Journal: BMC Systems Biology

Article Title: sybil – Efficient constraint-based modelling in R

doi: 10.1186/1752-0509-7-125

Figure Lengend Snippet: Running times for flux variability analysis. Running time of flux variability analysis in various software packages using the GNU Linear Programming Kit (GLPK). Time was measured in R with the function Rprof() and in MATLAB with the Profiler function. In both cases, the running time of a function is reported as "total time". For OptFlux, the Unix command top in delta mode was used. SBRT itself reports the elapsed time for flux variability analysis. For FASIMU, the "real time" reported by the Unix command time was used. For COBRApy, the Python module time was used. All simulations were run ten times on the same desktop PC (Intel Xeon, 2.8 GHz, running Mac OS 10.7). The reported running times are arithmetic means of these values.

Article Snippet: The MATLAB packages COBRA Toolbox and CellNetAnalyzer make use of glpkmex [ ], which provides high-level function calls to build and solve mathematical programming problems in one step.

Techniques: Software

Journal: BMC Systems Biology

Article Title: sybil – Efficient constraint-based modelling in R

doi: 10.1186/1752-0509-7-125

Figure Lengend Snippet: Running time for simulations of genome-wide genetic perturbations. Running time of genome-wide in silico perturbation experiments (single- and double-gene knockouts) using various software packages and different mathematical optimisation packages. a) For computation of single flux deletions, we used the functions oneFluxDel() in sybil, single_deletion() in COBRApy, singleRxnDeletion() in the COBRA Toolbox, and Exhaustive_single_deletion() in abcdeFBA. b-d) In sybil, we used the functions oneGeneDel() and doubleGeneDel() for simulations of single and pairwise knockout mutants, respectively. The same results were achieved with the COBRA Toolbox using functions singleGeneDeletion() and doubleGeneDeletion() , respectively. In COBRApy, we used functions single_deletion() and double_deletion . In OptFlux, the calculation of so called "critical genes" was used. The running times for COBRApy are extremely long when using the IBM ILOG CPLEX solver (* more than 24 hours for a simulation of all pairwise knockout mutants). The interface between COBRApy and IBM ILOG CPLEX seems not to support reusing a computed basis for re-solving an optimisation problem. Running times were obtained as in Figure .

Article Snippet: The MATLAB packages COBRA Toolbox and CellNetAnalyzer make use of glpkmex [ ], which provides high-level function calls to build and solve mathematical programming problems in one step.

Techniques: Genome Wide, In Silico, Software, Combined Bisulfite Restriction Analysis Assay, Knock-Out