Model Description Language (MDL): A Standard for Modeling and Simulation

Best Practices to Maximize the Use and Reuse of Quantitative and Systems Pharmacology Models: Recommendations From the United Kingdom Quantitative and Systems Pharmacology Network

“…When those parameters are reported, the data, knowledge, and assumptions that underwrite their values are often missing or their adequacy, quality, and quantity are poorly discussed. The paper in which the model is published provides its description but fails to provide the associated model file or programming code . The emergence of standardized markup languages (SBML), such as systems biology markup language, cell markup language (CellML), pharmacometrics markup language PharmML, or model description language (MDL), the existence of fully compatible modeling software (e.g., COPASI, SimBiology), and the availability of open source tools to translate between them (e.g., Systems Biology Workbench) should enable and encourage researchers to share their encoded model. However, although the provision of model files or computer code is encouraged by several scholarly journals, in practice some scientists are reluctant to give up their competitive advantage over other research groups.…”

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

“…As is the case for genomics data sets, journals could request authors to provide models in an established repository. Two such model repositories currently exist: BioModels geared toward cell‐ and molecular‐based systems models and DDMoRE for pharmacometrics. Consortiums have also been established to develop more comprehensive tissue‐ and disease‐focused models, such as DILIsym (drug‐induced liver injury), Certara's QSP Immunogenicity Consortium, or the Critical Path for Alzheimer's Disease; hence, these may serve in specific cases.…”

The Standard Output: A Tool‐Agnostic Modeling Storage Format

“…The DDMoRe project has addressed these shortcomings through the definition, implementation and integration of a set of standards into the so-called IOF. [6][7][8][9] Among these, the SO has been proposed as the tool-independent format for storing output typically produced from pharmacometric M&S tasks and workflows to guide the model building through assessment of the goodness-of-fit between the model and the dataset and the appropriateness of the underlying model assumptions, as well as to allow the reproducibility of the results. Developing a standardized output format across M&S tools allows better sharing of information, reusable code, and better integration of a wide variety of tools within a single pharmacometric workflow.…”