Distributing working versions of published mathematical models for biological systems via the internet

Abstract

Mathematical models are useful tools for investigating complex systems. By representing physiological systems as models, theories can be tested quantitatively against data from the system. Models can be used to explore new theories prior to experimentation and to design studies to optimize experimental resources. They can also be used as teaching tools to illustrate physiochemical principles. In spite of their usefulness and the time invested in developing models, published models are often underused due to the difficulty in obtaining working versions of the model. To address this problem we have designed a library for mathematical models of biological systems on the Internet. The library contains published models of biological systems in formats compatible with several modeling packages, from the fields of physiology, metabolism, endocrinology, biochemistry, and chemistry. The models can be viewed graphically, model solutions can be viewed as plots against data, and models can be downloaded to be run with software on the user's own system. The address of the library is: http://biomodel.georgetown.edu/model/. Investigators are invited to submit working versions of published models to the library. Models can be submitted electronically at the time a manuscript is accepted for publication. As journals go online, articles containing models can be linked to working versions of the models in the library. By increasing access to working versions of models, more of the investment in kinetic studies and model development can be realized. Once a model of interest has been located, a working version of the model can be accessed in a format compatible with one or more commonly used software packages. These include SAAM (Berman and Weiss, 1978; Berman et al., 1983; Boston et al., 1981), SAAM II (Foster et al., 1994), ACSL (Mitchell and Gauthier, 1986), and in the future, Scientist (Bogen, 1989) and MLAB (Knott, 1992). Using the menu on the browser, models can be downloaded to the user's system to be used with their own software. Although it might be helpful to be able to run a model on the library server, due to software license restrictions, SAAM (Berman and Weiss, 1978) is the only software package of those mentioned above that could potentially be run in this way. Criteria for submitting models to the library are that they have been published in a peer-review journal and that they have been fitted to data. Investigators are encouraged to cheek the web site or contact the library developers for the latest instructions prior to submitting a model.