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Ki MoSys: a web-based repository of experimental data for KInetic MOdels of biological SYStems

Rafael S Costa, André Veríssimo, Susana Vinga
2014 BMC Systems Biology  
Conclusions: KiMoSys is a web-based system that integrates a public data and associated model(s) repository with computational tools, providing the systems biology community with a novel application facilitating  ...  The kinetic modeling of biological systems is mainly composed of three steps that proceed iteratively: model building, simulation and analysis.  ...  For this purpose we have built KiMoSys a web-based repository oriented to kinetic modeling that provides a public data repository of published data in a structured format including annotations to external  ... 
doi:10.1186/s12918-014-0085-3 pmid:25115331 pmcid:PMC4236735 fatcat:s5prl75lmfdxfanozmal3jhh2m

KiMoSys 2.0: an upgraded database for submitting, storing and accessing experimental data for kinetic modeling

Hugo Mochão, Pedro Barahona, Rafael S Costa
2020 Database: The Journal of Biological Databases and Curation  
The KiMoSys (https://kimosys.org), launched in 2014, is a public repository of published experimental data, which contains concentration data of metabolites, protein abundances and flux data.  ...  It offers a web-based interface and upload facility to share data, making it accessible in structured formats, while also integrating associated kinetic models related to the data.  ...  This work was also supported by Fundação para a Ciência e a Tecnologia (FCT), through IDMEC, under LAETA, project UIDB/50022/2020. All past collaborators of KiMoSys are deeply acknowledged.  ... 
doi:10.1093/database/baaa093 pmid:33247931 fatcat:jgugf7g6gvhabka7l227f42njm

SBtab: a flexible table format for data exchange in systems biology

Timo Lubitz, Jens Hahn, Frank T. Bergmann, Elad Noor, Edda Klipp, Wolfram Liebermeister
2016 Bioinformatics  
SBtab is a table-based data format for Systems Biology, designed to support automated data integration and model building.  ...  The format comes with predefined table types for experimental data and SBML-compliant model structures and can easily be customized to cover new types of data.  ...  to the development of SBtab.  ... 
doi:10.1093/bioinformatics/btw179 pmid:27153616 pmcid:PMC4978929 fatcat:fzzxsohgp5bynik7iu3l54dp3i

Unifying the meaning of open and designing a new global open solutions policy framework

Glenn L. Hampson, L Kamerlin, H Hanahoe, C Graf
2020
Society's pursuit of open information solutions is disjointed.  ...  entities from a policy perspective.  ...  MATHEMATICAL & MODELING RESOURCES BioModels Database view FAIRsharing entry Kinetic Models of Biological Systems (KiMoSys) view FAIRsharing entry The Network Data Exchange (NDEx) view FAIRsharing  ... 
doi:10.13021/osi2020.2930 fatcat:pwhlnughzbey5b5jmyhfindnru