SysMod: the ISCB community for data-driven computational modelling and multi-scale analysis of biological systems

Abstract

Computational models of biological systems can exploit a broad range of rapidly developing approaches, including novel experimental approaches, bioinformatics data analysis, emerging modelling paradigms, data standards and algorithms. A discussion about the most recent advances among experts from various domains is crucial to foster data-driven computational modelling and its growing use in assessing and predicting the behaviour of biological systems. Intending to encourage the development of tools, approaches and predictive models, and to deepen our understanding of biological systems, the Community of Special Interest (COSI) was launched in Computational Modelling of Biological Systems (SysMod) in 2016. SysMod’s main activity is an annual meeting at the Intelligent Systems for Molecular Biology (ISMB) conference, which brings together computer scientists, biologists, mathematicians, engineers, computational and systems biologists. In the five years since its inception, SysMod has evolved into a dynamic and expanding community, as the increasing number of contributions and participants illustrate. SysMod maintains several online resources to facilitate interaction among the community members, including an online forum, a calendar of relevant meetings and a YouTube channel with talks and lectures of interest for the modelling community. For more than half a decade, the growing interest in computational systems modelling and multi-scale data integration has inspired and supported the SysMod community. Its members get progressively more involved and actively contribute to the annual COSI meeting and several related community workshops and meetings, focusing on specific topics, including particular techniques for computational modelling or standardisation efforts.

Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology

“…The workshop grew from a previous edition organised during [BC]2 2019 focused on logical modelling [ 1 ]. The second edition brought together scientists with various research backgrounds and from different working groups such as BioModels [ 2 ], a central repository of mathematical models of biological/biomedical processes; the Computational Modelling in Biology Network initiative (COMBINE) [ 3 ]; CoLoMoTo, [ 4 ]; SysMod, [ 5 ]; the Systems Biology Graphical Notation (SBGN) project [ 6 ]; the systems biology markup language (SBML) [ 7 ] and simulation experiment description markup language (SED-ML) [ 8 ], to exchange and expand on several key topics of common interest ( Figure 1 ).…”

Perspectives on computational modeling of biological systems and the significance of the SysMod community

“…Integration of single-cell data, for example, into CBMs of cell populations ( Damiani et al , 2019 , Wagner et al , 2021 ), has provided insights into the cellular heterogeneity of tumours, the tumour microenvironment, and the mechanisms of drug resistance in cancer therapy. Computational models that include single-cell data enhance our understanding of tumour evolution, the dynamics of cancer progression, and the biological processes in cancer ( Bakr et al , 2023 ), thereby informing more effective treatment strategies.…”

A guide for developing comprehensive systems biology maps of disease mechanisms: planning, construction and maintenance

“…Disease Maps approaches evolve together with other systems biology communities such as COMBINE ( Hucka et al, 2015 ), CoLoMoTo ( Niarakis et al, 2021 ), SysMod ( Dräger et al, 2021 ), SBGN ( Le Novère et al, 2009 ), SBML ( Keating et al, 2020 ) and FAIR ( Wilkinson et al, 2016 ) to enhance the accessibility and reusability of the resources ( Niarakis et al, 2022 ).…”