d2d开源项目

Contact:AndreasRaue-andreas.raue@fdm.uni-freiburg.de(forsupportissues,pleaseusetheissuesandforum,thanks!)

Cite:

Data2Dynamics:amodelingenvironmenttailoredtoparameterestimationindynamicalsystems.RaueA.,etal.Bioinformatics,31(21),3558-3560,2015.

LessonsLearnedfromQuantitativeDynamicalModelinginSystemsBiology.RaueA.,etal.PLOSONE,8(9),e74335,2013.

Video:SeehoweasymodelcalibrationcanbeusingD2DSoftwareinthisYouTubeVideo.ThevideoisrecordedinrealtimeonadualcorelaptopwiththeBachmannetal.2011exampleusingthefirstdataset.

Majorpurpose:EstablishingODEmodelsbasedonexperimentaldata.Thesoftwareisdesignedforbiochemicalreactionnetworks,butisnotlimitedtothis.

Keyfeature:Reliableandefficientparameterestimationtechniquesandstatisticalassessmentofparameter-,measurement-andpredictionuncertainties.

Somespecialfeatures:

Theframeworkcandealwithxperimentalerrorbarsbutalsoallowsfittingoferrorparameters(errormodels).

Modelinputscanbeimplementedasparameterizedfunctionsorcubicsplinesandcanbeestimatedtogetherwiththemodeldynamics(readmore).

Formodelcalibration,i.e.parameterestimation,bothstochasticanddeterministicnumericaloptimizationalgorithmscanbeused.

Foruncertaintyanalysisofmodelparameterandpredictions,theprofilelikelihoodapproachandMarkovchainMonteCarlosamplingapproachesareavailable(readmore).

Efficientnumericalcalculationofthedynamicsandderivativesinaparallelizedmanner(readmore).

L1regularizationofparameterfold-changescanbeused(readmore).

L2regularizationandincorporationofpriorknowledge

Identificationofinformativeexperimentaldesigns

Thesoftwareisopensourceandfreefornon-commercialusageandsupportsparallelization

AmorecomprehensivedescriptionoffeaturesisavailablefeaturespageintheWiki.

ThesoftwarewasawardedtwiceasbestperformerintheDialogueforReverseEngineeringAssessmentsandMethods(DREAM).2011intheEstimationofModelParametersChallenge(DREAM6)and2012intheNetworkTopologyandParameterInferenceChallenge(DREAM7).Readmoreaboutthisin:SteiertB.,etal.ExperimentalDesignforParameterEstimationofGeneRegulatoryNetworks.PLoSONE7(7),e40052,2012

PleasereadourWikiifyouareinterestedindetails.

CheckoutourWikiforinstallationinstructions.

Copyright©2016D2Ddevelopmentteam.Allrightsreserved.Copyrighttextandthirdpartysoftwarelicenseinformation.