Software Source Codes (mostly C)

ODEsim description source version 2 with batch file handling
STOsim description source
DomainDesign description source


ODEsim

ODEsim is a Ordinary Differential Equation software used for mass-action simulation of reaction kinetics. It is different from standard Matlab procedures on numerically solving ODEs in that it is user-friendly in the input of reactions. Reactions are inputted as "A + B -> C" and with listed reaction rates, and software will determine d[A]/dt from all inputted reactions as a back-end process. Has been tested relatively frequently, and no known bugs exist. Parameter input files are relatively straightfoward, but I will try to write up documentation at some point. Output is a tab-separated-values file which can be loaded up in Excel or Matlab for viewing. At some point I may write up front-end for outputting directly as a PS file.

STOsim

STOsim is a Stochastic Reactions simulation software. Reactions should be expressed in elementary form (i.e. all intermediates displayed), and number of molecules to be simulated should be small. Parameter file descriptions are in source code. This program has been moderately used, but source may not be as robust.

Domain Design

Domain Design is software that designs domains that have few interactions with each other. It uses a simplified algorithm to estimate the binding energy between domains, and adjusts this energy with ad-hoc penalties for things like GGGG (which is known to cause DNA quadroplexing). This even has an ANSI UI.