About

About PySB

PySB is an open source tool developed in the laboratory of Peter K. Sorger at Harvard Medical School by C. F. Lopez, J. L. Muhlich, and J. A. Bachman. PySB was motivated by the desire to create a mathematical representation of a “biological word model” in a manner that does not result in significant loss of information. Our approach aimed to embed a rules-based language formalism within a fully developed programming language. We wanted the language to be simple, flexible, extensible, and easy to learn. After much work, the idea to develop PySB in the Python programming language began to mature. At the time of release PySB consists of a set of core algorithms that allow the user to develop programs, similar to the way a user thinks about biology, using Python at a biological rules-language level. PySB also provides a set of biochemical macros to enable model creation and offers a novel paradigm in biological model building in a modular manner. PySB, through in-house developed code or through available Python modules, has the capablities to develop models of any arbitrary size, numerical integration using ODEs, numerical model analysis, computer experiment plotting, model visualization, symbolic math manipulations, and provides a base for users to develop interactions with any tools available in the Python programming language.

About the Developers

Carlos F. Lopez received his B.A. and B.S. from University of Miami, Ph. D. from University of Pennsylvania and trained as a postdoctoral fellow with Peter J. Rossky at University of Texas at Austin and Peter K Sorger at Harvard Medical School. He is now an assistant professor at Vanderbilt University, department of Cancer Biology where he continues to contribute to PySB.

Jeremy L. Muhlich received his B.S. from Johns Hopkins University and is a Staff member in the laboratory of Professor Peter K. Sorger. He is an active developer of PySB.

John A. Bachman received his B.S. from Harvard University and is working toward his Ph. D. at Harvard Medical School. He continues to contribute and use PySB for his work.

Peter K. Sorger received his A.B. from Harvard College, Ph.D. from

Trinity College Cambridge, U.K. and trained as a postdoctoral fellow with Harold Varmus and Andrew Murray at the University of California, San Francisco. Sorger is the Otto Krayer Professor of Systems Pharmacology at Harvard Medical School (HMS) and co-founder of the Open Microscopy Environment (OME), MIT’s Computational and Systems Biology Initiative (CSBi), the Council for Systems Biology in Boston (CSB2; www.csb2.org) and companies that include Merrimack Pharmaceuticals and Glencoe Software and serves on the scientific advisory and corporate boards of several other technology companies. He is director of the Center for Cell Decision Processes, an NIH Center of Excellence in Systems Biology and co-directs a new HMS program in Systems Pharmacology.