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MATLAB Applications in Bioinformatics Developing and Deploying Bioinformatics Applications with MATLAB MATLAB for Bioinformatics Kristen Amuzzini Biotech, Pharmaceutical, & Medical Industry The MathWorks, Inc. Presentation Layout MATLAB applications in Bioinformatics Customer success stories MATLAB & The Bioinformatics Toolbox Sequence analysis Microarray analysis Integrating MATLAB with other tools MATLAB as computational engine for Excel Questions/Answers & Wrap-up Bioinformatics Applications • Sequence analysis • Base calling algorithm design, sequence alignment, sequence building algorithms • 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 • Systems Biology • Interaction network identification, simulation of metabolic pathways, flux analysis Bioinformatics teams supporting multiple constituencies with multiple tools. • C/C++, Java, Perl • VB, Excel Macros • SQL • GUI Based tools • Freeware • SPLUS, R, SAS, Mathematica • Web based tools !!" #$% $$ &$"'($ )#$*+% $! ,-. )//0' +&1& (%( Using MATLAB, bioinformatics teams can support multiple constituencies. &1&23 % !!" #$% $$ &$"'($ )#$*+% $! ,-. )//0' +&1& (%( &1& (%( &(( )$("#$ $"!%&((" %$4#&1& $ “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.” 0$1!5&(("%$ User example: Genetic Sequence Base Calling User example: Breast Cancer Prognosis ($%"'(" !"$ !(3(!" 6((7($% #$ “Since MATLAB and the Image Processing Toolbox are fully integrated and the MATLAB platform is very good for matrix calculation, we did not have to spend time writing the low level image processing and the basic data analysis routines like vector and matrix calculations” “Our research scientists are happy with the quick feedback,” Dr. Dai says. “Using MathWorks tools, we can respond to their requests very fast, and it’s easy for the scientists to use these tools. Using the GUIs that we develop in MATLAB, they can access functions without having to remember the underlying code.” 89%#8 ($ :)$(% Academic users • Bioinformatics Teaching • MIT, Stanford, Cornell, Carnegie Mellon, … • Research • Sequencing • Base calling algorithm design • Sequence analysis • Computational biolinguistics • Microarray analysis • Statistical modeling of microarrays • Proteomics • Statistical modeling of protein-protein interaction • Systems Biology • Flux Analysis More than 600 textbooks for education and professional use, in 19 languages – Biosciences – Controls – Signal Processing – Image Processing – Mechanical Engineering – Mathematics – Natural Sciences – Environmental Sciences Thousands of universities teach students using MathWorks products. Industry Issues & Solutions • Integrating tools from various programming languages is difficult, closed source tools are not customizable, and freeware is often not supported. • There is no standard biological data format. • Applications must be easily deployable within organizations. • MATLAB is a supported, open architecture, user-friendly environment for data analysis across applications, algorithm development, and deployment. • MATLAB and the Bioinformatics Toolbox provides file format support for common data sources (web- based, sequences, microarray, etc.). • MATLAB’s deployment tools and user-interface design environment allow easy deployment of MATLAB based applications. [...]... deployment of MATLAB based applications © 2003 The MathWorks, Inc Further Information • Bioinformatics Toolbox Product page –Demos, technical literature, trial information –www.mathworks.com/products/bioinfo • MATLAB Central – File exchange and newsgroup access for MATLAB and Simulink users – www.mathworks.com/matlabcentral – Access to comp.soft-sys .matlab file exchange and newsgroup access for the MATLAB. .. Deploying Integrating and Deploying Bioinformatics Tools with Developing and Deploying Bioinformatics Bioinformatics Tools with MATLAB Applications with MATLAB MATLAB 17 © 2003 The MathWorks, Inc Connecting to MATLAB C/C++ Java Perl Excel / COM Database Toolbox Web Instrument Control Data Acquisition Image Acquisition File I/O © 2003 The MathWorks, Inc Deploying with MATLAB C/C++ Stand-alone COM Excel... supported MATLAB is a supported, open architecture, user-friendly environment for data analysis across applications, algorithm development, and deployment •There is no standard biological data format MATLAB and the Bioinformatics Toolbox provides file format support for common data sources (webbased, sequences, microarray, etc.) •Applications must be easily deployable within organizations MATLAB s...Robert Henson The MathWorks, Inc © 2003 The MathWorks, Inc Developing& The Deploying Bioinformatics MATLAB and Bioinformatics Toolbox The Bioinformatics Toolbox Applications with MATLAB 11 © 2003 The MathWorks, Inc The MathWorks Product Family Integrated for: technical computing, data analysis and visualization system modeling and simulation implementation of real-time... © 2003 The MathWorks, Inc What else could you do? Bioinformatics Statistics Signal Processing Neural Networks Image Processing Optimization © 2003 The MathWorks, Inc Robert Henson The MathWorks, Inc © 2003 The MathWorks, Inc Integrating and Deploying Bioinformatics Tools with Developing and Summary Deploying Bioinformatics Applications with MATLAB MATLAB 23 © 2003 The MathWorks, Inc Industry Issues... Deploying with MATLAB C/C++ Stand-alone COM Excel Web © 2003 The MathWorks, Inc Push Data into MATLAB Data I/O • Import Excel ranges into MATLAB • Export MATLAB data into Excel ranges • Evaluate MATLAB Statements in Excel © 2003 The MathWorks, Inc Computational Engine for Excel Spread Sheet Applications • MATLAB Excel Link can be the computational engine behind your Excel applications • Fast scalable... global alignment • Perform local alignment © 2003 The MathWorks, Inc Microarray Data Analysis Tutorial Example • Plot expression profiles for genes • Filter genes based on information content of profile • Perform hierarchical clustering • Perform K-means clustering • Perform Principal Component Analysis Reference: © 2003 DeRisi, JL, Iyer, VR, Brown, PO "Exploring the metabolic and genetic control of gene... MathWorks, Inc MATLAB Desktop Tools Launchpad: Start other tools and demos Command Window Workspace Browser: See your data Command History © 2003 The MathWorks, Inc Sequence Alignment Tutorial Example • Get human and mouse genes from GenBank • Look for open reading frames (ORFs) • Convert DNA sequences to amino acid sequences • Create a dotplot of the two sequences • Perform global alignment • Perform local... Toolboxes DAQ cards Instruments Databases and files Financial Datafeeds Stateflow Stateflow Code Generation PC-based real-time systems Desktop Applications Automated Reports © 2003 The MathWorks, Inc Bioinformatics Toolbox 1.0 • File I/O • FASTA, PDB, SCF, GPR, GAL • Web Connectivity • GenBank, EMBL, PIR, PDB • Sequence Analysis & Alignment 212 PYESFTFPELMRKGSYNPVTHIYTAQDVKEVIEYARLRGIR | | | . MATLAB Applications in Bioinformatics Developing and Deploying Bioinformatics Applications with MATLAB MATLAB for Bioinformatics Kristen Amuzzini Biotech,. Layout MATLAB applications in Bioinformatics Customer success stories MATLAB & The Bioinformatics Toolbox Sequence analysis Microarray analysis Integrating MATLAB with other tools MATLAB. development, and deployment. • MATLAB and the Bioinformatics Toolbox provides file format support for common data sources (web- based, sequences, microarray, etc.). • MATLAB s deployment tools
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