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AMIGO specifications

Information


Unique identifier OMICS_13998
Name AMIGO
Software type Package/Module
Interface Command line interface
Restrictions to use Academic or non-commercial use
Output data Given a problem definssary dition, AMIGO_Prep preprocesses generates neceirectories and code
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Requirements
Cytoscape, C complier
Maintained Yes

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Versioning


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Documentation


Maintainer


  • person_outline Eva Balsa-Canto

Publications for AMIGO

AMIGO citations

 (8)
library_books

A parallel metaheuristic for large mixed integer dynamic optimization problems, with applications in computational biology

2017
PLoS One
PMCID: 5557587
PMID: 28813442
DOI: 10.1371/journal.pone.0182186

[…] bles, one for each hyperedge. Thus, the obtained optimization problem contains 120 parameters, being 86 continuous and 34 binaries. We proceeded by implementing the model and experimental setup using AMIGO [] and exporting C code which could be used with the saCeSS2 method presented here.Considering saCeSS2, it is important to note that the cooperation between processes changes the systemic proper […]

library_books

Adaptive introgression from distant Caribbean islands contributed to the diversification of a microendemic adaptive radiation of trophic specialist pupfishes

2017
PLoS Genet
PMCID: 5552031
PMID: 28796803
DOI: 10.1371/journal.pgen.1006919

[…] ogression regions that have contributed to species divergence. For each of these regions, we looked for annotated genes and searched their gene ontology in the phenotype database ‘Phenoscape’ [–] and AmiGO2 [] for pertinent functions, particularly skeletal system effects. Skeletal features, particularly craniofacial morphologies such as jaw length, have extremely high rates of diversification amon […]

library_books

Scalable Parameter Estimation for Genome Scale Biochemical Reaction Networks

2017
PLoS Comput Biol
PMCID: 5256869
PMID: 28114351
DOI: 10.1371/journal.pcbi.1005331

[…] ivity analysis from symbolic model definitions. This way, the toolbox is easy-to-use and can easily be integrated with existing toolboxes. Also other MATLAB toolboxes for computational modeling, e.g. AMIGO [], Data2Dynamics [], MEIGO [] and SBtoolbox2 [] could be extended to exploit adjoint sensitivity analysis. In addition to adjoint sensitivity analysis, these MATLAB toolboxes could exploit forw […]

library_books

Reverse engineering of logic based differential equation models using a mixed integer dynamic optimization approach

2015
Bioinformatics
PMCID: 4565031
PMID: 26002881
DOI: 10.1093/bioinformatics/btv314

[…] g. S19) has a total of 109 hyperedges and 135 continuous parameters. To transform this network into logic-based ODEsl, we developed a parser that generates a C file and Matlab scripts compatible with AMIGO ().To use logic-based ODE models, all data should be in the [0,1] range and thus we simply normalized the data by rescaling it to this range. From the total 25 states present in the model, 16 co […]

call_split

BioPreDyn bench: a suite of benchmark problems for dynamic modelling in systems biology

2015
BMC Syst Biol
PMCID: 4342829
PMID: 25880925
DOI: 10.1186/s12918-015-0144-4
call_split See protocol

[…] value for each observable; and problem B6, where the weights are inversely related to the level of expression. More details are given in the next section. Note that the cost functions used in Matlab/AMIGO are not exactly the same as the ones used in COPASI, since in COPASI the weights are scaled so that for each experiment the maximal occurring weight is 1.The minimization of the objective functi […]

library_books

MEIGO: an open source software suite based on metaheuristics for global optimization in systems biology and bioinformatics

2014
BMC Bioinformatics
PMCID: 4025564
PMID: 24885957
DOI: 10.1186/1471-2105-15-136

[…] ing inner problems (e.g. simulations or even other optimization problems) to obtain explicit values for the objective function and/or the possible constraints. For example, CellNOpt [], SBToolbox [], AMIGO [] and Potterswheel [] use eSS for dynamic model calibration. Some recent successful applications of eSS in the field of systems biology can be found in [-]. It has also been shown that eSS outp […]

Citations

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AMIGO institution(s)
Bioprocess Engineering Group, IIM-CSIC, Vigo, Spain
AMIGO funding source(s)
EU FP7 project NICHE [ITN grant number 289384], Spanish MINECO/FEDER projects IMPROWINE [grant number AGL2015-67504-C3-2-R] and SYNBIOFACTORY [DPI2014-55276-C5-2-R]

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