special:Booksources&isbn=0521629713"><font color="#0066cc">ISBN 0-521-62971-3</font></a> </li> <li>Gilbert, D. <a class="external text" title="http://bib.oxfordjournals.org/cgi/content/abstract/5/3/300" rel="nofollow" href="http://bib.oxfordjournals.org/cgi/content/abstract/5/3/300"><em><font color="#0066cc">Bioinformatics software resources</font></em></a>. Briefings in Bioinformatics, Briefings in Bioinformatics, 2004 5(3):300-304. </li> <li>Keedwell, E., <em>Intelligent Bioinformatics: The Application of Artificial Intelligence Techniques to Bioinformatics Problems</em>. Wiley, 2005. <a class="internal" href="http://en.wikipedia.org/w/index.php?title=Special:Booksources&isbn=0470021756"><font color="#0066cc">ISBN 0-470-02175-6</font></a> </li> <li>Kohane, et al. <em>Microarrays for an Integrative Genomics.</em> The MIT Press, 2002. <a class="internal" href="http://en.wikipedia.org/w/index.php?title=Special:Booksources&isbn=026211271X"><font color="#0066cc">ISBN 0-262-11271-X</font></a> </li> <li>Lund, O. et al. <em>Immunological Bioinformatics.</em> The MIT Press, 2005. <a class="internal" href="http://en.wikipedia.org/w/index.php?title=Special:Booksources&isbn=0262122804"><font color="#0066cc">ISBN 0-262-12280-4</font></a> </li> <li>Michael S. Waterman, <em>Introduction to Computational Biology: Sequences, Maps and Genomes</em>. CRC Press, 1995. <a class="internal" href="http://en.wikipedia.org/w/index.php?title=Special:Booksources&isbn=0412993910"><font color="#0066cc">ISBN 0-412-99391-0</font></a> </li> <li>Mount, David W. <em>Bioinformatics: Sequence and Genome Analysis</em> Spring Harbor Press, May 2002. <a class="internal" href="http://en.wikipedia.org/w/index.php?title=Special:Booksources&isbn=0879696087"><font color="#0066cc">ISBN 0-87969-608-7</font></a> </li> <li>Pachter, Lior and <a title="Bernd Sturmfels" href="http://en.wikipedia.org/wiki/Bernd_Sturmfels"><font color="#0066cc">Sturmfels, Bernd</font></a>. "Algebraic Statistics for Computational Biology" Cambridge University Press, 2005. <a class="internal" href="http://en.wikipedia.org/w/index.php?title=Special:Booksources&isbn=0521857007"><font color="#0066cc">ISBN 0-521-85700-7</font></a> </li> <li>Pevzner, Pavel A. <em>Computational Molecular Biology: An Algorithmic Approach</em> The MIT Press, 2000. <a class="internal" href="http://en.wikipedia.org/w/index.php?title=Special:Booksources&isbn=0262161974"><font color="#0066cc">ISBN 0-262-16197-4</font></a> </li>
</ul>
<p> </p>
<h2p><span class="mw-headline"><font size="5">External links</font></span></h2p>
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<div style="FLOATfloat: left"><div class="floatnone"><span><a class="image" title="" href="http://en.wikipedia.org/wiki/Image:Wiktionary-logo-en.png"></a></span> </div>
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<div class="infobox sisterproject">
<div style="MARGINmargin-LEFTleft: 60px"><div style="MARGINmargin-LEFTleft: 10px"><a class="extiw" title="v:Topic:Bioinformatics" href="http://en.wikiversity.org/wiki/Topic:Bioinformatics"><font color="#0066cc"></font></a></div>
</div>
</div>
<li>
<ul>
<li>[http://bioinformatics.ws Bioinformatics.ws]: Bioinformatics wiki site.</li> <li>[http://biomatics.org Biomatics.org]</li> <li><a class="external text" title="http://bioinformatics.org/" rel="nofollow" href="http://bioinformatics.org/"><font color="#0066cc">Bioinformatics Organization (Bioinformatics.Org): The Open-Access Institute</font></a> </li> <li><a class="external text" title="http://www.embnet.org/" rel="nofollow" href="http://www.embnet.org/"><font color="#0066cc">EMBnet</font></a> </li> <li><a class="external text" title="http://www.ebi.ac.uk/" rel="nofollow" href="http://www.ebi.ac.uk/"><font color="#0066cc">European Bioinformatics Institute</font></a> </li> <li><a class="external text" title="http://www.embl.org/" rel="nofollow" href="http://www.embl.org/"><font color="#0066cc">European Molecular Biology Laboratory</font></a> </li> <li><a class="external text" title="http://www.iscb.org/" rel="nofollow" href="http://www.iscb.org/"><font color="#0066cc">The International Society for Computational Biology</font></a> </li> <li><a class="external text" title="http://www.ncbi.nlm.nih.gov/" rel="nofollow" href="http://www.ncbi.nlm.nih.gov/"><font color="#0066cc">National Center for Biotechnology Information</font></a> </li> <li><a class="external text" title="http://www.nih.gov" rel="nofollow" href="http://www.nih.gov/"><font color="#0066cc">National Institutes of Health homepage</font></a> </li> <li><a class="external text" title="http://www.open-bio.org/" rel="nofollow" href="http://www.open-bio.org/"><font color="#0066cc">Open Bioinformatics Foundation: umbrella non-profit organization supporting certain open-source projects in bioinformatics</font></a> </li> <li><a title="Swiss Institute of Bioinformatics" href="http://en.wikipedia.org/wiki/Swiss_Institute_of_Bioinformatics"><font color="#0066cc">Swiss Institute of Bioinformatics</font></a> </li> <li><a title="Wellcome Trust Sanger Institute" href="http://en.wikipedia.org/wiki/Wellcome_Trust_Sanger_Institute"><font color="#0066cc">Wellcome Trust Sanger Institute</font></a> </li>
</ul>
</li>
<li>Major Journals
<ul>
<li><a class="external text" title="http://www.almob.org/" rel="nofollow" href="http://www.almob.org/"><font color="#0066cc">Algorithms in Molecular Biology</font></a> </li> <li><a class="external text" title="http://bioinformatics.oupjournals.org/" rel="nofollow" href="http://bioinformatics.oupjournals.org/"><font color="#0066cc">Bioinformatics journal</font></a> </li> <li><a class="external text" title="http://www.biomedcentral.com/bmcbioinformatics" rel="nofollow" href="http://www.biomedcentral.com/bmcbioinformatics"><font color="#0066cc">BMC Bioinformatics journal</font></a> </li> <li><a class="external text" title="http://bib.oxfordjournals.org/" rel="nofollow" href="http://bib.oxfordjournals.org/"><font color="#0066cc">Briefings in Bioinformatics</font></a> </li> <li><a class="external text" title="http://www.la-press.com/evolbio.htm" rel="nofollow" href="http://www.la-press.com/evolbio.htm"><font color="#0066cc">Evolutionary Bioinformatics</font></a> </li> <li><a class="external text" title="http://www.genome.org" rel="nofollow" href="http://www.genome.org/"><font color="#0066cc">Genome Research</font></a> </li> <li><a class="external text" title="http://www.bepress.com/ijb/" rel="nofollow" href="http://www.bepress.com/ijb/"><font color="#0066cc">The International Journal of Biostatistics</font></a> </li> <li><a class="external text" title="http://www.liebertpub.com/publication.aspx?pub_id=31" rel="nofollow" href="http://www.liebertpub.com/publication.aspx?pub_id=31"><font color="#0066cc">Journal of Computational Biology</font></a> </li> <li><a class="external text" title="http://www.nature.com/msb/index.html" rel="nofollow" href="http://www.nature.com/msb/index.html"><font color="#0066cc">Molecular Systems Biology</font></a> </li> <li><a class="external text" title="http://compbiol.plosjournals.org" rel="nofollow" href="http://compbiol.plosjournals.org/"><font color="#0066cc">PLoS Computational Biology</font></a> </li> <li><a class="external text" title="http://www.bepress.com/sagmb/" rel="nofollow" href="http://www.bepress.com/sagmb/"><font color="#0066cc">Statistical Applications in Genetic and Molecular Biology</font></a> </li>
</ul>
</li>
<li>Other sites
<ul>
<li><a class="external text" title="http://www.biostatsresearch.com/repository/" rel="nofollow" href="http://www.biostatsresearch.com/repository/"><font color="#0066cc">The Collection of Biostatistics Research Archive</font></a> </li> <li><a class="external text" title="http://www.ornl.gov/TechResources/Human_Genome/research/informatics.html" rel="nofollow" href="http://www.ornl.gov/TechResources/Human_Genome/research/informatics.html"><font color="#0066cc">Human Genome Project and Bioinformatics</font></a> </li> <li><a class="external text" title="http://dmoz.org/Science/Biology/Bioinformatics/Research_Groups/" rel="nofollow" href="http://dmoz.org/Science/Biology/Bioinformatics/Research_Groups/"><font color="#0066cc">List of Bioinformatics Research Groups</font></a> at the <a title="Open Directory Project" href="http://en.wikipedia.org/wiki/Open_Directory_Project"><font color="#0066cc">Open Directory Project</font></a> </li>
</ul>
</li>
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<p>[http://bioinformatics.ws Bioinformatics.ws] | [http://biomics.org Biomics.org]<br />
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