Reference health
COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project
35/35 checkable references clean · checked 2026-07-14
Every reference with a DOI in the deposited reference list resolved to a known work in Crossref or DataCite at the dated check, and none carried a publisher retraction, withdrawal, or removal notice.
26 without a DOI — not checked. A reference deposited without a DOI is never matched by title or guessed at; it stays outside the checked set, and this line discloses that.
The 35 checked references that resolve
resolves10.1093/bioinformatics/btg015
The systems biology markup language (SBML): a medium for
representation and exchange of biochemical network models
resolves10.1098/rstb.2001.0910
Towards NeuroML: Model Description Methods for Collaborative Modelling in Neuroscience
resolves10.1038/nbt1156
Minimum information requested in the annotation of biochemical models (MIRIAM)
resolves10.1093/bioinformatics/btq069
SBRML: a markup language for associating systems biology data with models
resolves10.1186/1752-0509-5-198
Reproducible computational biology experiments with SED-ML - The Simulation Experiment Description Markup Language
resolves10.1016/j.pbiomolbio.2011.06.003
High-throughput functional curation of cellular electrophysiology models
resolves10.1038/nbt.2891
The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology
resolves10.1016/j.ecolmodel.2006.04.023
A standard protocol for describing individual-based and agent-based models
resolves10.1093/bioinformatics/btt018
Improving the reuse of computational models through version control
resolves10.1186/1752-0509-4-92
BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models
resolves10.1186/1471-2105-12-22
Revision history aware repositories of computational models of biological systems
resolves10.1093/nar/gkr1097
Identifiers.org and MIRIAM Registry: community resources to provide persistent identification
resolves10.1038/npre.2011.5846.1
Simulation Experiment Description Markup Language (SED-ML) : Level 1 Version 1
resolves10.1016/S0167-7799(01)01740-1
The Virtual Cell: a software environment for computational cell biology
resolves10.1016/j.pbiomolbio.2008.05.006
Practical application of CellML 1.1: The integration of new mechanisms into a human ventricular myocyte model
resolves10.1002/hep.27136
Integrated metabolic spatial‐temporal model for the prediction of ammonia detoxification during liver damage and regeneration
resolves10.1371/journal.pone.0066811
Integration of Biochemical and Electrical Signaling-Multiscale Model of the Medium Spiny Neuron of the Striatum
resolves10.7287/peerj.preprints.514v1
The CombineArchive Toolkit - facilitating the transfer of research results
resolves10.1186/2041-1480-5-41
Structuring research methods and data with the research object model: genomics workflows as a case study
The 26 references without a DOI — listed, not checked
no DOI — not checkedNumerical Markup Language. http://code.google.com/p/numl/. Accessed 09 April 2014.
no DOI — not checkedSmith LP, Hucka M, Hoops S, Finney A, Ginkel M, Myers CJ, Moraru I, Liebermeister W: Hierarchical Model Composition, Version 1 Release 2. Available from COMBINE 2013 http://identifiers.org/combine.specifications/sbml.level-3.version-1.comp.
no DOI — not checkedPharmacometrics Markup Language http://pharmml.org Accessed 12 Feb 2014
no DOI — not checkedHenkel R, Le Novère N, Wolkenhauer O, Waltemath D: Considerations of graph-based concepts to manage of computational biology models and associated simulations. GI-Jahrestagung. 2012, 2012: 1545-1551.
no DOI — not checkeddeb (file format) http://en.wikipedia.org/wiki/Deb_%28file_format%29. Accessed 12 Feb 2014.
no DOI — not checkedJAR (file format) http://en.wikipedia.org/wiki/JAR_%28file_format%29. Accessed 12 Feb 2014.
no DOI — not checked[OOXML] Office Open XML file formats. http://en.wikipedia.org/wiki/Office_Open_XML_file_formats. Accessed 12 Feb 2014.
no DOI — not checkedOpenDocument technical specification http://en.wikipedia.org/wiki/OpenDocument_technical_specification. Accessed 12 Feb 2014.
no DOI — not checkedThe Computational Modeling in Biology Initiative (COMBINE) http://co.mbine.org. Accessed 12 Feb 2014.
no DOI — not checkedZip (file format) http://en.wikipedia.org/wiki/Zip_%28file_format%29. Accessed 12 Feb 2014.
no DOI — not checked[ZipSpec] APPNOTE.TXT - .ZIP File Format Specification http://www.pkware.com/documents/casestudies/APPNOTE.TXT. Accessed 12 Feb 2014.
no DOI — not checkedResource Description Framework (RDF) http://www.w3.org/RDF/. Accessed 13 Feb 2014.
no DOI — not checkedIannella R, McKinney J: vCard Ontology. 2013 http://www.w3.org/TR/vcard-rdf/. Accessed 13 Feb 2014.
no DOI — not checkedDCMI Usage Board: DCMI Metadata Terms. 2012 http://dublincore.org/documents/dcmi-terms/. Accessed 13Feb 2014.
no DOI — not checkedWolf M, Wicksteed C: Date and Time Formats. 1997 http://www.w3.org/TR/NOTE-datetime. Accessed 13 Feb 2014.
no DOI — not checkedNilsson M, Powell A, Johnston P, Naeve A: Expressing Dublin Core metadata using the Resource Description Framework (RDF) http://dublincore.org/documents/dc-rdf/. Accessed 13 Feb 2014.
no DOI — not checkedIntegrated Python Based Modeling Environment http://tellurium.analogmachine.org. Accessed 2 July 2014.
no DOI — not checkedFDA center for drug evaluation and research: Model/Data Format. http://www.fda.gov/AboutFDA/CentersOffices/OfficeofMedicalProductsandTobacco/CDER/ucm180482.htm. Accessed 26 February 2014.
no DOI — not checkedTS-140. The record layout of a data set in SAS transport (XPORT) format. http://support.sas.com/techsup/technote/ts140.html. Accessed 26 February 2014.
no DOI — not checkedFunctional Curation for Cardiac Electrophysiology https://chaste.cs.ox.ac.uk/FunctionalCuration. Accessed 27 May 2014.
no DOI — not checkedSoiland-Reyes S: Wf4Ever Research Object Bundle 2013 http://purl.org/wf4ever/ro-bundle/2013-05-21/. Accessed 13 Feb 2014.
no DOI — not checkedUniversal Container Format: https://wikidocs.adobe.com/wiki/display/PDFNAV/Universal+Container+Format. Accessed 27 Feb 2014.
no DOI — not checkedSoiland-Reyes S, Gamble M: ro-combine-archive 0.1.0. ZENODO (2014). https://github.com/stain/ro-combine-archive doi:10.5281/zenodo.10439.
no DOI — not checkedEPUB Open Container Format (OCF) 3.0. http://www.idpf.org/epub/30/spec/epub30-ocf.html. Accessed 05 March 2014.
no DOI — not checkedOpen Packaging Convention. http://en.wikipedia.org/wiki/Open_Packaging_Convention. Accessed 05 March 2014.
no DOI — not checkedSmallbone K: Striking a balance with Recon 2.1. 2014, arXiv:1311.5696
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work were clean at the dated check: each resolved to a known work in a public registry, and none
carried a publisher retraction notice at that time. It says nothing about the quality, findings,
or importance of the work itself, and nothing about references deposited without a DOI.
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