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Computational modelling software and tools

Infobiotics Workbench (IBW) is a software platform designed to model and analyse systems and synthetic biology. IBW permits applying various computational techniques, such as modelling, simulation, verification and biocompilation. The simulation component includes various simulation algorithms implemented in a high-performance environment, whereas the verification part integrates various model checkers. The biocompilation component helps selecting appropriate devices into the designed system. This novel integrative approach makes IBW the only tool synthesising these different techniques in one tool. (See also EPSRC ROADBLOCK project.)

kPWorkbench is developed to support the computational analysis of membrane computing systems, in particular kernel P systems. kPWorkbench permits modeling, simulation and verification of membrane systems. The framework features a native simulator, a general-purpose large-scale agent-based simulation environment, and several model checkers to formally verify membrane systems. The tool also features a query language based on natural language statements to express system requirements.

FLAME is a generic agent-based modelling system, which can be used to develop applications in many areas, e.g. biology, economy, meteorology, engineering, etc. It generates a complete agent-based application, which can be compiled and built on the majority of computing systems ranging from laptops to HPC super computers.

FEDES is a Finite Element Data Exchange System for mapping finite element analysis data between different FE solvers and meshes with different element types and densities. Six commercial FE solvers are supported (ABAQUS, ANSYS, DEFORM, MARC, MORFEO, VULCAN). The FEA data outputted can be visualized with the open source program ParaView.