Software and Development Tools

CISBAN has developed a number of software tools for systems biology. CISBAN hosts a high power computing facility (10 x 8-core nodes) for data analysis and modeling. A range of research projects which have utilized our software tools are available in our research section.

For all of the software and development tools developed and maintained by the CISBAN in silico group, please see the Portal for Systems Biology of Ageing

Archiving data

  • FuGE, a data standard for describing laboratory protocols and for developing new data formats
  • Robot Object Database, a storage tools and database for high-throughput yeast data
  • SyMBA, a repository tool for storing, archiving, and retrieving multi-omics high throughput data and metadata

Modelling

  • BASIS, a collection of web-based services for the quantitative study of the biology of ageing. CaliBayes integrates GRID-based post-genomic data resources through Bayesian calibration of biological simulators
  • Model Format OWL, an aid to computational reasoning and validation of SBML models
  • pysbml, a package with python libraries that are useful in SBML modelling
  • SBML Shorthand, a tool to aid in the creation of SBML models
  • Saint, a lightweight integration environment for model annotation

Networks

  • CID provides integrated interactomes for different ageing-related model organisms
  • Relevant networks exploit the bias in datasets to generate networks that are relevant to particular biological questions