Models

The model can simulate the the dynamics of sigB dependent transcription at the transition to starvation. It is was developed along the comic in 'sigB-activation-comic_vol1'. Parameters were partly taken from Delumeau et al., 2002, J. Bact. and Igoshin et al., 2007, JMB. Parameter estimation was performed using experimental data from '0804_shake-flask'. Use the .m-file with matlab as: % reading initial conditions from the file: inic = sigb_model_liebal;

% performing the simulation: [t,y] = ...

The model describes the Entner-Doudoroff pathway in Sulfolobus solfataricus under temperature variation. The package contains source code written in FORTRAN as well as binaries for Mac OSX, Linux, and Windows. If compiling from source code, a FORTRAN compiler is required. On-line versions of the model are also available at: http://bioinfo.ux.uis.no/sulfosys http://jjj.biochem.sun.ac.za/sysmo/projects/Sulfo-Sys/index.html

The agent-based model involves the representation of each individual molecule of interest as an autonomous agent that exists within the cellular environment and interacts with other molecules according to the biochemical situation. FLAME environmet has beem used for agent-based development. The FLAME framework is an enabling tool to create agent-based models that can be run on high performance computers (HPCs). Models are created based upon extended finite state machines that include message input ...