INCF Program on Multiscale Modeling Workshop: From Cellular/Network Models to Tissue Simulation

Abstract

The INCF Program on Multiscale Modeling (MSM) aims to promote the development of software infrastructure to facilitate neural modeling across many different scales. A new focus of the Program could be to support the transition from single neuron (network) modeling to neural tissue simulation. The aim would be to develop model description languages and the software infrastructure required to leverage existing molecular, neuron, and network models to build neural tissue models that accommodate both virtual tissue and reconstructed tissue modeling within a single framework. The aim of this workshop was to assess the current state of the field and available software infrastructure for tissue modeling from within the field of neuroscience and other fields in order to broadly define an outline of the development needed. The INCF will take the recommendations of this workshop to determine the need for subsequent actions and follow-up workshops, in order to direct future activities within the MSM Program, including the formation of new Program task force(s) as needed. In addition, The INCF aims to integrate these efforts with other INCF Programs such as those currently in progress in the Digital Brain Atlasing Program, Standards for Data Sharing Program and the Program on Ontologies of Neural Structures. The participants of the workshop suggested that the INCF could establish a working group to investigate how to describe spatial structures at the micro-scale, including the investigation of annotated mesh formats, mesh outputs from EM reconstruction, coordinate transforms, and markup schemes (Digital Atlasing, SBML). Participants noted that a thematic workshop on topic of ‘How to model when you do not know the parameters’ would be useful, with computational biologists included as participants. The participants also recommended that the INCF should announce an open call in the form of a competition for interested parties who want to commit to commenting on the state of the field for some of the use cases recommended during the discussion. The candidates should respond with a plan which will be reviewed against a set of criteria set forth during the workshop. The INCF should then hold followup workshops around the use cases with the output of these workshops being a set of recommendations for actions by the INCF. One identified use case linking different levels involves advancing the understanding of the relationship of sub cellular processes and cellular level electrical behavior. Since the workshop, a proposal has been developed further by the community for a workshop on the topic ‘Methods in bridging subcellular and cellular level models’.