Bioinformatics
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© 2003 The MathWorks, Inc.
DMevAeTlLoApAiBMnpAgApTlpaLicnpAadlBitcifDoaonertipBsolinowosiynitifihnonrgMmBBAaiotiTiociLnsinAfofBormrmaatitcicss
Kristen Amuzzini Biotech, Pharmaceutical, & Medical Industry
© 2003 The MathWorks, Inc.
Bioinformatics Applications
• Sequence analysis
• Base calling algorithm design, sequence alignment, sequence building algorithms
Jim Labrenz, Applied Biosystems
© 2003 The ຫໍສະໝຸດ BaiduathWorks, Inc.
User example: Breast Cancer Prognosis
Rosetta Inpharmatics recently developed a tool that enables clinicians to determine a breast cancer patient’s prognosis based on the gene expression profile of the primary tumor.
Research Biologists •Prefer UI/Web based
tools •Want custom analyses
Bioinformatics Team •Algorithm development •Custom one-off analyses •Programs for biologists
▪ Sequence analysis ▪ Microarray analysis ▪ Integrating MATLAB with other tools ▪ MATLAB as computational engine for Excel ▪ Questions/Answers & Wrap-up
tools •Want custom analyses
Bioinformatics Team •Algorithm development •Custom one-off analyses •Programs for biologists
Software Engineers •C++, Java •Work off MATLAB
• Microarray analysis
• Image processing, QA/QC, data normalization, data analysis
• Proteomics
• Mass Spectrometry signal processing, protein marker identification and classification, peptide sequence identification, 2D-Gel image analysis
prototypes
MATLAB GUI’s, analyses
MATLAB prototypes / Applicatio ns
© 2003 The MathWorks, Inc.
User example: Genetic Sequence Base Calling
Complete draft of the human genome, accelerated by Applied Biosystems — using MATLAB algorithms.
Software Engineers •C++, Java •Work off MATLAB
prototypes
• C/C++, Java, Perl
• VB, Excel Macros
• SQL
• GUI Based tools
• Freeware
• SPLUS, R, SAS, Mathematica
“Having one integrated package is a big advantage. Using MATLAB and the MATLAB Compiler reduced my development time by a factor of 4 or 5.”
“MATLAB has always been ideal as an algorithm prototyping tool,” Labrenz concludes, “but the MATLAB Compiler and C/C++ Math and Graphics Libraries add a whole new dimension, allowing rapid delivery of sophisticated solutions.”
• Web based tools
© 2003 The MathWorks, Inc.
Using MATLAB, bioinformatics teams can support multiple constituencies.
Research Biologists •Prefer UI/Web based
• Systems Biology
• Interaction network identification, simulation of metabolic pathways, flux analysis
© 2003 The MathWorks, Inc.
Bioinformatics teams supporting multiple constituencies with multiple tools.
The MathWorks, Inc.
1
© 2003 The MathWorks, Inc.
Presentation Layout
▪ MATLAB applications in Bioinformatics ▪ Customer success stories ▪ MATLAB & The Bioinformatics Toolbox
DMevAeTlLoApAiBMnpAgApTlpaLicnpAadlBitcifDoaonertipBsolinowosiynitifihnonrgMmBBAaiotiTiociLnsinAfofBormrmaatitcicss
Kristen Amuzzini Biotech, Pharmaceutical, & Medical Industry
© 2003 The MathWorks, Inc.
Bioinformatics Applications
• Sequence analysis
• Base calling algorithm design, sequence alignment, sequence building algorithms
Jim Labrenz, Applied Biosystems
© 2003 The ຫໍສະໝຸດ BaiduathWorks, Inc.
User example: Breast Cancer Prognosis
Rosetta Inpharmatics recently developed a tool that enables clinicians to determine a breast cancer patient’s prognosis based on the gene expression profile of the primary tumor.
Research Biologists •Prefer UI/Web based
tools •Want custom analyses
Bioinformatics Team •Algorithm development •Custom one-off analyses •Programs for biologists
▪ Sequence analysis ▪ Microarray analysis ▪ Integrating MATLAB with other tools ▪ MATLAB as computational engine for Excel ▪ Questions/Answers & Wrap-up
tools •Want custom analyses
Bioinformatics Team •Algorithm development •Custom one-off analyses •Programs for biologists
Software Engineers •C++, Java •Work off MATLAB
• Microarray analysis
• Image processing, QA/QC, data normalization, data analysis
• Proteomics
• Mass Spectrometry signal processing, protein marker identification and classification, peptide sequence identification, 2D-Gel image analysis
prototypes
MATLAB GUI’s, analyses
MATLAB prototypes / Applicatio ns
© 2003 The MathWorks, Inc.
User example: Genetic Sequence Base Calling
Complete draft of the human genome, accelerated by Applied Biosystems — using MATLAB algorithms.
Software Engineers •C++, Java •Work off MATLAB
prototypes
• C/C++, Java, Perl
• VB, Excel Macros
• SQL
• GUI Based tools
• Freeware
• SPLUS, R, SAS, Mathematica
“Having one integrated package is a big advantage. Using MATLAB and the MATLAB Compiler reduced my development time by a factor of 4 or 5.”
“MATLAB has always been ideal as an algorithm prototyping tool,” Labrenz concludes, “but the MATLAB Compiler and C/C++ Math and Graphics Libraries add a whole new dimension, allowing rapid delivery of sophisticated solutions.”
• Web based tools
© 2003 The MathWorks, Inc.
Using MATLAB, bioinformatics teams can support multiple constituencies.
Research Biologists •Prefer UI/Web based
• Systems Biology
• Interaction network identification, simulation of metabolic pathways, flux analysis
© 2003 The MathWorks, Inc.
Bioinformatics teams supporting multiple constituencies with multiple tools.
The MathWorks, Inc.
1
© 2003 The MathWorks, Inc.
Presentation Layout
▪ MATLAB applications in Bioinformatics ▪ Customer success stories ▪ MATLAB & The Bioinformatics Toolbox