Biorithm  1.1

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:

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


  1. Building Biorithm
  2. Available Tools

Building Biorithm

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


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.


Biorithm 1.1 (Added 2012-07-27):

Biorithm 1.0 (Added 2011-09-22):

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