ABC-SysBio specifications

Information


Unique identifier OMICS_09022
Name ABC-SysBio
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Programming languages Python
Computer skills Advanced
Version 2.05
Stability Stable
Maintained Yes

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Documentation


Maintainer


  • person_outline Michael Stumpf <>

Publications for ABC-SysBio

ABC-SysBio in publications

 (13)
PMCID: 5929911
PMID: 29574056
DOI: 10.1016/j.cels.2018.02.008

[…] ny, nz) as,(equation 7)nx=xα˜zωδ˜x,ny=yα˜zωδ˜x,nz=zα˜zωδ˜x., the parameter exploration was carried out using bayesian sampling techniques through the approximate bayesian computation (abc) using abc-sysbio software (). the score functions, d(), are minimal for the optimal behavior scored. they were designed to capture a change from stable steady state to oscillations. this was evaluated […]

PMCID: 5843277
PMID: 29518130
DOI: 10.1371/journal.pone.0193981

[…] how to install abrox can be found online (see https://github.com/mertensu/abrox)., the main advantages of abrox compared to other software packages such as the r-package abc [] or the python module abc-sysbio [] are the domain-independence, meaning that it is not designed for a specific field of research, and its ease of use due to the gui. the software diyabc [] is another attempt […]

PMCID: 5625687
PMID: 29026441
DOI: 10.1186/s13036-017-0071-6

[…] to assess the potential of the 48 candidate architectures to reproduce the known characteristics of the system, we perform model selection based on approximate bayesian computation (abc) using the abc-sysbio software package. abc-sysbio combines bayes’ rule with sequential monte carlo (smc) approaches to solve parameter inference and model selection problems in systems biology [–]. […]

PMCID: 5565741
PMID: 28855977
DOI: 10.1016/j.csbj.2017.07.005

[…] often parameters of a given layer represent variables for an upward layer . it is therefore important to review common practices to perform this task., in , the authors present a platform named abc-sysbio which provides tools for parameter estimation and model selection in systems biology. parameter estimation is performed with approximate bayesian computation . abc-sysbio is designed […]

PMCID: 5425217
PMID: 28489927
DOI: 10.1371/journal.pone.0177336

[…] model comparison and parameter estimation were carried out with an approximate bayesian computation (abc) method combined with sequential monte carlo (smc) sampling, [] implemented in the abc-sysbio python package and complemented with the gpu-accelerated simulation tool, cudasim. [,] each experiment made up of a pair of p53 distributions were analysed independently., the model […]


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ABC-SysBio institution(s)
Centre for Bioinformatics, Division of Molecular Biosciences; Institute of Mathematical Sciences, Department of Epidemiology and Public Health, School of Public Health, and Centre for Integrative Systems Biology, Imperial College London, London, UK

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