COMBINE archive and OMEX format: one file to share all information to reproduce a modeling project
Open accessAbstract
BACKGROUND: With the ever increasing use of computational models in the biosciences, the need to share models and reproduce the results of published studies efficiently and easily is becoming more important. To this end, various standards have been proposed that can be used to describe models, simulations, data or other essential information in a consistent fashion. These constitute various separate components required to reproduce a given published scientific result. RESULTS: We describe the Open Modeling EXchange format (OMEX). Together with the use of other standard formats from the Computational Modeling in Biology Network (COMBINE), OMEX is the basis of the COMBINE Archive, a single file that supports the exchange of all the information necessary for a modeling and simulation experiment in biology. An OMEX file is a ZIP container that includes a manifest file, listing the content of the archive, an optional metadata file adding information about the archive and its content, and the files describing the model. The content of a COMBINE Archive consists of files encoded in COMBINE standards whenever possible, but may include additional files defined by an Internet Media Type. Several tools that support the COMBINE Archive are available, either as independent libraries or embedded in modeling software. CONCLUSIONS: The COMBINE Archive facilitates the reproduction of modeling and simulation experiments in biology by embedding all the relevant information in one file. Having all the information stored and exchanged at once also helps in building activity logs and audit trails. We anticipate that the COMBINE Archive will become a significant help for modellers, as the domain moves to larger, more complex experiments such as multi-scale models of organs, digital organisms, and bioengineering.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Each entity and activity in the final set has already been mentioned for provenance, modeling or documentation purposes, or experiment design of simulation studies, but they have not all been used together.
“Each entity and activity has already been mentioned for provenance, modeling or documentation purposes, or experiment design of simulation studies [1, 3–5, 8, 20, 21, 60–63], but they have not all been used together.”
From Relating simulation studies by provenance—Developing a family of Wnt signaling models (2021) · cites this paper as [61]
The Background discusses documenting models, simulation procedures, results, and metadata; Implementation > Metadata also discusses logs of actions and audit trails (pages unavailable). These passages support the claim that related concepts had been discussed for modeling, documentation, and provenance. They do not establish that every entity and activity in the citing document’s final set had been mentioned previously or that the full set had never been used together. (LLM, conf=0.82)
Experimental — accuracy not yet measuredThe inclusion of all necessary protocols and data needed to implement a model enables distribution of models via a single file, encouraging reuse and improving reproducibility.
“The inclusion of all necessary protocols and data needed to implement a model enables distribution of models via a single file encouraging reuse and improving reproducibility [55].”
From Adapting modeling and simulation credibility standards to computational systems biology (2023) · cites this paper as [55]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Hucka, M., Finney, A., Sauro, H. M., Bolouri, H., Doyle, J. C., Kitano, H., Arkin, A. P., Bornstein, B. J., Bray, D., Cornish-Bowden, A., et al. (2003) · Bioinformatics · doi:10.1093/bioinformatics/btg015 · Cited by 3,060 · see citing works
Self-citationA standard protocol for describing individual-based and agent-based models
Grimm, V., Berger, U., Bastiansen, F., Eliassen, S., Ginot, V., Giske, J., GOSS‐CUSTARD, J. D., Grand, T. C., Heinz, S. K., Huse, G., et al. (2006) · Ecological Modelling · doi:10.1016/j.ecolmodel.2006.04.023 · Cited by 2,988 · see citing works
Uniform Resource Identifiers (URI): Generic Syntax
Berners‐Lee, T., Fielding, R. T., & Masinter, L. M. (1998) · doi:10.17487/rfc2396 · Cited by 1,749 · see citing works
A Whole-Cell Computational Model Predicts Phenotype from Genotype
Karr, J. R., Sanghvi, J. C., Macklin, D. N., Gutschow, M. V., Jacobs, J. M., Bolival, B., Assad-Garcia, N., Glass, J. I., & Covert, M. W. (2012) · Cell · doi:10.1016/j.cell.2012.05.044 · Cited by 1,300 · see citing works
A community-driven global reconstruction of human metabolism
Thiele, I., Swainston, N., Fleming, R. M. T., Hoppe, A., Sahoo, S., Aurich, M. K., Haraldsdottir, H., Mo, M. L., Rolfsson, O., Stobbe, M. D., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2488 · Cited by 1,019 · see citing works
Self-citationThe systems biology graphical notation.
Novère, N. L., Hucka, M., Mi, H., Moodie, S., Schreiber, F., Sorokin, A., Demir, E., Wegner, K., Aladjem, M. I., Wimalaratne, S. M., et al. (2009) · Nature Biotechnology · doi:10.1038/nbt.1558 · Cited by 903 · see citing works
Self-citationTen Simple Rules for Reproducible Computational Research
Sandve, G. K., Nekrutenko, A., Taylor, J., & Hovig, E. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003285 · Cited by 880 · see citing works
Uniform Resource Identifier (URI): Generic Syntax
Berners‐Lee, T., Fielding, R., & Masinter, L. (2005) · doi:10.17487/rfc3986 · Cited by 818 · see citing works
Minimum information requested in the annotation of biochemical models (MIRIAM)
Novère, N. L., Finney, A., Hucka, M., Bhalla, U. S., Campagne, F., Collado-Vides, J., Crampin, E. J., Halstead, M., Klipp, E., Mendes, P., et al. (2005) · Nature Biotechnology · doi:10.1038/nbt1156 · Cited by 622 · see citing works
Self-citationLi, C., Donizelli, M., Rodriguez, N., Dharuri, H., Endler, L., Chelliah, V., Li, L., He, E., Henry, A., Stefan, M. I., et al. (2010) · BMC Systems Biology · doi:10.1186/1752-0509-4-92 · Cited by 597 · see citing works
Self-citationThe Virtual Cell: a software environment for computational cell biology
Loew, L. M., & Schaff, J. C. (2001) · Trends in biotechnology · doi:10.1016/s0167-7799(01)01740-1 · Cited by 406 · see citing works
Controlled vocabularies and semantics in systems biology
Courtot, M., Juty, N., Knüpfer, C., Waltemath, D., Zhukova, A., Dräger, A., Dumontier, M., Finney, A., Golebiewski, M., Hastings, J., et al. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.77 · Cited by 316 · cited 1× · see citing works
“The modeling and simulation life cycle includes several steps [10] which need to be documented and described in order to be reproduced.”
BackgroundSelf-citationAccessible Reproducible Research
Mesirov, J. P. (2010) · Science · doi:10.1126/science.1179653 · Cited by 311 · see citing works
Galdzicki, M., Clancy, K., Oberortner, E., Pocock, M., Quinn, J. Y., Rodríguez, C., Roehner, N., Wilson, M., Adam, L., Anderson, J. C., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.2891 · Cited by 288 · see citing works
Self-citationWaltemath, D., Adams, R., Bergmann, F. T., Hucka, M., Kolpakov, F., Miller, A. K., Moraru, I., Nickerson, D., Sahle, S., Snoep, J., et al. (2011) · BMC Systems Biology · doi:10.1186/1752-0509-5-198 · Cited by 269 · see citing works
Self-citationIdentifiers.org and MIRIAM Registry: community resources to provide persistent identification
Juty, N., Novère, N. G. L., & Laibe, C. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr1097 · Cited by 205 · see citing works
Self-citationModelling cellular systems with PySCeS
Olivier, B. G., Rohwer, J. M., & Hofmeyr, J. S. (2004) · Bioinformatics · doi:10.1093/bioinformatics/bti046 · Cited by 180 · see citing works
Self-citationMinimum Information About a Simulation Experiment (MIASE)
Waltemath, D., Adams, R., Beard, D. A., Bergmann, F. T., Bhalla, U. S., Britten, R., Chelliah, V., Cooling, M. T., Cooper, J., Crampin, E. J., et al. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1001122 · Cited by 168 · see citing works
Self-citationTowards NeuroML: Model Description Methods for Collaborative Modelling in Neuroscience
Goddard, N., Hucka, M., Howell, F. W., Cornelis, H., Shankar, K., & Beeman, D. (2001) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2001.0910 · Cited by 131 · see citing works
Self-citationSchliess, F., Hoehme, S., Henkel, S., Ghallab, A., Driesch, D., Böttger, J., Guthke, R., Pfaff, M., Hengstler, J. G., Gebhardt, R., et al. (2014) · Hepatology · doi:10.1002/hep.27136 · Cited by 112 · see citing works
FieldML: concepts and implementation
Christie, G. R., Nielsen, P. M. F., Blackett, S. A., Bradley, C. P., & Hunter, P. J. (2009) · Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences · doi:10.1098/rsta.2009.0025 · Cited by 102 · see citing works
A short introduction to CellML
Hedley, W., Nelson, M. R., Bellivant, D. P., & Nielsen, P. F. (2001) · Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences · doi:10.1098/rsta.2001.0817 · Cited by 101 · see citing works
Software support for SBGN maps: SBGN-ML and LibSBGN
van Iersel, M., Villéger, A. C., Czauderna, T., Boyd, S. E., Bergmann, F., Luna, A., Demir, E., Sorokin, A., Doğrusöz, U., Matsuoka, Y., et al. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts270 · Cited by 87 · see citing works
Self-citationSBRML: a markup language for associating systems biology data with models
Dada, J. O., Spasic, I., Paton, N., & Mendes, P. (2010) · Bioinform. · doi:10.1093/bioinformatics/btq069 · Cited by 66 · see citing works
Media Type Specifications and Registration Procedures
Freed, N., & Klensin, J. (2005) · doi:10.17487/rfc4288 · Cited by 64 · see citing works
Wolstencroft, K., Owen, S., du Preez, F. B., Krebs, O., Müller, W., Goble, C., & Snoep, J. L. (2011) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/b978-0-12-385118-5.00029-3 · Cited by 56 · see citing works
High-throughput functional curation of cellular electrophysiology models
Cooper, J., Mirams, G. R., & Niederer, S. (2011) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2011.06.003 · Cited by 49 · see citing works
Self-citationSBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3
Smith, L. P., Hucka, M., Hoops, S., Finney, A., Ginkel, M., Myers, C. J., Moraru, I. I., & Liebermeister, W. (2015) · Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics · doi:10.1515/jib-2015-268 · Cited by 48 · see citing works
Self-citationJSim, an open-source modeling system for data analysis
Butterworth, E. A., Jardine, B., Raymond, G. M., Neal, M. L., & Bassingthwaighte, J. B. (2013) · F1000Research · doi:10.12688/f1000research.2-288.v1 · Cited by 47 · see citing works
SBML Level 3 package: Hierarchical Model Composition, Version 1 Release 3
Smith, L. P., Hucka, M., Hoops, S., Finney, A., Ginkel, M., Myers, C. J., Moraru, I. I., & Liebermeister, W. (2015) · PubMed · doi:10.2390/biecoll-jib-2015-268 · Cited by 41 · see citing works
Self-citationMattioni, M., & Novère, N. G. L. (2013) · PLoS ONE · doi:10.1371/journal.pone.0066811 · Cited by 38 · see citing works
Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3)
Bergmann, F. T., Cooper, J., König, M., Moraru, I., Nickerson, D., Le Novère, N., Olivier, B. G., Sahle, S., Smith, L., & Waltemath, D. (2018) · Journal of Integrative Bioinformatics · doi:10.1515/jib-2017-0086 · Cited by 37 · see citing works
Self-citationWolf, M., & Wicksteed, C. (1997) · Cited by 32 · see citing works
Perreault, S. (2011) · doi:10.17487/rfc6350 · Cited by 27 · see citing works
Nickerson, D. P., & Buist, M. L. (2008) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2008.05.006 · Cited by 26 · see citing works
Self-citationHettne, K. M., Dharuri, H. K., Zhao, J., Wolstencroft, K., Belhajjame, K., Soiland‐Reyes, S., Mina, E., Thompson, M., Cruickshank, D. G., Verdes-Montenegro, L. L., et al. (2014) · Journal of Biomedical Semantics · doi:10.1186/2041-1480-5-41 · Cited by 25 · see citing works
Self-citationImproving the reuse of computational models through version control
Waltemath, D., Henkel, R., Hälke, R., Scharm, M., & Olaf Wolkenhauer, A. (2013) · Bioinformatics · doi:10.1093/bioinformatics/btt018 · Cited by 23 · see citing works
Self-citationRevision history aware repositories of computational models of biological systems
Miller, A. K., Yu, T., Britten, R. D., Cooling, M. T., Lawson, J., Cowan, D., Garny, A., Halstead, M. D. B., Hunter, P. J., Nickerson, D. P., et al. (2011) · BMC Bioinformatics · doi:10.1186/1471-2105-12-22 · Cited by 19 · see citing works
Self-citationSimulation Experiment Description Markup Language (SED-ML) : Level 1 Version 1Preprint
Waltemath, D., Bergmann, F. T., Adams, R., & Novère, N. L. (2011) · Nature Precedings · doi:10.1038/npre.2011.5846.1 · Cited by 13 · see citing works
Self-citationStriking a balance with Recon 2.1Preprint
B, K. S. A. (2013) · arXiv (Cornell University) · doi:10.48550/arxiv.1311.5696 · Cited by 10 · see citing works
Henkel, R., Novère, N. G. L., Olaf Wolkenhauer, A., & Waltemath, D. (2012) · Cited by 10 · see citing works
Self-citationSoiland‐Reyes, S., & Gamble, M. (2014) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.10439 · Cited by 1 · see citing works
Self-citationThe CombineArchive Toolkit - facilitating the transfer of research resultsPreprint
Scharm, M., Wendland, F., Peters, M., Wolfien, M., Theile, T., & Waltemath, D. (2014) · doi:10.7287/peerj.preprints.514v1 · Cited by 1 · see citing works
Self-citation
Flagged first, then by citations
1 of the 44 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
BioModels—15 years of sharing computational models in life science
Malik-Sheriff, R. S., Glont, M., Nguyen, T. V. N., Tiwari, K., Roberts, M. G., Xavier, A., Vu, M. T., Men, J., Maire, M., Kananathan, S., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz1055 · Cited by 361 · see citing works
Self-citationSBML Level 3: an extensible format for the exchange and reuse of biological models
Keating, S. M., Waltemath, D., König, M., Zhang, F.-K., Dräger, A., Chaouiya, C., Bergmann, F. T., Finney, A., Gillespie, C. S., Helikar, T., et al. (2020) · Molecular Systems Biology · doi:10.15252/msb.20199110 · Cited by 270 · see citing works
Self-citationProceedings of the 2017 Winter Simulation Conference
Chan, W.-M., D’Ambrogio, A., Zacharewicz, G., Mustafee, N., Wainer, G., & Page, E. (2017) · HAL · Cited by 251 · see citing works
Tellurium: An extensible python-based modeling environment for systems and synthetic biology
Choi, K., Medley, K., König, M., Stocking, K., Smith, L. P., Gu, S., & Sauro, H. M. (2018) · Biosystems · doi:10.1016/j.biosystems.2018.07.006 · Cited by 164 · see citing works
Self-citationHucka, M., Nickerson, D. P., Bader, G. D., Bergmann, F., Cooper, J., Demir, E., Garny, A., Golebiewski, M., Myers, C. J., Schreiber, F., et al. (2015) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2015.00019 · Cited by 118 · see citing works
Self-citationCOPASI and its applications in biotechnology
Bergmann, F., Hoops, S., Klahn, B., Kummer, U., Mendes, P., Pahle, J., & Sahle, S. (2017) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2017.06.1200 · Cited by 108 · see citing works
Self-citationPEtab—Interoperable specification of parameter estimation problems in systems biology
Schmiester, L., Schälte, Y., Bergmann, F. T., Camba, T., Dudkin, E., Egert, J., Fröhlich, F., Fuhrmann, L., Hauber, A. L., Kemmer, S., et al. (2021) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1008646 · Cited by 96 · see citing works
Self-citationImmune digital twins for complex human pathologies: applications, limitations, and challenges
Niarakis, A., Laubenbacher, R., An, G. C., Ilan, Y., Fisher, J., Flobak, Å., Reiche, K., Martínez, M. R., Geris, L., Ladeira, L., et al. (2024) · npj Systems Biology and Applications · doi:10.1038/s41540-024-00450-5 · Cited by 104 · see citing works
BioModels: expanding horizons to include more modelling approaches and formats
Glont, M., Nguyen, T. V. N., Graesslin, M., Hälke, R., Ali, R., Schramm, J., Wimalaratne, S. M., Kothamachu, V. B., Rodriguez, N., Swat, M. J., et al. (2018) · Nucleic Acids Research · doi:10.1093/nar/gkx1023 · Cited by 89 · see citing works
Self-citationi B io S im 3: A Tool for Model-Based Genetic Circuit Design
Watanabe, L. H., Nguyen, T., Zhang, M., Zundel, Z., Zhang, Z., Madsen, C. K., Roehner, N., & Myers, C. J. (2018) · ACS Synthetic Biology · doi:10.1021/acssynbio.8b00078 · Cited by 82 · see citing works
Harmonizing semantic annotations for computational models in biology
Neal, M. L., König, M., Nickerson, D., Mısırlı, G., Kalbasi, R., Dräger, A., Atalag, K., Chelliah, V., Cooling, M. T., Cook, D. L., et al. (2019) · Briefings in Bioinformatics · doi:10.1093/bib/bby087 · Cited by 74 · see citing works
Self-citationThe Cardiac Electrophysiology Web Lab
Cooper, J., Scharm, M., & Mirams, G. R. (2016) · Biophysical Journal · doi:10.1016/j.bpj.2015.12.012 · Cited by 58 · see citing works
Self-citationImproving Collaboration by Standardization Efforts in Systems Biology
Dräger, A., & Palsson, B. Ã. (2014) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2014.00061 · Cited by 57 · see citing works
Tellurium notebooks—An environment for reproducible dynamical modeling in systems biology
Medley, J., Choi, K., König, M., Smith, L. P., Gu, S., Hellerstein, J., Sealfon, S., & Sauro, H. (2018) · PLoS Comput. Biol. · doi:10.1371/journal.pcbi.1006220 · Cited by 58 · see citing works
Self-citationMemote: A community driven effort towards a standardized genome-scale metabolic model test suitePreprint
Lieven, C., Beber, M. E., Olivier, B. G., Bergmann, F., Ataman, M., Babaei, P., Bartell, J. A., Blank, L. M., Chauhan, S., Correia, K., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/350991 · Cited by 55 · see citing works
Self-citationKinetic modeling of cell metabolism for microbial production
Costa, R. S., Hartmann, A., & Vinga, S. (2015) · Journal of Biotechnology · doi:10.1016/j.jbiotec.2015.12.023 · Cited by 53 · see citing works
Community standards to facilitate development and address challenges in metabolic modeling
Carey, M. A., Dräger, A., Beber, M. E., Papin, J. A., & Yurkovich, J. T. (2020) · Molecular Systems Biology · doi:10.15252/msb.20199235 · Cited by 49 · see citing works
Waltemath, D., & Wolkenhauer, O. (2016) · IEEE Transactions on Biomedical Engineering · doi:10.1109/tbme.2016.2555481 · Cited by 49 · see citing works
Self-citationBest Practices for Making Reproducible Biochemical Models
Porubsky, V. L., Goldberg, A. P., Rampadarath, A. K., Nickerson, D. P., Karr, J. R., & Sauro, H. M. (2020) · Cell Systems · doi:10.1016/j.cels.2020.06.012 · Cited by 45 · see citing works
Self-citationEnzymeML—a data exchange format for biocatalysis and enzymology
Range, J., Halupczok, C., Lohmann, J., Swainston, N., Kettner, C., Bergmann, F. T., Weidemann, A., Wittig, U., Schnell, S., & Pleiss, J. (2021) · The FEBS Journal · doi:10.1111/febs.16318 · Cited by 32 · see citing works
Self-citationClosing the gap between formats for storing layout information in systems biology
Hoksza, D., Gawron, P., Ostaszewski, M., Hasenauer, J., & Schneider, R. (2019) · Briefings in Bioinformatics · doi:10.1093/bib/bbz067 · Cited by 32 · see citing works
Waltemath, D., Golebiewski, M., Blinov, M. L., Gleeson, P., Hermjakob, H., Hucka, M., Inau, E. T., Keating, S., König, M., Krebs, O., et al. (2020) · Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics · doi:10.1515/jib-2020-0005 · Cited by 38 · see citing works
Self-citationRenz, A., Widerspick, L., & Dräger, A. (2021) · Genes · doi:10.3390/genes12060796 · Cited by 38 · see citing works
Simulation Experiment Description Markup Language (SED-ML) Level 1 Version 3 (L1V3)
Bergmann, F. T., Cooper, J., König, M., Moraru, I., Nickerson, D., Le Novère, N., Olivier, B. G., Sahle, S., Smith, L., & Waltemath, D. (2018) · Journal of Integrative Bioinformatics · doi:10.1515/jib-2017-0086 · Cited by 37 · see citing works
Self-citationBuecherl, L., & Myers, C. J. (2022) · Current Opinion in Microbiology · doi:10.1016/j.mib.2022.102155 · Cited by 36 · see citing works
The JWS online simulation database
Peters, M., Eicher, J. J., van Niekerk, D. D., Waltemath, D., & Snoep, J. L. (2017) · Bioinformatics · doi:10.1093/bioinformatics/btw831 · Cited by 36 · see citing works
Self-citationNickerson, D. P., Atalağ, K., de Bono, B., Geiger, J., Goble, C., Hollmann, S., Lonien, J., Müller, W., Regierer, B., Stanford, N., et al. (2016) · Interface Focus · doi:10.1098/rsfs.2015.0103 · Cited by 32 · see citing works
Self-citationNiarakis, A., Waltemath, D., Glazier, J. A., Schreiber, F., Keating, S., Nickerson, D. P., Chaouiya, C., Siegel, A., Noël, V., Hermjakob, H., et al. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac212 · Cited by 32 · see citing works
Self-citationDrawert, B., Trogdon, M., Salman Zubair, T. O. O. R., Petzold, L. R., & Hellander, A. (2016) · SIAM Journal on Scientific Computing · doi:10.1137/15m1014784 · Cited by 29 · see citing works
Benito-Vaquerizo, S., Olm, I. P., de Vroet, T., Schaap, P. J., Sousa, D. Z., dos Santos, V. A. P. M., & Diez, M. S. (2022) · Microbial Cell Factories · doi:10.1186/s12934-022-01841-1 · Cited by 27 · see citing works
BioSimulators: a central registry of simulation engines and services for recommending specific tools
Shaikh, B., Smith, L. P., Vasilescu, D., Marupilla, G., Wilson, M., Agmon, E., Agnew, H., Andrews, S., Anwar, A., Beber, M., et al. (2022) · Nucleic Acids Res. · doi:10.1093/nar/gkac331 · Cited by 31 · see citing works
Genetic Circuit Dynamics: Hazard and Glitch Analysis
Fontanarrosa, P., Doosthosseini, H., Borujeni, A. E., Dorfan, Y., Voigt, C. A., & Myers, C. J. (2020) · ACS Synthetic Biology · doi:10.1021/acssynbio.0c00055 · Cited by 27 · see citing works
High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032
Feierabend, M., Renz, A., Zelle, E., Nöh, K., Wiechert, W., & Dräger, A. (2021) · Frontiers in Microbiology · doi:10.3389/fmicb.2021.750206 · Cited by 27 · see citing works
FSK-Lab – An open source food safety model integration tool
Aparicio, M. D. A., Buschhardt, T., Swaid, A., Valentin, L., Mesa-Varona, O., Günther, T., Plaza‐Rodríguez, C., & Filter, M. (2018) · Microbial Risk Analysis · doi:10.1016/j.mran.2018.09.001 · Cited by 26 · see citing works
Adapting modeling and simulation credibility standards to computational systems biology
Tatka, L. T., Smith, L. P., Hellerstein, J. L., & Sauro, H. M. (2023) · Journal of Translational Medicine · doi:10.1186/s12967-023-04290-5 · Cited by 25 · see citing works
Self-citationBASICO: A simplified Python interface to COPASI
Bergmann, F. (2023) · The Journal of Open Source Software · doi:10.21105/joss.05553 · Cited by 25 · see citing works
Self-citationPleiss, J. (2021) · ChemCatChem · doi:10.1002/cctc.202100822 · Cited by 24 · see citing works
SemGen: a tool for semantics-based annotation and composition of biosimulation models
Neal, M. L., Thompson, C. T., Kim, K., James, R. C., Cook, D. L., Carlson, B. E., & Gennari, J. H. (2018) · Bioinformatics · doi:10.1093/bioinformatics/bty829 · Cited by 24 · see citing works
Payne, D. D., Renz, A., Dunphy, L. J., Lewis, T., Dräger, A., & Papin, J. (2021) · bioRxiv · doi:10.1038/s41540-021-00198-2 · Cited by 22 · see citing works
Organizing genome engineering for the gigabase scale
Bartley, B., Beal, J., Karr, J. R., & Strychalski, E. A. (2020) · Nature Communications · doi:10.1038/s41467-020-14314-z · Cited by 23 · see citing works
Towards standardization guidelines for in silico approaches in personalized medicine
Brunak, S., Collin, C. B., Cathaoir, K. Ó., Golebiewski, M., Kirschner, M. W., Kockum, I. S., Moser, H., & Waltemath, D. (2020) · Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics · doi:10.1515/jib-2020-0006 · Cited by 22 · see citing works
Self-citationRelating simulation studies by provenance—Developing a family of Wnt signaling models
Budde, K., Smith, J., Wilsdorf, P., Haack, F., & Uhrmacher, A. M. (2021) · PLOS Computational Biology · doi:10.1371/journal.pcbi.1009227 · Cited by 23 · see citing works
“This could be achieved, for example, by publishing a COMBINE archive [61], which is a “single file that aggregates all data files and information necessary to reproduce a simulation study in computational biology” [102].”
BackgroundShaikh, B., Marupilla, G., Wilson, M., Blinov, M. L., Moraru, I. I., & Karr, J. R. (2021) · Nucleic Acids Research · doi:10.1093/nar/gkab411 · Cited by 21 · see citing works
Automatic Reuse, Adaption, and Execution of Simulation Experiments via Provenance Patterns
Wilsdorf, P., Wolpers, A., Hilton, J., Haack, F., & Uhrmacher, A. M. (2022) · ACM Transactions on Modeling and Computer Simulation · doi:10.1145/3564928 · Cited by 21 · see citing works
Curating and comparing 114 strain-specific genome-scale metabolic models of Staphylococcus aureus
Renz, A., & Dräger, A. (2021) · npj Systems Biology and Applications · doi:10.1038/s41540-021-00188-4 · Cited by 21 · see citing works
Organizing genome engineering for the gigabase scale
Bartley, B., Beal, J., Karr, J. R., & Strychalski, E. A. (2020) · RePEc: Research Papers in Economics · Cited by 20 · see citing works
Specifications of Standards in Systems and Synthetic Biology
Schreiber, F., Bader, G. D., Golebiewski, M., Hucka, M., Kormeier, B., Novère, N. G. L., Myers, C. J., Nickerson, D. P., Sommer, B., Waltemath, D., et al. (2015) · PubMed · doi:10.2390/biecoll-jib-2015-258 · Cited by 20 · see citing works
Self-citationTellurium: A Python Based Modeling and Reproducibility Platform for Systems BiologyPreprint
Choi, K., Medley, K., Cannistra, C., König, M., Smith, L. P., Stocking, K., & Sauro, H. M. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/054601 · Cited by 20 · see citing works
Self-citationContext, Composition, Automation, and Communication: The C 2 AC Roadmap for Modeling and Simulation
Uhrmacher, A. M., Frazier, P. I., Hähnle, R., Klügl, F., Lorig, F., Ludäscher, B., Nenzi, L., Ruiz-Martín, C., Rumpe⋆, B., Szabo, C., et al. (2024) · ACM Transactions on Modeling and Computer Simulation · doi:10.1145/3673226 · Cited by 21 · see citing works
Asif, K., O’Rourke, D., Legione, A. R., Shil, P. K., Marenda, M. S., & Noormohammadi, A. H. (2021) · PLoS ONE · doi:10.1371/journal.pone.0261122 · Cited by 19 · see citing works
Akberdin, I. R., Kiselev, I. N., Pintus, S. S., Sharipov, R., Vertyshev, A. Y., Виноградова, О. Л., Викторович, П. Д., & Kolpakov, F. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms221910353 · Cited by 19 · see citing works
Smith, L. P., Bergmann, F. T., Garny, A., Helikar, T., Karr, J., Nickerson, D., Sauro, H., Waltemath, D., & König, M. (2021) · Journal of Integrative Bioinformatics · doi:10.1515/jib-2021-0021 · Cited by 17 · see citing works
Self-citationSpecifications of standards in systems and synthetic biology: status and developments in 2020
Schreiber, F., Sommer, B., Czauderna, T., Golebiewski, M., Gorochowski, T. E., Hucka, M., Keating, S. M., König, M., Myers, C., Nickerson, D., et al. (2020) · Journal of Integrative Bioinformatics · doi:10.1515/jib-2020-0022 · Cited by 17 · see citing works
Self-citationCOMODI: an ontology to characterise differences in versions of computational models in biology
Scharm, M., Waltemath, D., Mendes, P., & Wolkenhauer, O. (2016) · Journal of Biomedical Semantics · doi:10.1186/s13326-016-0080-2 · Cited by 14 · see citing works
Self-citationMichael, C. T., Almohri, S. A., Linderman, J. J., & Kirschner, D. E. (2024) · Frontiers in Systems Biology · doi:10.3389/fsysb.2023.1283341 · Cited by 16 · see citing works
Standards, dissemination, and best practices in systems biology
Shin, J., Porubsky, V., Carothers, J., & Sauro, H. M. (2023) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2023.102922 · Cited by 15 · see citing works
Self-citationGuidelines for benchmarking of optimization-based approaches for fitting mathematical models
Kreutz, C. (2019) · Genome biology · doi:10.1186/s13059-019-1887-9 · Cited by 15 · see citing works
SynBiopython: an open-source software library for Synthetic Biology
Yeoh, J. W., Swainston, N., Végh, P., Zulkower, V., Carbonell, P., Holowko, M. B., Gopalacharyulu, P. V., & Poh, C. L. (2021) · Synthetic Biology · doi:10.1093/synbio/ysab001 · Cited by 15 · see citing works
Practical steps to digital organism models, from laboratory model species to ‘Crops in silico
Millar, A. J., Urquiza‐García, U., Freeman, P. L., Hume, A. C., Plotkin, G. D., Sorokina, O., Zardilis, A., & Zieliński, T. (2018) · Journal of Experimental Botany · doi:10.1093/jxb/ery435 · Cited by 15 · see citing works
Casini, I., McCubbin, T., Esquivel-Elizondo, S., Luque, G. G., Evseeva, D., Fink, C., Beblawy, S., Youngblut, N. D., Aristilde, L., Huson, D. H., et al. (2023) · iScience · doi:10.1016/j.isci.2023.108016 · Cited by 14 · see citing works
Practical Resources for Enhancing the Reproducibility of Mechanistic Modeling in Systems Biology
Blinov, M., Gennari, J., Karr, J. R., Moraru, I., Nickerson, D., & Sauro, H. (2021) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2021.06.001 · Cited by 18 · see citing works
Self-citationGolebiewski, M., Bader, G. D., Gleeson, P., Gorochowski, T. E., Keating, S., König, M., Myers, C. J., Nickerson, D. P., Sommer, B., Waltemath, D., et al. (2024) · Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics · doi:10.1515/jib-2024-0015 · Cited by 12 · see citing works
Self-citationSimulation Experiment Schemas –Beyond Tools and Simulation Approaches
Wilsdorf, P., Dombrowsky, M., Uhrmacher, A. M., Zimmermann, J., & van Rienen, U. (2019) · Winter Simulation Conference · doi:10.1109/wsc40007.2019.9004710 · Cited by 13 · see citing works
First Genome-Scale Metabolic Model of Dolosigranulum pigrum Confirms Multiple Auxotrophies
Renz, A., Widerspick, L., & Dräger, A. (2021) · Metabolites · doi:10.3390/metabo11040232 · Cited by 13 · see citing works
Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2016
Schreiber, F., Bader, G. D., Gleeson, P., Golebiewski, M., Hucka, M., Novère, N. L., Myers, C., Nickerson, D., Sommer, B., & Walthemath, D. (2016) · Journal of Integrative Bioinformatics · doi:10.2390/biecoll-jib-2016-289 · Cited by 21 · see citing works
Self-citationDesign patterns of biological cells
Andrews, S. S., Wiley, H. S., & Sauro, H. M. (2024) · BioEssays · doi:10.1002/bies.202300188 · Cited by 13 · see citing works
Self-citationPublishing reproducible dynamic kinetic models
Porubsky, V. L., Smith, L. P., & Sauro, H. M. (2020) · Briefings in Bioinformatics · doi:10.1093/bib/bbaa152 · Cited by 12 · see citing works
Self-citationTouré, V., Novère, N. G. L., Waltemath, D., & Olaf Wolkenhauer, A. (2018) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1005740 · Cited by 12 · see citing works
Self-citationOpen modeling and exchange (OMEX) metadata specification version 1.0
Neal, M. L., Gennari, J. H., Waltemath, D., Nickerson, D. P., & König, M. (2020) · Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics · doi:10.1515/jib-2020-0020 · Cited by 12 · see citing works
Self-citationOMEX metadata specification (version 1.2)
Gennari, J. H., König, M., Misirli, G., Neal, M. L., Nickerson, D. P., & Waltemath, D. (2021) · Journal of Integrative Bioinformatics · doi:10.1515/jib-2021-0020 · Cited by 11 · see citing works
Self-citationvan Kampen, A. H. C., Mahamune, U., Jongejan, A., van Schaik, B. D. C., Balashova, D., Lashgari, D., Pras‐Raves, M. L., Wever, E. J. M., Dane, A. D., García-Valiente, R., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-52446-8 · Cited by 14 · see citing works
Scharm, M., & Waltemath, D. (2016) · F1000Research · doi:10.12688/f1000research.9379.1 · Cited by 11 · see citing works
Self-citationSynBioSuite: A Tool for Improving the Workflow for Genetic Design and Modeling.
Sents, Z., Stoughton, T. E., Buecherl, L., Thomas, P. J., Fontanarrosa, P., & Myers, C. (2023) · ACS Synthetic Biology · doi:10.1021/acssynbio.2c00597 · Cited by 7 · see citing works
New workflow predicts drug targets against SARS-CoV-2 via metabolic changes in infected cells
Leonidou, N., Renz, A., Mostolizadeh, R., & Dräger, A. (2023) · PLoS Comput. Biol. · doi:10.1371/journal.pcbi.1010903 · Cited by 6 · see citing works
A community approach to whole-cell modeling
Singla, J., & White, K. L. (2021) · Current Opinion in Systems Biology · doi:10.1016/j.coisb.2021.03.009 · Cited by 11 · see citing works
Executable Simulation Model of the Liver
König, M. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-801238-3.11682-4 · Cited by 10 · see citing works
Towards the human nasal microbiome: Simulating D. pigrum and S. aureus
Mostolizadeh, R., Gloeckler, M., & Dräger, A. (2022) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2022.925215 · Cited by 10 · see citing works
Myers, C. J., Bader, G. D., Gleeson, P., Golebiewski, M., Hucka, M., Novère, N. G. L., Nickerson, D. P., Schreiber, F., & Waltemath, D. (2017) · Winter Simulation Conference · doi:10.1109/wsc.2017.8247840 · Cited by 10 · see citing works
Self-citationThe systems biology simulation core library
Panchiwala, H., Shah, S., Planatscher, H., Zakharchuk, M., König, M., & Dräger, A. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab669 · Cited by 10 · see citing works
Leonidou, N., Ostyn, L., Coenye, T., Crabbé, A., & Dräger, A. (2024) · Microbiology Spectrum · doi:10.1128/spectrum.04006-23 · Cited by 9 · see citing works
Modeling Enzyme Kinetics: Current Challenges and Future Perspectives for Biocatalysis
Pleiss, J. (2024) · Biochemistry · doi:10.1021/acs.biochem.4c00501 · Cited by 9 · see citing works
Evaluating Tools for Enhancing Reproducibility in Computational Scientific Experiments
Costa, L., Barbosa, S., & Cunha, J. (2024) · ACM Conference on Reproducibility and Replicability (ACM REP) · doi:10.1145/3641525.3663623 · Cited by 9 · see citing works
SED-ML web tools: generate, modify and export standard-compliant simulation studies
Bergmann, F., Nickerson, D. P., Waltemath, D., & Scharm, M. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw812 · Cited by 9 · see citing works
Self-citationSpecifications of Standards in Systems and Synthetic Biology: Status and Developments in 2017
Schreiber, F., Bader, G. D., Gleeson, P., Golebiewski, M., Hucka, M., Keating, S. M., Novère, N. L., Myers, C., Nickerson, D., Sommer, B., et al. (2018) · Journal of Integrative Bioinformatics · doi:10.1515/jib-2018-0013 · Cited by 9 · see citing works
Self-citationSpecifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019
Schreiber, F., Sommer, B., Bader, G. D., Gleeson, P., Golebiewski, M., Hucka, M., Keating, S. M., König, M., Myers, C., Nickerson, D., et al. (2019) · Journal of Integrative Bioinformatics · doi:10.1515/jib-2019-0035 · Cited by 15 · see citing works
Self-citationKönig, M., Gleeson, P., Golebiewski, M., Gorochowski, T. E., Hucka, M., Keating, S. M., Myers, C. J., Nickerson, D. P., Sommer, B., Waltemath, D., et al. (2023) · Journal of Integrative Bioinformatics · doi:10.1515/jib-2023-0004 · Cited by 6 · see citing works
Self-citationOlm, I. P., Benito-Vaquerizo, S., Dubaere, C., dos Santos, V. A. P. M., Diez, M. S., & Sousa, D. Z. (2025) · Environmental Science & Technology · doi:10.1021/acs.est.4c14794 · Cited by 9 · see citing works
Minimum Information Required to Annotate Food Safety Risk Assessment Models (MIRARAM)
Filter, M., Sundermann, E. M., Mesa-Varona, O., Buschhardt, T., de Abechuco, E. L., & Georgiadis, M. (2020) · Food Research International · doi:10.1016/j.foodres.2020.109952 · Cited by 8 · see citing works
libOmexMeta: enabling semantic annotation of models to support FAIR principles
Welsh, C., Nickerson, D. P., Rampadarath, A., Neal, M. L., Sauro, H. M., & Gennari, J. H. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab445 · Cited by 8 · see citing works
Self-citationSmith, L. P., Bergmann, F., Garny, A., Helikar, T., Karr, J. R., Nickerson, D. P., Sauro, H. M., Waltemath, D., & König, M. (2024) · Berichte aus der medizinischen Informatik und Bioinformatik/Journal of integrative bioinformatics · doi:10.1515/jib-2024-0008 · Cited by 7 · see citing works
Self-citationStanford, N., Scharm, M., Dobson, P. D., Golebiewski, M., Hucka, M., Kothamachu, V. B., Nickerson, D. P., Owen, S., Pahle, J., Wittig, U., et al. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9736-7_17 · Cited by 7 · see citing works
Self-citationFitzpatrick, R., & Stefan, M. I. (2022) · Neuroinformatics · doi:10.1007/s12021-022-09584-5 · Cited by 6 · see citing works
Excel–SBOL Converter: Creating SBOL from Excel Templates and Vice Versa
Mante, J. V., Abam, J., Samineni, S. P., Pötzsch, I. M., Singh, P., Beal, J., & Myers, C. J. (2023) · ACS Synthetic Biology · doi:10.1021/acssynbio.2c00521 · Cited by 6 · see citing works
Bayesian estimation reveals that reproducible models in Systems Biology get more citations
Höpfl, S., Pleiss, J., & Radde, N. E. (2023) · Scientific Reports · doi:10.1038/s41598-023-29340-2 · Cited by 6 · see citing works
Leonidou, N., Xia, Y., Friedrich, L., Schütz, M., & Dräger, A. (2024) · PLoS Pathogens · doi:10.1371/journal.ppat.1012528 · Cited by 6 · see citing works
Mimoza: web-based semantic zooming and navigation in metabolic networks
Zhukova, A., & Sherman, D. J. (2015) · BMC Systems Biology · doi:10.1186/s12918-015-0151-5 · Cited by 5 · see citing works
Dynamic Flux Balance Analysis Models in SBMLPreprint
König, M., Watanabe, L. H., Grzegorzewski, J., & Myers, C. (2018) · bioRxiv · doi:10.1101/245076 · Cited by 4 · see citing works
Who's afraid of synthetic data? Hybrid approaches to deliver medical digital twins
Vanin, J., Hagar, A., & Glazier, J. A. (2026) · Informatics in Medicine Unlocked · doi:10.1016/j.imu.2026.101737 · Cited by 6 · see citing works
Specifications of standards in systems and synthetic biology: status and developments in 2021
Schreiber, F., Gleeson, P., Golebiewski, M., Gorochowski, T., Hucka, M., Keating, S. M., König, M., Myers, C., Nickerson, D., Sommer, B., et al. (2021) · Journal of Integrative Bioinformatics · doi:10.1515/jib-2021-0026 · Cited by 6 · see citing works
Self-citationSimulation Experiment Description Markup Language (SED-ML)
Waltemath, D., & Novère, N. L. (2014) · Encyclopedia of Computational Neuroscience · doi:10.1007/978-1-4614-7320-6_377-6 · Cited by 8 · see citing works
Self-citation
- Authors
- Bergmann, F. T., Adams, R., Moodie, S., Cooper, J., Glont, M., Golebiewski, M., Hucka, M., Laibe, C., Miller, A. K., Nickerson, D. P., Olivier, B. G., Rodriguez, N., Sauro, H. M., Scharm, M., Soiland-Reyes, S., Waltemath, D., Yvon, F., & Le Novère, N.
- Affiliations
- Heidelberg University (DE)
- Research Space (United Kingdom) (GB)
- European Bioinformatics Institute (GB)
- University of Oxford (GB)
- Heidelberg Institute for Theoretical Studies (DE)
- California Institute of Technology (US)
- University of Auckland (NZ)
- Vrije Universiteit Amsterdam (NL)
- University of Washington (US)
- University of Rostock (DE)
- ORCID
- Venue
- BMC Bioinformatics
- Published
- 2014-12
- Volume
- 15
- Issue
- 1
- Pages
- 369-369
- ISSN
- 1471-2105 (ISSN-L)
- PMC
- PMC4272562
- OpenAlex
- W2096951208
- Cited by
- 173
- References
- 44
- Citations by year
- 2026: 10 · 2025: 10 · 2024: 19 · 2023: 23 · 2022: 16 · 2021: 25 · 2020: 18 · 2019: 10 · 2018: 15 · 2017: 6 · 2016: 11 · 2015: 7 · 2014: 2 · 2013: 1
- FWCI
- 16.81
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- BMC Bioinformatics (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Research Explorer (The University of Manchester) (publishedVersion, cc-by)
- VU Research Portal (publishedVersion, other-oa)
- arXiv (Cornell University) (submittedVersion)
- CaltechAUTHORS (California Institute of Technology) (submittedVersion, cc-by)
- UCL Discovery (University College London) (submittedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion, other-oa)
- arXiv (Cornell University)
- Funders
- Microsoft Research
- European Commission (283359, 270192)
- ZonMw (40-41009-98-10038)
- Bundesministerium für Bildung und Forschung (FKZ 031, FKZ 0316194, 0316194)
- Innovative Medicines Initiative (115156)
- Maurice Wilkins Centre for Molecular Biodiscovery
- National Institutes of Health (NIH P50, GM094503)
- Engineering and Physical Sciences Research Council (EP/I017909, EP/I017909/1)
- Biotechnology and Biological Sciences Research Council (BB/M013189/1, BBS/E/B/000C0419)
- National Institute of General Medical Sciences (GM070923, R01GM070923, P50GM094503, R01GM081070)
- FP7 Information and Communication Technologies
- Topics
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Keywords
- model exchange, model reproducibility, model metadata, audit trail, multiscale modeling, digital organisms
- MeSH terms
- Archives, Computer Simulation, Humans, Software, Information Storage and Retrieval, Computational Biology, Internet, Databases, Nucleic Acid
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
