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BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems

N. Le Novere
2006 Nucleic Acids Research  
BioModels Database ( biomodels/), part of the international initiative, provides access to published, peerreviewed, quantitative models of biochemical and cellular systems  ...  This allows the users to search accurately for the models they need.  ...  Bard Ermentrout, Sarah Keating, Joanne Matthews and Nicolas Rodriguez for sharing their code. Funding to pay the Open Access publication charges for this article was provided by EMBL.  ... 
doi:10.1093/nar/gkj092 pmid:16381960 pmcid:PMC1347454 fatcat:zx5xzxueqvgvja2p3hp3uft3by

BioModels: ten-year anniversary

Vijayalakshmi Chelliah, Nick Juty, Ishan Ajmera, Raza Ali, Marine Dumousseau, Mihai Glont, Michael Hucka, Gaël Jalowicki, Sarah Keating, Vincent Knight-Schrijver, Audald Lloret-Villas, Kedar Nath Natarajan (+8 others)
2014 Nucleic Acids Research  
BioModels ( is a repository of mathematical models of biological processes.  ...  A large set of models is curated to verify both correspondence to the biological process that the model seeks to represent, and reproducibility of the simulation results as described in the corresponding  ...  ACKNOWLEDGEMENTS The BioModels team would also like to express their gratitude to the Computational Systems Biology community, in particular members of the SBML forum, not only for models contributed,  ... 
doi:10.1093/nar/gku1181 pmid:25414348 pmcid:PMC4383975 fatcat:amkctztvwzddbpmb4hr5bj5xau

BioModels: Content, Features, Functionality, and Use

N Juty, R Ali, M Glont, S Keating, N Rodriguez, MJ Swat, SM Wimalaratne, H Hermjakob, N Le Novère, C Laibe, V Chelliah
2015 CPT: Pharmacometrics & Systems Pharmacology  
BioModels is a reference repository hosting mathematical models that describe the dynamic interactions of biological components at various scales.  ...  Most model components are cross-linked with external resources to facilitate interoperability. A large proportion of models are manually curated to ensure reproducibility of simulation results.  ...  This work received support from the Biotechnology and Biological Sciences Research Council (BioModels, BB/J019305/  ... 
doi:10.1002/psp4.3 pmid:26225232 pmcid:PMC4360671 fatcat:4ki3pd2zdze5pdvtqo4qhjbi3a

BioModels-15 years of sharing computational models in life science

2019 Nucleic Acids Research  
To provide a platform to support universal sharing, easy accessibility and model reproducibility, BioModels (, a repository for mathematical models, was established in  ...  The models submitted to BioModels are curated to verify the computational representation of the biological process and the reproducibility of the simulation results in the reference publication.  ...  ACKNOWLEDGEMENTS We would like to acknowledge the COMBINE community for the support and numerous contributions over the years.  ... 
doi:10.1093/nar/gkz1055 pmid:31701150 pmcid:PMC7145643 fatcat:kbsg5oncwfan3aq4h5arm3bo5i

BioModels: expanding horizons to include more modelling approaches and formats

Mihai Glont, Tung V N Nguyen, Martin Graesslin, Robert Hälke, Raza Ali, Jochen Schramm, Sarala M Wimalaratne, Varun B Kothamachu, Nicolas Rodriguez, Maciej J Swat, Jurgen Eils, Roland Eils (+5 others)
2017 Nucleic Acids Research  
BioModels serves as a central repository of mathematical models representing biological processes.  ...  This new system allows submitting and sharing of a wide range of models with improved support for formats other than SBML.  ...  Special thanks to the DKFZ for valuable contributions and for setting up the initial structure of JUMMP. FUNDING  ... 
doi:10.1093/nar/gkx1023 pmid:29106614 pmcid:PMC5753244 fatcat:3e4bpcbu7bh2dklf7v4vxeduwu

BioModelKit – An Integrative Framework for Multi-Scale Biomodel-Engineering

Mary-Ann Blätke
2018 Journal of Integrative Bioinformatics  
BMK is accessible through a public web interface (, where users can interact with the modules stored in a database, and make use of the model composition features.  ...  BioModelKit (BMK) approaches this challenge by offering an integrative and versatile framework for biomodel-engineering based on a modular modelling concept with the purpose: (i) to represent knowledge  ...  ; and Wolfgang Marwan for supporting the development of BMK by his supervision.  ... 
doi:10.1515/jib-2018-0021 pmid:30205646 fatcat:ioefzk6bffa5tcu64m3jcx3r64

Combining computational models, semantic annotations and simulation experiments in a graph database

Ron Henkel, Olaf Wolkenhauer, Dagmar Waltemath
2015 Database: The Journal of Biological Databases and Curation  
Abstract Model repositories such as the BioModels Database, the CellML Model Repository or JWS Online are frequently accessed to retrieve computational models of biological systems.  ...  The introduced concept notably improves the access of computational models and associated simulations in a model repository.  ...  Acknowledgements The authors thank Rebekka Alm for implementing part of the SED-ML storage and Markus Wolfien for creating and encoding the SED-ML files used in this article.  ... 
doi:10.1093/database/bau130 pmid:25754863 pmcid:PMC4352687 fatcat:mkeroo4ot5fhrhxoxokbydyauq

OUP accepted manuscript

2018 Database: The Journal of Biological Databases and Curation  
The occurrences of frequent patterns may give insight into the encoding of central biological processes, evaluate postulated biological motifs or serve as a similarity measure for models that share common  ...  Our workflow can be applied to a custom set of models or to models already existing in our graph database MaSyMoS.  ...  Acknowledgements The authors like to thank Faiz Muhammad Khan for the many fruitful discussions and Martin Scharm for helping with scripting issues. Conflict of interest. None declared.  ... 
doi:10.1093/database/bay051 pmid:29992320 pmcid:PMC6030809 fatcat:3qnywfjsezgmrdyz3s5cfs7ae4

Metabolic pathway databases and model repositories

Abraham A. Labena, Yi-Zhou Gao, Chuan Dong, Hong-li Hua, Feng-Biao Guo
2017 Quantitative Biology  
The number of biological Knowledge bases/databases storing metabolic pathway information and models has been growing rapidly.  ...  The three model repositories reviewed do not offer a brief description of the models' characteristics such as simulation conditions.  ...  This article is a review article and does not contain any studies with human or animal subjects performed by any of the authors.  ... 
doi:10.1007/s40484-017-0108-3 fatcat:j6osebecqjehzj6lkchtldkwke

Databases for multilevel biophysiology research available at

Yoshiyuki Asai, Takeshi Abe, Li Li, Hideki Oka, Taishin Nomura, Hiroaki Kitano
2015 Frontiers in Physiology  
PH database BioModels CellML repository URL Model curation Ontology-based search * a PHML has the ability to import a whole SBML model into modules, and employs SBML-PHML hybrid modeling to describe hierarchical  ...  among three databases, the PH Database, BioModels, and the CellML Repository.  ...  Aird for reviewing the manuscript, and the reviewers for comments on an earlier version of this paper.  ... 
doi:10.3389/fphys.2015.00251 pmid:26441671 pmcid:PMC4563878 fatcat:vn4juasdavbltpajmeknd566sy

PathCase-SB architecture and database design

Ali Cakmak, Xinjian Qi, Sarp A Coskun, Mitali Das, En Cheng, A Cicek, Nicola Lai, Gultekin Ozsoyoglu, Z Ozsoyoglu
2011 BMC Systems Biology  
The current PathCase-SB system provides a databaseenabled framework and web-based computational tools towards facilitating the development of kinetic models for biological systems.  ...  Therefore, the tasks of (a) integrating under a single database environment regulatory metabolic networks and existing models, and (b) building tools to help with modeling and analysis are desirable and  ...  Acknowledgements and Funding Authors acknowledge (a) guidance and contributions of (late) Marco Cabrera for his early contributions to PathCase-SB architecture and database design, (b) PathCase-SB design  ... 
doi:10.1186/1752-0509-5-188 pmid:22070889 pmcid:PMC3229461 fatcat:lvc74inelzhnlf2huwpzj4w2ba

Comparison of human cell signaling pathway databases—evolution, drawbacks and challenges

Saikat Chowdhury, Ram Rup Sarkar
2015 Database: The Journal of Biological Databases and Curation  
Elucidating the complexities of cell signaling pathways is of immense importance to gain understanding about various biological phenomenon, such as dynamics of gene/protein expression regulation, cell  ...  solutions for future database development, which could be useful to the whole scientific community.  ...  Conflict of interest: None declared.  ... 
doi:10.1093/database/bau126 pmid:25632107 pmcid:PMC4309023 fatcat:b6y4vbdg7rfdrac5z3htaxdcji

CellCircuits: a database of protein network models

H. C. Mak, M. Daly, B. Gruebel, T. Ideker
2007 Nucleic Acids Research  
We demonstrate how such a repository of network models is a novel systems biology resource by performing several meta-analyses not currently possible with existing databases.  ...  We envision CellCircuits as a clearinghouse in which theorists may distribute or revise models in need of validation and experimentalists may search for models or specific hypotheses relevant to their  ...  Funding to pay the Open Access publication charges for this article was provided by the National Science Foundation (NSF 0425926). Conflict of interest statement. None declared.  ... 
doi:10.1093/nar/gkl937 pmid:17135207 pmcid:PMC1751555 fatcat:2jfmnrpwarakzm6f7noeedonsa

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 (, launched in 2014, is a public repository of published experimental data, which contains concentration data of metabolites, protein abundances and flux data.  ...  We believe that this new version will improve its role as a valuable resource for the systems biology community. Database URL:  ...  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

Resources for integrative systems biology: from data through databases to networks and dynamic system models

Aylwin Ng, Borisas Bursteinas, Qiong Gao, Ewan Mollison, Marketa Zvelebil
2006 Briefings in Bioinformatics  
In systems biology, biologically relevant quantitative modelling of physiological processes requires the integration of experimental data from diverse sources.  ...  deluge of experimental data held in numerous public databases.  ...  Acknowledgements The authors thank Anne Ridley and Buzz Baum for very helpful discussions, David Sims and Konstantinos Lykostratis for suggesting several useful websites for inclusion into the list of  ... 
doi:10.1093/bib/bbl036 pmid:17040977 fatcat:lfu4hga62zegdalxxvex3ugfju
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