COPASI

Biochemistry specialists who are involved into various undertakings that imply the simulation of biochemical network models need an efficient solution for managing their experiments. COPASI is here to help them achieve the required results easier, through its array of simulation and analysis tools for biochemical networks dynamics.

COPASI offers users a minimalist interface that houses numerous tools that will help users set the values for the different parameters which characterize the model. People will be able to easily switch between concentration and particle number display, in accordance with the requirements of the current model. Nevertheless, novice users will require a thorough documentation process since the application does require advanced knowledge of biochemistry.

The utility provides a set of predefined model examples that will help inexperienced users practice and get a grasp of its features and handling. For each particular model, users can add their own annotations and the model’s corresponding URL, if applicable. In order to enhance the model referencing, COPASI offers a well defined author, reference and description text entry system.

People will be able to apply state changes to their models (initial state and initial state update) and the application will allow them to verify the models. The resulting check-up reports contain detailed information about the validity of each model component.

Having the different compartments, species, reactions and events distributed hierarchically, COPASI provides extensive parametrization for each model component. In addition to its main biochemical and mathematical constituents, the utility also offers task customization and output specifications for the selected models.

Addressing mostly advanced users who are involved in the field of biochemistry, this application will provide a solid tool for defining the parameters of biochemical network models. It will allow people to parametrize their models with increased detail, thanks to its array of predefined functions and mathematical equations. This software package implies advanced knowledge of biochemistry and novice users are advised to document themselves prior to using it.