The Wolfram Solution forBioinformaticsPull 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 Wolfram 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. |
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Wolfram technologies include thousands of built-in functions that let you:
- Model biological systems with Wolfram SystemModeler
- Rapidly search the human genome
- Generate sequence alignments in a computable form
- Quickly visualize large-scale sequence alignments
- Rapidly compare gene structures
- Visualize biological reaction networks with Wolfram SystemModeler
- Generate accurate protein renderings using integrated protein structure, element, and color data
- Instantly visualize protein sequence alignments
- Use built-in protein structure data to generate Ramachandran plots, visualize protein folds, and more
- Visualize gene interaction networks
- 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
Analyzing processes in the glucose-insulin system with Wolfram SystemModeler
Visualizing protein folds using built-in protein structure data
Does your current tool set have these advantages?
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Free-form linguistic input produces immediate results without the need for syntax
Unique to Wolfram technologies -
Built-in curated genomic and proteomic data, ready for use without preprocessing
Unique to Wolfram technologies -
High-level language with automated interface construction for quick prototyping of applications
BioPerl, BioJava, and BioPython require extensive programming to prototype interactive applications -
Powerful integrated statistical and graphical tools for analyzing genomic, proteomic, and other data
R projects like Bioconductor focus on genomic data only -
Built-in high-level computation and automatic report generation
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
Extensive programming is required to parallelize processes in all other systems -
Complete high-level workflow enabled by symbolic function architecture
R does not have symbolic functionality built in
Studying glycolytic oscillations in yeast cells with Wolfram SystemModeler
Showing the global alignment of two protein sequences on an alignment wheel
Bioinformatics specific capabilities:
- 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 »
- Functions for contiguous and non-contiguous common subsequences »
- Sequence alignment using local or global methods such as Smith–Waterman, Needleman–Wunsch, and more »
- Partitioning data using cluster analysis, nearest neighbors, and more »
- 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 Wolfram Language programs into C code, for standalone use or integration with other systems
Wolfram SystemModeler is the most complete physical modeling and simulation tool for high-fidelity modeling. Capabilities include:
- Use the built-in BioChem library to model biological systems »
- Import and export Systems Biology Markup Language (SBML) models »
- Visualize biological reaction networks »
- Connect seamlessly with Mathematica for the ultimate integrated modeling, simulation, and analysis workflow
Organizations Using Wolfram Technologies
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