Biorithm

Biorithm is a C++ package that includes several libraries and software tools to analyze data in molecular systems biology. This software has been developed in T. M. Murali's research group over a number of years. The tools available in Biorithm cover a wide range of application areas in computational biology. Many of these applications focus on integrating multiple flavors of biological data to improve interpretation of the data:

• The ActiveNetworks tool in Biorithm is useful for integrating microarray data with various types of interaction networks to compute cellular response networks.
• The allied NetworkLego software allows the Boolean combination of multiple response networks in order to dissect condition-specific and cross-condition responses.
• The GAIN software can predict the biological functions of genes whose function is currently unknown.
• Through the implementation of several functional enrichment algorithms, Biorithm can incorporate functional annotations of genes (e.g., from the Gene Ontology) with expression measurements to assess the functional coherence of a collection of genes.
• The Network Reconciliation algorithms integrate gene expression data with an underlying molecular interaction network by applying smoothing functions over the network.
• Biorithm also includes several generic data mining tools, including tools to compute biclusters or truth tables in binary matrices.

With the increasing availability of high-throughput biological data, such tools are extremely useful in helping biologists interpret biological phenomena.

Index

1. Building Biorithm
2. Available Tools

Building Biorithm

Currently, Biorithm has been successfully built on the following operating systems:

• Ubuntu 10.04, 11.04, 12.04

Prerequisites

Biorithm makes use of several third-party libraries. Please install the following libraries using the appropriate software management tool for your operating system (e.g., apt or Synaptic for Ubuntu).

1. libgsl - libgsl0-dev
2. C++ boost libraries - libboost1.40-dev libboost-regex-dev libboost-filesystem-dev libboost-system-dev
   Note: Your software repository may have a different version than 1.40. If it is recent enough, you can likely install that version of boost.
3. Doxygen - doxygen is only needed if the user wants to generate a local copy of this html documentation.

In Ubuntu, you can install all the necessary libraries with the following command:
sudo apt-get install doxygen libgsl0-dev libboost1.40-dev libboost-regex-dev libboost-filesystem-dev libboost-system-dev

You may need to replace the version number of the boost libraries depending on your operating system. Alternatively, you can open the Synaptic Package Manager, which is a GUI frontend to APT. There you can search individually for each prerequisite and mark it for installation.

Steps for Building Biorithm

1. Download the most recent version of Biorithm: Biorithm 1.1
2. Install all required Prerequisites
3. Unpack biorithm.tar.gz: tar -xvzf biorithm.tar.gz
4. Move to the newly-unpacked directory: cd biorithm-1.1
5. Issue the configuration command: ./configure
6. Build the software using make: make
7. Optionally, generate a local copy of this html documentation: make docs

Available Tools

Several tools are comprehensively documented, with detailed explanations of each tool and examples of how to use them. Some other tools may not be fully-documented (yet), but you can always move to an appropriate directory (e.g., apriori) and run the tool with the -h flag (e.g., ./apriori -h) to obtain instructions on basic usage with brief descriptions of each option and their default values.

Biorithm directories that begin with "lib" refer to libraries, and there will not be any tools available in those directories that the user can directly run. Most of the other directories contain usable tools.

History

Biorithm 1.1 (Added 2012-07-27):

• Added the Network Reconciliation tool.
• Added several new options to the biograph tool.
• GAIN changes:
  • Added options to filter functions by the number of genes they annotate.
  • Bugfixes and implementation improvements for SinkSource, SinkSource+, and GeneMANIA.
  • Removed creation of an extraneous output file.
  • General code cleanup.
  • Improved documentation.
• Improved libgraph documenatation.

Biorithm 1.0 (Added 2011-09-22):

• First version of Biorithm.
• Available tools include:
  • ActiveNetworks and NetworkLego
  • Bicluster Miner
  • Biograph
  • BiVoC
  • Functional Enrichment
  • GAIN
  • Process GO
  • Truthiness Miner
  • xMotif
• Available libraries include:
  • libapriori
  • libexpression
  • libfun
  • libgeewhiz
  • libgraph
  • libutil