PharmML in Action: an Interoperable Language for Modeling and Simulation

Bizzotto, Roberto; Comets, Emmanuelle; Smith, George S.; Yvon, Florent; Kristensen, Niels Buus; Swat, Maciej

doi:10.1002/psp4.12213

Cited by 7 publications

(5 citation statements)

References 35 publications

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“…QSP models should ultimately be provided in an open‐source, standardized format. Although no single standard currently exists, there are a number of options, such as SBML, PharmML, and PK‐Sim/MoBi . However, given the extra effort required to do so and the fact that QSP work is rarely scripted in such platforms, such a requirement may simply impede publication rather than enhance sharing at this point.…”

Section: Best Practice Recommendations For Publishing Qsp Modelsmentioning

confidence: 99%

Reproducibility of Quantitative Systems Pharmacology Models: Current Challenges and Future Opportunities

Kirouac

Cicali

Schmidt

2019

CPT Pharmacom & Syst Pharma

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The provision of model code is required for publication in CPT: Pharmacometrics & Systems Pharmacology , enabling quantitative systems pharmacology (QSP) model availability. A searchable repository of published QSP models would enhance model accessibility. We assess the feasibility of establishing such a resource based on 18 QSP models published in this journal. However, because of the diversity of software platforms (nine), file formats, and functionality, such a resource is premature. We evaluated 12 of the models (those coded in R, PK ‐Sim/ MoBi, and MATLAB) for functionality. Of the 12, only 4 were executable in that figures from the associated manuscript could be generated via a “run” script. Many researchers are aware of the challenges involved in repurposing published models. We offer some ideas to enable model sharing going forward, including annotation guidelines, standardized formats, and the inclusion of “run” scripts. If practitioners can agree to some minimum standards for the provision of model code, model reuse and extension would be accelerated.

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Section: Best Practice Recommendations For Publishing Qsp Modelsmentioning

confidence: 99%

Reproducibility of Quantitative Systems Pharmacology Models: Current Challenges and Future Opportunities

Kirouac

Cicali

Schmidt

2019

CPT Pharmacom & Syst Pharma

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“…The new infrastructure removes this technical hindrance, allowing authors to submit models encoded in the format of their choice including Python, Mathematica or Matlab SimBiology, and regardless of the modelling approach employed (Figure 1 ). To foster interoperability and model reuse, the new system offers enhanced technical support for open formats such as SBML, PharmML ( 7 ) or COMBINE Archive ( 8 ). This expansion of scope for submissions offers more modelling communities the ability to leverage BioModels for dissemination, exchange and reuse of the models that they develop.…”

Section: Multiformat Model Submissionmentioning

confidence: 99%

BioModels: expanding horizons to include more modelling approaches and formats

Glonț

Nguyen

Graesslin

et al. 2017

Nucleic Acids Research

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BioModels serves as a central repository of mathematical models representing biological processes. It offers a platform to make mathematical models easily shareable across the systems modelling community, thereby supporting model reuse. To facilitate hosting a broader range of model formats derived from diverse modelling approaches and tools, a new infrastructure for BioModels has been developed that is available at http://www.ebi.ac.uk/biomodels. This new system allows submitting and sharing of a wide range of models with improved support for formats other than SBML. It also offers a version-control backed environment in which authors and curators can work collaboratively to curate models. This article summarises the features available in the current system and discusses the potential benefit they offer to the users over the previous system. In summary, the new portal broadens the scope of models accepted in BioModels and supports collaborative model curation which is crucial for model reproducibility and sharing.

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“…Our BioModels team helped launch PharmML, a flexible format for exchanging computational models in pharmaceutical R&D, in 2016 ( 15 ). PharmML is a key component of the Innovative Medicines Initiative-funded DDMoRe model repository ( http://repository.ddmore.eu/ ) ( 32 ), which supports inter-organizational collaboration on models to improve the design of cost-effective, reliable clinical trials of new and re-purposed drugs. The Proteomics team, in collaboration with the Proteomics Standards Initiative, has led the development of the proBed and proBAM standard formats, aimed at representing proteogenomics results ( https://www.biorxiv.org/content/early/2017/06/20/152579 ).…”

Section: Data Integrationmentioning

confidence: 99%

The European Bioinformatics Institute in 2017: data coordination and integration

Cook

Bergman

Cochrane

et al. 2017

Nucleic Acids Research

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The European Bioinformatics Institute (EMBL-EBI) supports life-science research throughout the world by providing open data, open-source software and analytical tools, and technical infrastructure (https://www.ebi.ac.uk). We accommodate an increasingly diverse range of data types and integrate them, so that biologists in all disciplines can explore life in ever-increasing detail. We maintain over 40 data resources, many of which are run collaboratively with partners in 16 countries (https://www.ebi.ac.uk/services). Submissions continue to increase exponentially: our data storage has doubled in less than two years to 120 petabytes. Recent advances in cellular imaging and single-cell sequencing techniques are generating a vast amount of high-dimensional data, bringing to light new cell types and new perspectives on anatomy. Accordingly, one of our main focus areas is integrating high-quality information from bioimaging, biobanking and other types of molecular data. This is reflected in our deep involvement in Open Targets, stewarding of plant phenotyping standards (MIAPPE) and partnership in the Human Cell Atlas data coordination platform, as well as the 2017 launch of the Omics Discovery Index. This update gives a birds-eye view of EMBL-EBI’s approach to data integration and service development as genomics begins to enter the clinic.

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PharmML in Action: an Interoperable Language for Modeling and Simulation

Cited by 7 publications

References 35 publications

Reproducibility of Quantitative Systems Pharmacology Models: Current Challenges and Future Opportunities

Reproducibility of Quantitative Systems Pharmacology Models: Current Challenges and Future Opportunities

BioModels: expanding horizons to include more modelling approaches and formats

The European Bioinformatics Institute in 2017: data coordination and integration

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