Computational Methods in Systems Biology
292 F. Camporesi et al. Fig. 1.Two rules. (left) Two proteins may bind. (right) The protein on the left may activate the right s ...
KADE: A Tool to Compile Kappa Rules into (Reduced) ODE Models 293 2 ODEs Generation with KADE KaDEgenerates the differential sem ...
294 F. Camporesi et al. reactions. LastlyErodetakes the first convention for reaction rate constants in the differential setting ...
KADE: A Tool to Compile Kappa Rules into (Reduced) ODE Models 295 k 1 k 2 k 3 Fig. 3.Sites are equivalent, if the corrected rate ...
296 F. Camporesi et al. 4 Benchmarks We test the reduction power and the time efficiency of our framework on three families of m ...
KADE: A Tool to Compile Kappa Rules into (Reduced) ODE Models 297 (a) kinetase/phosphatase model. (b) multi-phosphorylation site ...
298 F. Camporesi et al. Feret, J., Danos, V., Krivine, J., Harmer, R., Fontana, W.: Internal coarse-graining of molecular syste ...
KADE: A Tool to Compile Kappa Rules into (Reduced) ODE Models 299 Camporesi, F., Feret, J., L ́y, K.Q.: KaDE: a tool to compile ...
Database of Dynamic Signatures Generated by Regulatory Networks (DSGRN) Bree Cummins^1 , Tomas Gedeon1(B), Shaun Harker^2 , and ...
Database of Dynamic Signatures Generated 301 dynamics across hundreds of networks with data allowing rigorous exploration of the ...
302 B. Cummins et al. Switching Systems of Regulatory Networks.A regulatory network involv- ingNgenes is often modeled by a syst ...
Database of Dynamic Signatures Generated 303 constant are semi-algebraic sets, and that the decomposition of parameter space int ...
304 B. Cummins et al. XY 00 10 01 20 11 21 FC FP (a) (b) (c) 00 10 01 20 11 21 FC^0010 01 20 11 21 FC FP (d) (e) (f) (g) 00 10 0 ...
Database of Dynamic Signatures Generated 305 YOX1 SBF HCM1 SFF SWI5 CdH1 YOX1 SBF HCM1 SFF SWI5 CdH1 X 7 X 8 4400 4410 4420 4430 ...
306 B. Cummins et al. be considered a representation of such unchecked progression through the cell cycle. While the original ne ...
Database of Dynamic Signatures Generated 307 each type of node has to be precomputed using Cylindrical Algebraic Decom- position ...
308 B. Cummins et al. Bogomolov, S., Schilling, C., Bartocci, E., Batt, G., Kong, H., Grosu, R.: Abstraction-based parameter sy ...
PINT: A Static Analyzer for Transient Dynamics of Qualitative Networks with IPython Interface Lo ̈ıc Paulev ́e(B) CNRS, LRI UMR ...
310 L. Paulev ́e correctness (under-approximations, satisfying sufficient conditions) or complete- ness (over-approximations, sa ...
PINT: A Static Analyzer for Transient Dynamics of Qualitative Networks 311 Fig. 1.(a) graphical representation of an automata ne ...
«
8
9
10
11
12
13
14
15
16
17
»
Free download pdf