The Computational Modelling in Biology Network in 2024: Standards and services for the computational physiology community and beyond

Presentation delivered at the 2024 VPH Conference.

Abstract

The Computational Modelling in Biology Network (https://co.mbine.org/) coordinates the development and dissemination of community standards and formats in systems biology and related fields. It ensures that previously independent standardisation initiatives develop a set of interoperable and non-overlapping standards covering all aspects of modelling in biology and medicine. The global effort is led by the COMBINE coordination board with representatives of all COMBINE standards. Building on the experience of mature projects, which already have stable specifications, software support, user-base and community governance, COMBINE helps foster and support fledgling efforts. As those efforts mature, they may become part of the core set of COMBINE standards.

Our presentation will introduce the COMBINE governance and core standards for modelling (CellML, NeuroML, SBOL, SBML), graphical network representation (SBGN, SBOL Visual), simulation encoding (SED-ML), dissemination of modelling studies (COMBINE archive), and handling of metadata (OMEX). We will discuss the available resources and community support specifically for the computational physiology community. An overview of ongoing projects and open challenges to extend the COMBINE standards will be given, as well as examples for implementation in tools and models, e.g. in the context of Virtual Human Twins and personalized medicine. We invite the audience to participate in the standards’ development and evaluation.

COMBINE supports FAIR and TRUSTed efforts and infrastructures in systems medicine, thereby fostering reuse of simulation studies, reproducibility and interoperability of model-based results. We share our experiences of cooperating with model repositories such as Biomodels or the Physiome Model Repository, and with international efforts such as the Reproducibility Center or the Disease Map community. The development of open software and libraries, standard-enabled workflows, and the contribution to open science efforts (EOSC, FAIRsharing) are also part of our work. We also contribute to formal ISO standards for data sharing in life sciences (ISO 20691) and modelling in personalised medicine (ISO/TS 9491-1).