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: ? ? a) A portable library that can be used to determine unit consistency in a model; ? ? 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. ? ? ?
| Choi, Kiri; Medley, J Kyle; König, Matthias et al. (2018) Tellurium: An extensible python-based modeling environment for systems and synthetic biology. Biosystems 171:74-79 |
| Bedaso, Yosef; Bergmann, Frank T; Choi, Kiri et al. (2018) A portable structural analysis library for reaction networks. Biosystems 169-170:20-25 |
| Bartley, Bryan A; Kim, Kyung; Medley, J Kyle et al. (2017) Synthetic Biology: Engineering Living Systems from Biophysical Principles. Biophys J 112:1050-1058 |
| Bergmann, Frank T; Nickerson, David; Waltemath, Dagmar et al. (2017) SED-ML web tools: generate, modify and export standard-compliant simulation studies. Bioinformatics 33:1253-1254 |
| Choi, Kiri; Smith, Lucian P; Medley, J Kyle et al. (2016) phraSED-ML: A paraphrased, human-readable adaptation of SED-ML. J Bioinform Comput Biol 14:1650035 |
| Medley, J Kyle; Goldberg, Arthur P; Karr, Jonathan R (2016) Guidelines for Reproducibly Building and Simulating Systems Biology Models. IEEE Trans Biomed Eng 63:2015-20 |
| Somogyi, Endre T; Bouteiller, Jean-Marie; Glazier, James A et al. (2015) libRoadRunner: a high performance SBML simulation and analysis library. Bioinformatics 31:3315-21 |
| Neal, Maxwell L; Cooling, Michael T; Smith, Lucian P et al. (2014) A reappraisal of how to build modular, reusable models of biological systems. PLoS Comput Biol 10:e1003849 |
| Bergmann, Frank T; Adams, Richard; Moodie, Stuart et al. (2014) COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project. BMC Bioinformatics 15:369 |
| Neal, M L; Galdzicki, M; Gallimore, J T et al. (2014) A C library for retrieving specific reactions from the BioModels database. Bioinformatics 30:129-30 |
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