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Industry Solutions for Biotechnology and Medicine

Bioinformatics

Pull in your data or ours, apply sophisticated symbolic and numeric analysis, visualize, generate interactive reports or instant applications—all in one system, with one integrated workflow.

The Mathematica bioinformatics solution seamlessly integrates specialized capabilities—like built-in computable genome and protein data and sequence alignment—while providing the most automated and reliable computation, development, and deployment environment available.

Using built-in curated human genome and protein data suitable for computation

A protein fold visualization using built-in protein structure data

Key Capabilities

Why Choose Mathematica

Ways to Use

Mathematica includes thousands of built-in functions for computation, modeling, visualization, development, and deployment »
Bioinformatics specific capabilities include:
Built-in access to continually updated data on the standard human genome »
Integrated load-on-demand data on all reference human proteins »
Fast exact-match searches for sequences in the human genome »
Integrated access to gene structure information, gene function metadata, and ontology
Built-in chromosome and banding information
Easy import of Affymetrix, GenBank, EDF, FASTA, NEXUS, PDB, and other data formats »
Sequence alignment using local or global methods such as Smith-Waterman, Needleman-Wunsch, and more »
Functions for contiguous and non-contiguous common subsequences »
Partitioning data using cluster analysis, nearest neighbors, and more »

Includes bioinformatics data immediately suitable for computation
Genome Data »
Integrated access to the entire DNA sequence of the human genome
Protein Data »
Built-in data on all reference human proteins
Chemical Data »
Detailed physical, chemical, and molecular properties of more than 34,000 compounds
Free-form linguistic input produces immediate results without the need for syntax »
Built-in graph theory functions for determining shortest paths, graph isomorphisms, and more
Extensive linking and connectivity capabilities to databases, and Java, C, and .NET codes »
Advanced string and general list manipulations, including regular expression notation »
Automatically convert compilable Mathematica programs into C code, for standalone use or integration with other systems
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Why Choose Mathematica

Key Capabilities

Why Choose Mathematica

Ways to Use

Compare Mathematica to your current tools. Do they have these advantages?
Free-form linguistic input produces immediate results without the need for syntax »
Competitor note: Unique to Mathematica
Built-in curated genomic and proteomic data, ready for use without preprocessing
Competitor note: Unique to Mathematica
High-level language with automated interface construction for quick prototyping of applications »
Competitor note: BioPerl, BioJava, and BioPython require extensive programming to prototype interactive applications
Powerful integrated statistical and graphical tools for analyzing genomic, proteomic, and other data »
Competitor note: R projects like Bioconductor focus on genomic data only
Built-in high-level computation and automatic report generation »
Competitor note: BioPerl, BioJava, and BioPython do not include automatic report generation

Easy-to-use parallel computing capabilities for solving computation- or data-intensive problems on multicore computers »
Competitor note: Extensive programming is required to parallelize processes in all other systems
Complete high-level workflow enabled by symbolic function architecture »
Competitor note: R does not have symbolic functionality built-in
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Ways to Use

Key Capabilities

Why Choose Mathematica

Ways to Use

Rapidly develop and test algorithms
Easily integrate legacy data with ready-to-use curated genomic and protein data in a powerful computational environment
Construct interactive applications and deploy them immediately with the Wolfram CDF Player
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Key Capabilities

BIOSCIENCES CASE STUDIES

Case Studies

Some Major Organizations using Mathematica

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—Zhilan Feng

Professor of Mathematics, Purdue University

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