Software Systems and Databases

  • Kaichu - a Master-Worker cluster computing system written in Java. The system can piggy back on a batch clustering system such as Condor where Sancho workers act as individual jobs. Sancho can efficiently process small jobs (execution time in order of seconds) alleviating the need to adjust or aggregate jobs which is a common issue with less dynamic systems. Sancho was developed by Maciej Trybilo under the supervision of David Gilbert.
  • OBM (an Ontology of BioModelling) aims to support the recording and sharing of knowledge about theconstruction and analysis of biological models. OBM follows a structural approach for the engineering of biochemical network models. It aims to provide consistent logical definitions of the principle entities involved to the typical phases of biomodelling, e.g. identification of tasks and requirements for a model construction, modelling domain of interest, selection of tools for model construction, analysis, and validation, exploration of a model, reporting. Currently OBI is at an initial stage of the development. This effort is being led by Larisa Soldatova in collaboration with Pam Gao and David Gilbert.
  • MC2(PLTLc)a Monte Carlo Model Checker for properties written in Probabilistic Linear-time Temporal Logic with numerical constraints (PLTLc). The model checker takes as input a set of traces in the form of a simulation output file.  It also takes as input a query file containing a list of PLTLc properties, and returns for each property the probability that the set of traces satisfies the property. MC2(PLTLc) can operate with stochastic/deterministic simulation output, deterministic parameter scan output or even wet-lab data. MC2(PLTLc) was developed by Robin Donaldson at the Bioinformatics Research Centre in the University of Glasgow under the supervision of David Gilbert.
  • BioNessieLite - the command-line version of the BioNessie simulator that can simulate biochemical pathway models in SBML and can also perform parameter scans.  Simulation and parameter scan results are textual, keeping with the lightweight approach.  The command-line interaction allows for easy distribution across a computer cluster and integrates well with the MC2(PLTLc) model checker. BioNessie Lite was developed was developed by Robin Donaldson and Xuan Liu at the Bioinformatics Research Centre in the University of Glasgow under the supervision of David Gilbert.  
  • BioNessie - a free, state-of-the-art platform-independent BioModel engineering environment for biochemical networks that supports the development, simulation and analysis of biochemical network models. It provides a full user-friendly Graphical User Interface (GUI) which allows the user to import, create, edit and export the biochemical models with the SBML (Systems Biology Markup Language) standard. The unique Concurrent Versions System (CVS) design helps users to keep track of the version history of their SBML models during construction and subsequent modification. BioNessie supports multi-thread/core parameter scan, sensitivity analysis, parameter estimation (model fitting) and model checking.  BioNessie was developed by Xuan Liu at the University of Glasgow and Brunel University under the supervision of David Gilbert.
  • Multiscale models and analysis. Developed by Ovidiu Parvu while a PhD student at Brunel University under the supervision of David Gilbert.

Page last updated: Monday 01 September 2014