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cuda-sim specifications


Unique identifier OMICS_09023
Name cuda-sim
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Python
Parallelization CUDA
Computer skills Advanced
Version 0.07
Stability Stable
Maintained Yes


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Publication for cuda-sim

cuda-sim citations


The feasibility of genome scale biological network inference using Graphics Processing Units

PMCID: 5360040
PMID: 28344638
DOI: 10.1186/s13015-017-0100-5

[…] used for stiff problems. Stiff solvers require more memory to record previous time steps and matrices used for solving implicit equations. The Thompson version of LSODA is used by Zhou et al. in the CUDA-sim package written in Python¬†[]. Zhou et al. report a speedup of around 50 fold, on a single Tesla C2050 GPU relative to a single Intel Core i7 Extreme Edition CPU, for a single non-stiff ODE wh […]


Ptch1 and Gli regulate Shh signalling dynamics via multiple mechanisms

Nat Commun
PMCID: 4396374
PMID: 25833741
DOI: 10.1038/ncomms7709
call_split See protocol

[…] model, which relies on the transcriptional regulation of Gli, the degradation of rates of Gli was fixed and Ptch1 regulation by Gli was disabled.We used ABC performed with the software ABC-SysBio and cuda-sim to analyse our model. This technique can be used to determine an approximate representation of the parameter space for which a model is able to satisfy a particular target. We stereotyped the […]


A theoretical framework for the regulation of Shh morphogen controlled gene expression

PMCID: 4197706
PMID: 25294939
DOI: 10.1242/dev.112573
call_split See protocol

[…] sing Mathematica 9.0 (Wolfram Research). The network model was analysed using ABC-SysBio (; ), an ABC () suite designed to run in parallel on graphics processing units (GPUs) using the python package cuda-sim (Zhou et al., 2011). The input gradient of GliA and GliR described in was discretised into 100 positions. At each position the ODEs describing the TF dynamics were solved to steady state (10 […]

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cuda-sim institution(s)
Centre for Bioinformatics, Division of Molecular Biosciences; Institute of Mathematical Sciences, and Centre for Integrative Systems Biology, Imperial College London, London, UK

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