Continued Development and Maintenance of the Systems Biology Workbench

University Of Washington, Seattle WA

Investigators

Linked publications & trials

Abstract

[unreadable] DESCRIPTION (provided by applicant): This application is to provide programming support to enable the continued maintenance and development of the Systems Biology Workbench (SBW) and related software libraries. SBW is a large collection of software tools for enabling the simulation and analysis of kinetic models of cellular networks. This software have proved most useful in the study of problems related to biomedical research, in particular our work on the p53/Mdm2 response to DNA damage and our stem cell differentiation model would not have been possible without this resource. Many of the tools in SBW can be used as standalone applications but when connected to the SBW communications backbone, the tools may be used seamlessly together. This permits software applications to be written in different languages, potentially, running on different platforms to work together. All SBW compliant applications can read and, often write, standard SBML Level 2. This enables computational models to be easily shared between SBW and any other SBML compliant tool set. In this application we wish to request resources to continue to maintain the software and to contribute further improvements to its functionality. Maintenance of SBW requires ensuring that the different tools can run on the three main platforms - Mac, Linux and Windows - particularly as they are updated. In addition we need to continue to maintain and assist in the growth of the SBML ODE and stochastic test suite which are essential tools that we use in our development process. In addition to maintaining the current software we also wish to extent functionality in certain areas. We wish to propose four focus areas for further development, these include: [unreadable] [unreadable] a) A portable library that can be used to determine unit consistency in a model; [unreadable] [unreadable] b) A portable library for translation between SBML and CellML; c) Develop a composition framework and software libraries to enable models to be constructed from other submodels; d) To port our successful visual design editor, JDesigner, to the Mac and Linux platforms. Many of these developments will directly affect the computational community. Placing much of the planned functionality into portable libraries will enable other developers to reuse this work in their own projects. All code will be open source and hosted on sourceforge. [unreadable] [unreadable] [unreadable]