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Presenter: Bradley Green What is Bioinformatics? Brief History of Bioinformatics Development Computer Science and Bioinformatics Current Applications What the future holds Original Definition – “Study of information processes in biotic systems” Retrieve, Organize, Analyze New and ever changing field Bioinformatics is a field supported by ◦ Computer Science ◦ Engineering ◦ Mathematics Develop software Tools ◦ Generate biological data and knowledge Alvin Kabat (1978) ◦ Led research in biological sequence analysis Was strictly used as an organizational tool Assisted in the development of nucleotide sequence data bases and software Increase understanding of biological processes Apply computational techniques Post 1980’s Impact Bioinformatics as a Computer Scientist ◦ The application of computer science to the analysis of biological data ◦ Genome Research ◦ DNA Sequencing ◦ Creation and advancement of databases and algorithms ◦ Computational methods to solve practical problems ◦ 3D generation of various biological systems ◦ Develop software used to discover and analyze biological networks Analyzing biological information involves the application of: ◦ ◦ ◦ ◦ ◦ ◦ Algorithms in AI Soft Computing Data mining Image system theory Information theory Statistics Tools Used ◦ Java, XML, Perl, C, C++, Ruby, Python, R, SQL, CUDA, MATLAB, and spread sheet applications Computer scientists responsible for mass advancements ◦ Developed technologies ◦ Diagnosis ◦ Applications and devices Drastic changes in biomedicine ◦ Captured information stored in biotic systems ◦ Develop into applicable technology and data Research Methods ◦ ◦ ◦ ◦ Able to research at cellular levels Predictive and diagnostic methods Complex biological systems Interactions in Biotics Command-line tools and scripts to complex and advanced graphical programs ◦ Developed using common programming languages Bioinformatics software Some capabilities Organizations: Open Bioinformatics Foundation and EBI ◦ BioConducter, BioRuby, BioPython, BioJava, EMBOSS, Taverna workbench ◦ Limited to machines installed with software ◦ Analyzing biotic sequences ◦ Modeling cells ◦ Testing methods ◦ Annual Bioinformatics Open Source Conference Web services ◦ Not always open source ◦ Browser based applications ◦ Superior to local software in certain cases Allows user to share mass quantities of data ◦ Promotes synthesis of research and applications ◦ Not limited to accessing data from one location Ensures multiple parties are updated consistently SOAP and REST ◦ Sequence Search Services, Multiple Sequence Alignment, Biological Sequence Analysis ◦ Bioinformatics workflow management systems Research in progress: ◦ Amino-acid sequencing ◦ DNA sequencing ◦ Genome research Diagnose and treat illness far in advance Understand unknown concepts of the brain and high level functioning Advancement of technology and capabilities ◦ Medical Research ◦ Clinical Research Simulate virus and infection Origin of the gene Further the concept of the cell Promote computer scientists Bioinformatics." Wikipedia. Wikimedia Foundation, 25 Feb. 2013. Web. 25 Feb. 2013 Neuman, Joseph A., Ofer Isakov, and Noam Shomron. "Briefings in Bioinformatics." Analysis of Insertion†“deletion from Deep-sequencing Data: Software Evaluation for Optimal Detection. Oxford Journals, n.d. Web. 25 Feb. 2013. Cohen, Jacques. "Bioinformatics- An Introduction for Computer Scientists." ACM Computing Surveys 36.2 (2004): 123-56. Cse.spsu.edu. Web.