We are regularly developing software for our projects. Most of them are freely available as open-source projects. Here is the list of our recent projects.
Portfolio
BioNetGen
Bionetgen Implementation of the Heat Shock Response Bogdan Iancu has implemented the Bionetgen source code of the Heat Shock Response. It can be downloaded as a zip-file from here .
Gene Assembly Simulator
Download GeneAssemblySimulator.jar_.zip GeneAssemblySimulator.jar_.tar.gz Demo https://webswing.combio.org/gas/ User: demo, password: demo Tutorial Creating a new drawing area To be able to draw a new graph you have to create a new drawing area. By clicking on the icon �in the toolbar or choosing �New Graph� in file menu, a new internal window will popup where it is …
Heat Shock Response – Petri Net
Petri Net Implementation of the Heat Shock Response Diana-Elena Gratie has built Petri net models of the heat shock response. They can be downloaded as a zip-file from here . The latest standard and colored Petri net models are available here.
Heat Shock Response – PRISM
PRISM Implementation of the Heat Shock Response Sepinoud Azimi has implemented the PRISM source code of the Heat Shock Response. It can be downloaded as a zip-file from here .
Heat Shock Response Simulator
Kristian Nylund has developed Heat Shock Simulator. Links: Stand-alone Java application should be downloaded from here . In-browser demo can be accessed from here. User/password: demo/demo
WEBRSIM – Reaction System Simulator
This page provides a Web interface to the brsim reaction system simulator. For more information about how to describe reaction systems and their contexts, see the project page. Example 1: A Binary Counter In Example 3 of paper [1], the authors show how binary counters can be built with reaction systems. In short, the idea …