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FW: MISM Seminar Series - Eran Agmon [Hybrid]
by Weyhmiller, Aubrie Anne 21 Sep '26

21 Sep '26

From: mism-ops(a)duke.edu When: 10:00 - 11:00 October 8, 2026 Subject: MISM Seminar Series - Eran Agmon [Hybrid] Location: https://duke.zoom.us/j/99104284020?jst=1; Hock Plaza - Room #214 (CRTP Classroom) Title: Compositional systems biology: An executable framework for connecting models across scales Abstract: Biological systems are organized across interacting scales, from molecular networks and metabolic pathways to cells, tissues, microbial communities, and their environments, yet many computational models remain difficult to connect, reuse, or extend beyond the scale or formalism for which they were originally built. In this talk, I will introduce Compositional Systems Biology, an approach for building multiscale biological models from interoperable processes with explicit interfaces, shared state representations, and well-defined orchestration patterns governing when and how model components are executed. At the core of this work is Vivarium, an open-source platform for multiscale simulation that integrates diverse modeling formalisms -- including ODEs, stochastic kinetics, constraint-based models, agent-based dynamics, and rule-based logic -- within a unified execution framework. I will describe how this framework has been used in whole-cell modeling, including vEcoli, a comprehensive model of E. coli integrating mechanistic submodels of metabolism, transcription, translation, macromolecular synthesis, and cell division, and then discuss how the same compositional principles are being extended toward microbial systems, host-microbiome interactions, and spatially resolved multicellular tissue models. Throughout the talk, I will emphasize how executable composition can link biological structure to function, support transparent model reuse and validation, and create new opportunities for collaborative modeling across systems biology, computational medicine, and tissue-scale simulation. Bio: Eran Agmon is an Assistant Professor at the University of Connecticut School of Medicine and a member of the Center for Cell Analysis and Modeling. His research focuses on software infrastructure and theory for compositional, multiscale biological modeling, motivated by a longstanding interest in cells as both integrated molecular systems and adaptive agents that function within, respond to, and reshape their environments. He is a Principal Investigator on DARPA’s Simulating Microbial Systems program, where his group is developing hybrid simulations of E. coli that integrate mechanistic, agent-based, and constraint-based models, and a co-Investigator with the Center for Reproducible Biomedical Modeling, contributing to community standards, reusable simulation pipelines, and infrastructure for interoperable computational biology. His current work extends compositional modeling approaches to whole-cell simulation, microbial systems in the ocean and gut, and spatially resolved multicellular tissue models. Dr. Agmon completed a postdoctoral fellowship at Stanford University, where he worked on the E. coli whole-cell model, and earned his PhD in Informatics and Cognitive Science from Indiana University. Zoom: https://duke.zoom.us/j/99104284020?jst=1 Meeting ID: 991 0428 4020 Location: Hock Plaza - Room #214 (CRTP Classroom) ________________________________ This seminar series is organized by the Center for Multiscale Immune Systems Modeling<https://immunescale.org/> (MISM), funded by NIAID/NIH (U54AI191253).

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Scrum Summary
by Weyhmiller, Aubrie Anne 09 Jul '26

09 Jul '26

Hi all, Below is the AI-generated summary from scrum today. The notes are also captured in this agenda<https://docs.google.com/document/d/1ia68ZAkPUMWCNE0YUhvpfSr5kkvsttqAO_P_49H…>. On Tuesday July 14, we will review POC-2 after the journal club and prepare for a demo in the following weeks. Best, Aubrie Quick recap The team held a general check-in meeting to discuss progress on their POC2 development work, focusing on model upload and annotation functionality. Aubrie noted she still needs to update the data access layer to match new meta schemas, while Griffin reported completing the global auth context ticket and finishing model execution work including a runs history page. Harit discussed merging recent PRs and working on architectural cleanup with polling functionality for pod status tracking, while also developing a new endpoint for launching annotation pods. Yaphet provided updates on updating the access layer for new schemas and creating backend APIs to parse metadata packages, with Phil working on model upload functionality that's currently waiting on Harit's annotation pod implementation. The team discussed the workflow for handling model annotations, including status updates and UI polling mechanisms, with Yaphet suggesting a fire-and-forget approach where discovery calls execution and the UI separately monitors status changes. The conversation ended with a discussion about demo scheduling, with the team planning an internal demo on Tuesday followed by a presentation to Ashok on Wednesday and potentially to Nupin and Jason the following Monday. Next steps Aubrie * Update the data access layer to match the new meta schemas. * Send an email to Ashok and Rupan to schedule an in-person demo for the following week. Griffin * Open a PR for the model execution work, including the runs history page, by tomorrow. * Take over the work on the upload view from Phil after Phil is done. * Review and adjust the new endpoints created by Yaphet for displaying package files. Harit * Merge the PR for architectural cleanup and polling in the execution platform. * Complete the work on the new endpoint for firing off the annotation pod (MISM 271), aiming for a PR by tomorrow or Monday. * Work on modifying the run process to parameterize on different entry points, aiming for a PR early next week. Phil * Integrate the polling loop for annotation status into the UI upload page. Yaphet * Finish testing and open a PR for the model discovery work (parsing metadata YAML, new endpoints). * Look into building a Docker container for running composites locally, with the approach of mounting model files. Summary Team Progress and Blockers Update The team conducted a general check-in where Aubrie discussed updating the data access layer to match new meta schemas, which is needed for clock two and not currently blocked. Griffin reported completing the global auth context ticket and finishing model execution work including a runs history page, with plans to open a PR by tomorrow and take over Phil's upload view work. Harit mentioned merging several PRs and having a currently reviewed PR for architectural cleanup, while also working on a new endpoint for annotation pods that is blocking Phil's work. Model Upload and Workflow Updates Phil reported progress on model upload functionality but is waiting for Hari's work on launching the imitation pod. Yaphet discussed his work on updating the access layer for the new schema, including creating endpoints to help display package files for review. The team discussed how to handle status updates after annotation completion, with Yaphet explaining the new registration status workflow and Harit raising questions about reporting progress back to model discovery. Model Annotation Workflow Implementation The team discussed implementing a single call to execution for model annotation with status updates tracked in the database. Phil clarified how the UI would handle waiting for annotation completion, with Griffin confirming that the UI could show a waiting state and use polling to check status periodically. Yaphet outlined the workflow where annotations would move from "pending review" to "approved" states, with the search page displaying only approved and actively versioned models. Harit agreed to work on exposing different entry points in model metadata for parameterized runs and committed to sending a PR for this modification early the following week. POC Demo Planning Meeting The team discussed plans for demonstrating their POC (Proof of Concept) work. They agreed to have an internal demo on Tuesday before Journal Club to identify any issues, followed by a presentation to Ashok on Wednesday and then to Nupin and Jason on Monday the 20th. Griffin confirmed that the model execution feature branch is ready to merge, while Phil's upload component will remain on a separate feature branch until design improvements are completed. The team clarified that the original demo scheduled for Tuesday was actually for Journal Club, which will focus on reviewing the Vivarium paper, with the POC demo happening separately. Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her

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MISM Interns University Affiliations
by Weyhmiller, Aubrie Anne 08 Jun '26

08 Jun '26

Hi Kayla, It was great seeing you and the interns last week! Our team is evaluating if the infrastructure we are building can support MISM interns. Part of that is authentication based on their university affiliation. Are you able to share their organizations with us? Essentially, we need to know what institutions they are with so we can evaluate if a potential authentication tool supports their institutes' single sign on. Best, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her

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[For Review] MISM MDSC Vivarium Workshop Solution
by Weyhmiller, Aubrie Anne 28 May '26

28 May '26

Hi Ashok, The technical team has drafted a potential path forward<https://docs.google.com/document/d/1TekRFe_9FoQDU9aBWmBoPSXEULYW-rjobdtvOz7…> <https://docs.google.com/document/d/1TekRFe_9FoQDU9aBWmBoPSXEULYW-rjobdtvOz7…> for supporting a MISM Vivarium training as described by Kevin Flores (email subject: connecting for summer vivarium workshop). I have copied that email content below for further context. We can discuss this further next week at our MISM RENCI internal meeting at 2 PM on Wednesday 6/3. Otherwise, we can discuss async or set up an additional meeting. Best, Aubrie From: Kevin Flores <kbflores(a)ncsu.edu<mailto:kbflores@ncsu.edu>> Date: Wednesday, May 27, 2026 at 9:45 AM To: Krishnamurthy, Ashok Kumar <ashok(a)renci.org<mailto:ashok@renci.org>> Cc: John Hickey <john.hickey(a)duke.edu<mailto:john.hickey@duke.edu>> Subject: connecting for summer vivarium workshop Hi John and Ashok, I'm connecting you guys because one of John's students (Bobby Ni) will be training the summer interns on using Vivarium sometime in Mid-June (Bobby has a prelim exam early June). Ashok mentioned being able to support this training, and that members of the MDSC team would want to attend. John, I'll be reaching out to Grace to help schedule the Vivarium training with Bobby since I'll be traveling for work for the next month (I get back June 24th). Best, Kevin Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her

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