Transcript Technical Presentation: Bioinformatics

Presenter:
Bradley Green
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What is Bioinformatics?
Brief History of Bioinformatics
Development
Computer Science and Bioinformatics
Current Applications
What the future holds
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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
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Develop software Tools
◦ Generate biological data and knowledge
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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
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Post 1980’s
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Impact
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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
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Analyzing biological information involves the
application of:
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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
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Computer scientists responsible for mass
advancements
◦ Developed technologies
◦ Diagnosis
◦ Applications and devices
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Drastic changes in biomedicine
◦ Captured information stored in biotic systems
◦ Develop into applicable technology and data
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Research Methods
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Able to research at cellular levels
Predictive and diagnostic methods
Complex biological systems
Interactions in Biotics
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Command-line tools and scripts to complex and
advanced graphical programs
◦ Developed using common programming languages
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Bioinformatics software
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Some capabilities
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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
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Web services
◦ Not always open source
◦ Browser based applications
◦ Superior to local software in certain cases
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Allows user to share mass quantities of data
◦ Promotes synthesis of research and applications
◦ Not limited to accessing data from one location
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Ensures multiple parties are updated consistently
SOAP and REST
◦ Sequence Search Services, Multiple Sequence Alignment,
Biological Sequence Analysis
◦ Bioinformatics workflow management systems
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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
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Bioinformatics." Wikipedia. Wikimedia
Foundation, 25 Feb. 2013. Web. 25 Feb. 2013
Neuman, Joseph A., Ofer Isakov, and Noam
Shomron. "Briefings in Bioinformatics." Analysis
of Insertionâ€
“deletion from Deep-sequencing
Data: Software Evaluation for Optimal Detection.
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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.