Developing and for

MATLAB Deploying Bioinformatics

Bioinformatics
MATLAB Applications in Bioinformatics
Applications with MATLAB

Kristen Amuzzini

© 2003 The MathWorks, Inc.

Biotech, Pharmaceutical, & Medical Industry
The MathWorks, Inc.

1
© 2003 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

© 2003 The MathWorks, Inc.

 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

© 2003 The MathWorks, Inc.

 Bioinformatics teams supporting multiple
constituencies with multiple tools.

Research Biologists Bioinformatics Team Software Engineers

• Prefer UI/Web based • Algorithm development • C++, Java
tools • Custom one-off analyses • Work off MATLAB
• Want custom analyses • Programs for biologists prototypes

• C/C++, Java, Perl

• VB, Excel Macros
• SQL
• GUI Based tools
• Freeware
• SPLUS, R, SAS, Mathematica
• Web based tools
© 2003 The MathWorks, Inc.
 Using MATLAB, bioinformatics teams can support
multiple constituencies.

Research Biologists Bioinformatics Team Software Engineers

• Prefer UI/Web based • Algorithm development • C++, Java
tools • Custom one-off analyses • Work off MATLAB
• Want custom analyses • Programs for biologists prototypes

MATLAB GUI’s, MATLAB

analyses 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.

“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.”

Jim Labrenz, Applied Biosystems

© 2003 The MathWorks, 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.

“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.”
© 2003 The MathWorks, Inc.
 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

© 2003 The MathWorks, Inc.

 Thousands of universities teach students using
MathWorks products.
More than 600 textbooks for education and professional use, in 19
languages
– Biosciences – Mechanical Engineering
– Controls – Mathematics
– Signal Processing – Natural Sciences
– Image Processing – Environmental Sciences

© 2003 The MathWorks, Inc.

 Industry Issues & Solutions

•Integrating tools from various •MATLAB is a supported, open

programming languages is architecture, user-friendly
difficult, closed source tools are environment for data analysis across
not customizable, and freeware is applications, algorithm development,
often not supported. and deployment.

•There is no standard biological •MATLAB and the Bioinformatics

data format. Toolbox provides file format support
for common data sources (web-
based, sequences, microarray, etc.).

•MATLAB’s deployment tools and

•Applications must be easily
user-interface design environment
deployable within organizations.
allow easy deployment of MATLAB
based applications.
© 2003 The MathWorks, Inc.
Developing
MATLAB &and
The Deploying Bioinformatics
Bioinformatics Toolbox
The Bioinformatics Toolbox
Applications with MATLAB

© 2003 The MathWorks, Inc.

Robert Henson

The MathWorks, Inc.

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© 2003 The MathWorks, Inc.
 The MathWorks Product Family

Integrated for:
 technical computing, data analysis and visualization
 system modeling and simulation
 implementation of real-time embedded software

Blocksets
Code Generation
Stateflow
Stateflow
Toolboxes

PC-based real-time
systems
DAQ cards
Instruments Desktop Applications
Databases and files Automated Reports
Financial Datafeeds

© 2003 The MathWorks, Inc.

 Bioinformatics Toolbox 1.0

• File I/O
• FASTA, PDB, SCF, GPR, GAL
• Web Connectivity
• GenBank, EMBL, PIR, PDB 212 PYESFTFPELMRKGSYNPVTHIYTAQDVKEVIEYARLRGIR
| | | :| | | : |: | : : : |: | | | : | |
| : | :: | ::
• Sequence Analysis & Alignment 321 PYISRYYPELAVHGAYSE -SETYSEQDVREVAEFAKIYGVQ

• Needleman-Wunsch, Smith-Waterman
• DNA/RNA/AA conversions, pattern searching
• Microarray Normalization & Visualization
• Lowess, global mean, MAD (median absolute deviation)
• Protein Visualization
• Atomic composition, molecular weight, hydrophobicity profile

© 2003 The 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 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 expression on a genomic scale." Science. 1997 Oct 24;278(5338):680-6. The MathWorks, Inc.
 Integrating and Deploying
Integrating
Developing
and Deploying
and Deploying
Bioinformatics
Bioinformatics
Tools with
Bioinformatics Tools with MATLAB
ApplicationsMATLAB
with MATLAB

© 2003 The MathWorks, Inc.

Robert Henson

The MathWorks, Inc.

17
© 2003 The MathWorks, Inc.
 Connecting to MATLAB

C/C++
Java Excel / COM
Perl
Database
Toolbox

Web

Instrument Control
Data Acquisition File I/O
Image Acquisition

© 2003 The MathWorks, Inc.

 Deploying with MATLAB

C/C++ COM Excel

Stand-alone 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 solution

MLPutMatrix("data",B2:H43)

MLPutMatrix("Genes",A2:A43)

MLPutMatrix("TimeSteps",B1:H1)

MLEvalString("clustergram(data,'RowLabels',…

Genes,'ColLabels',TimeSteps)")
© 2003 The MathWorks, Inc.
 What else could you do?

Bioinformatics Signal Processing Image Processing

Statistics Neural Networks Optimization

© 2003 The MathWorks, Inc.

Integrating
Developing
and Deploying
and Summary
Deploying
Bioinformatics
Bioinformatics
Tools with
Applications
MATLAB
with MATLAB

© 2003 The MathWorks, Inc.

Robert Henson

The MathWorks, Inc.

23
© 2003 The MathWorks, Inc.
 Industry Issues & Solutions

•Integrating tools from various •MATLAB is a supported, open

programming languages is architecture, user-friendly
difficult, closed source tools are environment for data analysis across
not customizable, and freeware is applications, algorithm development,
often not supported. and deployment.

•There is no standard biological •MATLAB and the Bioinformatics

data format. Toolbox provides file format support
for common data sources (web-
based, sequences, microarray, etc.).

•MATLAB’s deployment tools and

•Applications must be easily
user-interface design environment
deployable within organizations.
allow easy 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 & Simulink user community

© 2003 The MathWorks, Inc.