SYSTEMS

A software package developed by a professor at the Virginia Bioinformatics Institute (VBI) and his colleagues to help researchers better understand the workings of biochemical networks now features an open source license, offering an ever wider range of benefits to its users.

In development for over a decade, COPASI (Complex Pathway Simulator) involves an international collaboration between VBI Professor Pedro Mendes' research groups at Virginia Tech and the University of Manchester and Professor Ursula Kummer's group at the University of Heidelberg. Allowing users with limited experience in mathematics to develop models and simulations of biochemical networks, COPASI supports the Systems Biology Markup Language (SBML) standard for systems biology software and provides researchers the computational tools needed to investigate how a system is working through the construction of biochemical models. COPASI is also used by advanced modelers since it includes sophisticated algorithms. One of COPASI's main features is the ability to automatically adjust model parameters to reproduce experimental results, which helps to justify the validity of the chosen model.

COPASI has always been available through an open source format for individual users, but the software's new license agreement, which is approved by the Open Source Initiative (OSI), allows commercial users to freely use the software. This enhanced availability is included with the release of the newest version (4.6.33) of the software.

"Through our new Artistic License 2.0 licensing scheme, everyone will have the opportunity to download and use future versions of COPASI free of charge," explains Stefan Hoops, VBI senior project manager and one of the technical leads of the project. "The new license is also compatible with more software libraries and other academic software programs, which will allow the development team to enhance the quality and functionality of COPASI. Third parties will now be able to develop and distribute software packages that use the program and it can also be included in other software bundles, such as Linux distributions. Researchers from across the globe will now be able to integrate COPASI in their own software projects and freely distribute results."

The COPASI development team continues to make improvements to the software package, with the ultimate goal of helping to further the understanding of cellular and molecular behavior by facilitating the quantitative interpretation of modern experiments. COPASI is designed to meet the real needs of life scientists in a powerful package that every biologist can use, not just experts in systems biology. Development of COPASI has been funded by the National Institutes of Health, the German Ministry of Science, the Klaus Tschira Foundation, the Commonwealth of Virginia, and the British Biotechnology and Biological Sciences Research Council.