Requirements for CellML Libmesh integration

Requirements Specification

Project : CellML-Libmesh Integration

Owner: Shane Blackett (s.blackett@auckland.ac.nz)

Initially Jagir 08/11/06

Initial Draft

Project Description

CellML is the widely used model representation methodology at Auckland Bioengineering institute. Significant effort has been undertaken to model biological phenomena, represent using CellML and to simulate these models using CMISS (the computational work horse).

The Open CMISS project aims at developing the computational back-end on a scalable, distributed environment. Libmesh has been chosen as the mesh solver above which the CMISS capabilities will be developed.

Hence it is imperative that Libmesh should be integrated with CellML components in-order to enable smooth transition from the current environment to the new environment.

Functional Requirements

The following section lists the functional requirements that the integration components are expected to meet.

Transform CellML representation of the model to machine executable code

• That can be linked with OpenCMISS
• Will conform to an interface standard between the cell model and OpenCMISS
• Conforms to debugging and tracing standard of Open CMISS

Desirable Features

The following section lists the non-functional requirements that the integration components are expected to meet.

Provide interfaces to utilize external solvers like CVODES

Minimal memory utilization

• Distributed across processes.
• Sharing parameters that do not vary from cell to cell.
  • Can be handled at compile time perhaps.

Cross-platform portability (compile time only)