Hi Aubria and MISM MDSC crew, Pleasure to meet you earlier this week. Attaching the slides I showed you, and I am going straight down to the questions below within your email’s text (response in blue). ~Eran From: Weyhmiller, Aubrie Anne <aubriew@renci.org> Date: Wednesday, July 29, 2026 at 11:34 AM To: Agmon,Eran <agmon@uchc.edu> Cc: Weyhmiller, Aubrie Anne via Mism-external <mism-external@lists.renci.org> Subject: Re: Journal Club Tomorrow 11 AM *** Attention: This is an external email. *** Use caution responding, opening attachments or clicking on links. Report Suspicious<https://us-phishalarm-ewt.proofpoint.com/EWT/v1/ADdU39pX!fttTL2ogMToHCUbjjjBuWC-HF6Bc_2SS6eyrf033Mct-gLQadBsH2zvO2i98w8J_YCQ-qjhfmHn7g-kgaudWePa-B5qb8adkfSBLo0j4Cd8SSH3YPATWij72Bc2Ajob8zZzczoc2Qw$> Hi Eran, Thank you for joining us yesterday, we really enjoyed learning more about Vivarium and discussing how our teams can potentially work together. Below is a (long) list of questions our team has for you. We also expressed interest in meeting again prior to your October MISM visit. We will chat internally about timing and topics and reach back out to you 😊 Yes please! MDSC Questions for Eran * How do you decide the level of metadata required for Vivarium models? * Does Vivarium follow MIRIAM? We require metadata that supports execution, composition, interpretation, and reproducibility: typed inputs and outputs, units, configuration, update behavior, dependencies, version, provenance. Additional metadata should capture the model’s assumptions and intended reuse. Not following MIRIAM. * What other groups are developing vivarium models, or converting their models to vivarium? There are a few, most of them linked to my lab’s collaborations, but some also independent. This includes the Covert Lab’s E. coli whole-cell model, C-CoMP microbial ecosystem modeling, Build-a-Cell in silico cell efforts, Open Virtual Tissues, the Allen Institute for Cell Science, the Center for Reproducible Biomedical Modeling/ BioSimulations, and some groups integrating SBML, COBRA, spatial, agent-based, and tissue models. * What kinds of meetings do you/your lab attend? * For modeling * For standards and FAIR? We attend COMBINE, Society for Mathematical Biology, International Society for Systems Biology sometimes, IMAG Multiscale Modeling meetings. COMBINE is the main standard meeting in systems biology. * Could vivarium be used for the individual and population scales, not just cells/tissues? What would that take? Yes, Vivarium is scale and method independent. This requires the appropriate schemas, simulation processes, and appropriate mappings within-host and population-level variables. * Are their lessons that we can take from the bigraph/compartmental hierarchy that might extend to multiscale models that use many distinct agent types? The hierarchy separates what an entity is, where it is, and how it interacts. Distinct agent types can share common interfaces while retaining specialized internal models. This enables heterogeneous agents to coexist, move between compartments, exchange information, and be added or removed dynamically. The Bigraph framework is a generalized approach to modeling “the space and motion of communicating agents" * How do we think about communicating uncertainty when uncertainty at one scale can magnify at another scale? Uncertainty should be represented at each model interface, propagated through ensembles or probabilistic distributions, and reported locally between interfaces and for final outcomes. * The platform we are building may need to inform responses to future outbreaks. What validation, versioning, provenance, or compatibility checking may we want to consider as we develop the platform if there is the potential for bad models to be combined with good models? Every component should have a versioned contract, provenance record, validation evidence, applicable domain, units, and assumptions. Composition includes automated checks for interface compatibility, units, timescales, semantic meaning, parameter ranges, and validation status * As a disease platform, we may need to host/run large models. How might we want to think about that now in the early stages of development? Design early for containerized components, data references, checkpointing, parallel execution, cloud/HPC scheduling, resource declarations, and reproducible environments. Models should run locally when small but move to distributed infrastructure without changing their scientific interfaces. Vivarium helps with all of this. * Where and how in vivarium 2 are: * Agents used * LLMs used Agents are used in surrounding tools to help wrap simulators, generate process contracts, assemble composites, search documentation, explain models, and operate the Vivarium Workbench. There are no LLMs in the core engine. Viva-superpowers is the ai-specific repo that knows how to interact with vivarium: https://github.com/vivarium-collective/viva-superpowers * What are the minimum requirements to run workbench with a setup similar to what was demoed? Do you have links to any documentation? Here is some info about the software: https://vivariumlab.com/software/. I demoed the E. Coli whole-cell model in vivarium 2: https://github.com/vivarium-collective/v2ecoli. If you go through that readme there is a lot of information about how to run it, including a markdown file you can give to claude so it will get everything running for you: https://github.com/vivarium-collective/v2ecoli/blob/main/docs/first-run-agen.... Creating and running your own repo takes a little bit more, because you have to identify the components and templates that you need. Thanks again, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her From: Weyhmiller, Aubrie Anne via Mism-external <mism-external@lists.renci.org> Date: Monday, July 27, 2026 at 12:28 To: Agmon,Eran <agmon@uchc.edu> Cc: Weyhmiller, Aubrie Anne via Mism-external <mism-external@lists.renci.org> Subject: [Mism-external] Journal Club Tomorrow 11 AM Hi Eran, We are looking forward to chatting with you tomorrow at 11 AM ET! I see you accepted the calendar invite. Please let me know if you have any questions. Best, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her