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Vivarium: an Interface and Engine for Integrative Multiscale Modeling in Computational Biology

Agmon, Eran and Spangler, Ryan K. and Skalnik, Christopher J. and Poole, William and Peirce, Shayn M. and Morrison, Jerry H. and Covert, Markus W. (2021) Vivarium: an Interface and Engine for Integrative Multiscale Modeling in Computational Biology. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20210429-132053775

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Abstract

Motivation: This paper introduces Vivarium – software born of the idea that it should be as easy as possible for computational biologists to define any imaginable mechanistic model, combine it with existing models, and execute them together as an integrated multiscale model. Integrative multiscale modeling confronts the complexity of biology by combining heterogeneous datasets and diverse modeling strategies into unified representations. These integrated models are then run to simulate how the hypothesized mechanisms operate as a whole. But building such models has been a labor-intensive process that requires many contributors, and they are still primarily developed on a case-by-case basis with each project starting anew. New software tools that streamline the integrative modeling effort and facilitate collaboration are therefore essential for future computational biologists. Results: Vivarium is a Pythonic software for building integrative multiscale models. It provides an interface that makes individual models into modules that can be wired together in large composite models, parallelized across multiple CPUs, and run with Vivarium’s simulation engine. Vivarium’s utility is demonstrated by building composite models that combine several modeling frameworks: agent based models, ordinary differential equations, stochastic reaction systems, constraint-based models, solid-body physics, and spatial diffusion. This demonstrates just the beginning of what is possible – future efforts can integrate many more types of models and at many more biological scales. Availability: The models, simulation pipelines, and notebooks developed for this paper are available at the vivarium-notebooks repository: https://github.com/vivarium-collective/vivarium-notebooks. Vivarium-core is available at https://github.com/vivarium-collective/vivarium-core, and has been released on PyPI. The Vivarium Collective (https://vivarium-collective.github.io) is a repository of freely-available Vivarium processes and composites, including the processes used in Section 3. Supplementary materials provide with an extensive methodology section, with several code listings that demonstrate the basic interfaces.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/2021.04.27.441657DOIDiscussion Paper
https://github.com/vivarium-collective/vivarium-notebooksRelated ItemModels, simulation pipelines, and notebooks
https://github.com/vivarium-collective/vivarium-coreRelated ItemVivarium-core
https://vivarium-collective.github.ioRelated ItemVivarium Collective
ORCID:
AuthorORCID
Agmon, Eran0000-0003-1279-2474
Spangler, Ryan K.0000-0002-6080-3142
Peirce, Shayn M.0000-0001-5857-5606
Covert, Markus W.0000-0002-5993-8912
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license. Version 1 - April 28, 2021. Version 2 - September 15, 2021. We thank two anonymous reviewers for their thoughtful comments, which were significant in shaping the discussion section. We thank Jeremy Zucker for reporting a bug in the vivarium-cobra library, Richard Murray for discussion and feedback on the paper, and the Build-A-Cell community for organizing workshop discussions that helped motivate the use of Vivarium as a general model integration software tool. This work was supported by the Paul G. Allen Frontiers Group via an Allen Discovery Center at Stanford, as well as NIGMS of the National Institutes of Health under award number F32GM137464 to E.A., and NSF grant CBET-1903477 to W.P. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. The authors have declared no competing interest.
Funders:
Funding AgencyGrant Number
Paul G. Allen Frontiers GroupUNSPECIFIED
NIH Postdoctoral FellowshipF32GM137464
NSFCBET-1903477
Subject Keywords:Integrative modeling; Multiscale modeling; Computational biology
Record Number:CaltechAUTHORS:20210429-132053775
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20210429-132053775
Official Citation:Vivarium: an Interface and Engine for Integrative Multiscale Modeling in Computational Biology. Eran Agmon, Ryan K. Spangler, Christopher J. Skalnik, William Poole, Shayn M. Peirce, Jerry H. Morrison, Markus W. Covert. bioRxiv 2021.04.27.441657; doi: https://doi.org/10.1101/2021.04.27.441657
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:108871
Collection:CaltechAUTHORS
Deposited By: George Porter
Deposited On:29 Apr 2021 22:03
Last Modified:16 Sep 2021 16:12

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