Model Description Language (MDL): A Standard for Modeling and Simulation
Open accessAbstract
Recent work on Model Informed Drug Discovery and Development (MID3) has noted the need for clarity in model description used in quantitative disciplines such as pharmacology and statistics.1-3 Currently, models are encoded in a variety of computer languages and are shared through publications that rarely include original code and generally lack reproducibility. The DDMoRe Model Description Language (MDL) has been developed primarily as a language standard to facilitate sharing knowledge and understanding of models.
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Two model repositories currently exist: BioModels, geared toward cell- and molecular-based systems models, and DDMoRE, for pharmacometrics.
“Two such model repositories currently exist: BioModels25 geared toward cell‐ and molecular‐based systems models and DDMoRE26 for pharmacometrics.”
From Reproducibility of Quantitative Systems Pharmacology Models: Current Challenges and Future Opportunities (2019) · cites this paper as [26]
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Cites
Workgroup, E. M., Marshall, S., Burghaus, R., Cosson, V, Cheung, S., Chenel, M., DellaPasqua, O., Frey, N., Hamrén, B., Harnisch, L., et al. (2016) · CPT: Pharmacometrics & Systems Pharmacology · doi:10.1002/psp4.12049 · Cited by 373 · see citing works
Self-citationModel-Based Drug Development: A Rational Approach to Efficiently Accelerate Drug Development
Milligan, P. A., Brown, M. J., Marchant, B., Martin, S. W., van der Graaf, P. H., Benson, N., Nucci, G., Nichols, D. J., Boyd, R. A., Mandema, J. W., et al. (2013) · Clinical Pharmacology & Therapeutics · doi:10.1038/clpt.2013.54 · Cited by 238 · see citing works
Hucka, M., Finney, A., Doyle, J. C., Kitano, H., Kovitz, B., Shapiro, B. E., Funahashi, A., Matthews, J., Bornstein, B., Keating, S., et al. (2004) · Systems Biology · doi:10.1049/sb:20045008 · Cited by 232 · see citing works
Swat, M. J., Moodie, S., Wimalaratne, S., Kristensen, N. R., Lavielle, M., Mari, A., Magni, P., Smith, M. K., Bizzotto, R., Pasotti, L., et al. (2015) · CPT Pharmacometrics & Systems Pharmacology · doi:10.1002/psp4.57 · Cited by 39 · see citing works
Self-citationProposed best practice for projects that involve modelling and simulation
O’Kelly, M., Anisimov, V. V., Campbell, C., & Hamilton, S. (2016) · Pharmaceutical Statistics · doi:10.1002/pst.1789 · Cited by 17 · see citing works
ProbOnto: ontology and knowledge base of probability distributions
Swat, M. J., Grenon, P., & Wimalaratne, S. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw170 · Cited by 16 · see citing works
Self-citationImplementing a Domain-specific Language for Model-based Drug Development
Kokash, N., Moodie, S., Smith, M. K., & Holford, N. H. G. (2015) · Procedia Computer Science · doi:10.1016/j.procs.2015.08.348 · Cited by 5 · see citing works
Self-citationLewis Sheiner ISoP/UCSF Lecturer Award: From Drug Use to Statistical Models and Vice Versa
Mentré, F. (2014) · CPT Pharmacometrics & Systems Pharmacology · doi:10.1038/psp.2014.52 · Cited by 4 · see citing works
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Cucurull‐Sanchez, L., Chappell, M. J., Chelliah, V., Amy Cheung, S. Y., Derks, G., Penney, M., Phipps, A., Malik‐Sheriff, R. S., Timmis, J., Tindall, M. J., et al. (2019) · CPT: Pharmacometrics & Systems Pharmacology · doi:10.1002/psp4.12381 · Cited by 61 · see citing works
Kirouac, D. C., Cicali, B., & Schmidt, S. (2019) · CPT: Pharmacometrics & Systems Pharmacology · doi:10.1002/psp4.12390 · Cited by 46 · see citing works
“Two such model repositories currently exist: BioModels 25 geared toward cell-and molecular-based systems models and DDMoRE 26 for pharmacometrics.”
Method
- Authors
- Smith, M. K., Moodie, S. L., Bizzotto, R., Blaudez, E., Borella, E., Carrara, L., Chan, P., Chenel, M., Comets, E., Gieschke, R., Harling, K., Harnisch, L., Hartung, N., Hooker, A. C., Karlsson, M. O., Kaye, R., Kloft, C., Kokash, N., Lavielle, M., Lestini, G., Magni, P., Mari, A., Mentré, F., Muselle, C., Nordgren, R., Nyberg, H. B., Parra‐Guillén, Z. P., Pasotti, L., Rode‐Kristensen, N., Sardu, M. L., Smith, G. R., Swat, M. J., Terranova, N., Yngman, G., Yvon, F., Holford, N., & on behalf of the DDMoRe consortium
- Affiliations
- Pfizer (United Kingdom) (GB)
- Eight Pillars Ltd Edinburgh UK
- CNR Institute of Neurosciences Padova Italy
- Lixoft Orsay France
- University of Pavia (IT)
- Servier (France) (FR)
- Inserm (FR)
- F. Hoffmann-La Roche AG (CH)
- Uppsala University (SE)
- Freie Universität Berlin (DE)
- Mango Solutions Chippenham UK
- Leiden University (NL)
- Institut national de recherche en sciences et technologies du numérique (FR)
- Freie Univeristät Berlin Germany
- Novo Nordisk A/S Bagsværd Denmark
- Merck Serono S.A. (Switzerland) (CH)
- Scientific Computing Group, Cyprotex Discovery Limited, Macclesfield Crewe UK
- European Bioinformatics Institute (GB)
- Uppsala Universitet Sweden
- Corresponding author
- Smith, Mike K.
- ORCID
- Moodie, Stuart L.
- Bizzotto, Roberto
- Chan, Phylinda
- Chenel, Marylore
- Comets, Emmanuelle
- Gieschke, Ronald
- Harnisch, Lutz
- Hartung, Niklas
- Hooker, Andrew C.
- Karlsson, Mats O.
- Kloft, Charlotte
- Kokash, Natallia
- Lavielle, Marc
- Lestini, Giulia
- Magni, Paolo
- Mentré, France
- Nordgren, Rikard
- Nyberg, Henrik B.
- Pasotti, Lorenzo
- Swat, Maciej J.
- Terranova, Nadia
- Yvon, Florent
- Venue
- CPT: Pharmacometrics & Systems Pharmacology
- Publisher
- Wiley
- Published
- 2017-07-12
- Volume
- 6
- Issue
- 10
- Pages
- 647-650
- ISSN
- 2163-8306 (ISSN-L)
- PMC
- PMC5658286
- OpenAlex
- W2628982289
- Cited by
- 17
- References
- 8
- Citations by year
- 2024: 1 · 2022: 2 · 2021: 1 · 2020: 3 · 2019: 3 · 2018: 7
- FWCI
- 5.71
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- CPT Pharmacometrics & Systems Pharmacology (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- CNR ExploRA (submittedVersion, other-oa)
- ResearchSpace (University of Auckland) (submittedVersion)
- Funders
- European Federation of Pharmaceutical Industries and Associations (FP7/20072013)
- European Commission (115156, 2007–2013, FP7 2007-2013, FP7/2007)
- Innovative Medicines Initiative (FP7/2007‐2013, 115156)
- Topics
- Social Sciences › Decision Sciences › Information Systems and Management › Scientific Computing and Data Management
- Physical Sciences › Computer Science › Information Systems › Research Data Management Practices
- Physical Sciences › Computer Science › Computational Theory and Mathematics › Modeling and Simulation Systems
- Keywords
- model description language, model description, modeling and simulation, language norms, model sharing, reproducibility, statistical models
- MeSH terms
- Computer Simulation, Models, Statistical
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