March 2026 - Mism-external - lists.renci.org

Example Model from John Hickey
by Weyhmiller, Aubrie Anne 31 Mar '26

31 Mar '26

Hi Cliburn, In a recent meeting, you mentioned John Hickey's U01 influenza model project as a use case for testing model interoperability between different platforms. Are you able to share a manuscript, GitHub, or any relevant resources? Best, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her

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Journal Club – Tuesday 3/24 from 11 - 12 @ RENCI (Attendance + Details)
by Peterson, Gabi 24 Mar '26

24 Mar '26

Hi everyone, This is a friendly reminder that our first journal club meeting will take place this upcoming Tuesday, 3/24, from 11:00 am - 12:00 pm at the RENCI office. A Zoom option will be available, but we encourage in-person attendance when possible to support team building. We will discuss the pre-read paper below and brainstorm how to structure this meeting moving forward. Ashok has also kindly offered to provide lunch—more details to come. Required attendees (please attend in person or via Zoom): * Ashok * Isma * Aubrie * Nrupen All others are strongly encouraged to attend, though we understand you may have conflicting priorities. Required pre-read: * CURE Principles<https://drive.google.com/file/d/1XrJ2D57-7q5VQniGqzp_rbpmFZWeak6d/view?usp=…> (estimated read time: 30 - 60 min) * This paper describes specific FAIR (CURE) guidelines for mechanistic models. This is applicable to MDSC when thinking about how to build a FAIR platform for models and baseline requirements for submitted models. As you read, think about how MDSC can apply and promote these principles (and what principles are missing). What we need from you: * Confirm whether you will attend in person or via Zoom * Let us know if this meeting is not on your calendar * Keep an eye out for a follow-up email with lunch details Location details: RENCI 100 Europa Dr, Suite 590 Chapel Hill, NC 27517 Parking & building access: * Covered parking is available at the Europa Center * Enter through the main entrance (across from the parking lot), turn right, and take the elevators on the east (right) side to the 5th floor * Exit the elevators, turn right, then immediately left into the long hallway * Continue to the second set of elevators, then enter through the double doors for Suite 589 * The Franklin Conference Room is just past the kitchen Please reach out if you have any questions. Looking forward to seeing you all there! Best, Gabi Gabi Peterson, PMP (she/her/hers) Research Project Manager Renaissance Computing Institute University of North Carolina at Chapel Hill 100 Europa Drive, Suite 540 Chapel Hill, NC 27517-7583

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Urgent: Azure Environment Configuration Blocker for MDSC Platform
by Gilani, Isma 13 Mar '26

13 Mar '26

Hi Nrupen and Ashok, I wanted to provide an update from this morning’s meeting with Duke IT regarding the Azure environment required to support MDSC platform development (including Kubernetes clusters and public VMs for iRODS). We reviewed the proposed platform architecture and no concerns were raised. However, Duke IT cannot provision the necessary permissions, resources, or configurations until they understand the sensitivity level of the data that will flow through the system. As a result, development in the Azure environment is currently blocked until this information is clarified. To proceed, Duke IT has asked us to provide the following: * A data flow diagram showing where data originates, how it moves through the system, and what is exposed through APIs * RENCI is actively working on this * The data sensitivity level of information entering or leaving the platform * We will need to get this information from the RPs ASAP. Cliburn may have more info as well. * To our knowledge, RP1 may have sensitive data from private BCR repertoire data. * To our knowledge, RP3 may have sensitive data as well. We are less sure what that data is and where it comes from. * Which Duke HPC systems the project will use (identified vs. de-identified patient data environments) * Confirmation of user onboarding and identity management (we indicated MDSC would manage onboarding and users will not require direct Azure access) * Incident response ownership (I indicated Duke) * Responsibility for maintaining the Kubernetes clusters and VMs in the subscription (initially stated Duke) The immediate next step is to clarify the data sensitivity questions and produce the data flow diagram so Duke IT can determine the appropriate environment configuration. I recommend that we make this the first agenda item in Monday’s meeting so we can resolve the open questions quickly. Afterward, we will need to schedule a follow-up call with Duke IT and Duke Health CP to review the responses. It would be helpful for Nrupen to join that discussion. Best, Isma

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Request for RP Feedback on FAIR for Various Models
by Weyhmiller, Aubrie Anne 06 Mar '26

06 Mar '26

Hi Cliburn, As you know, MDSC is in the process of writing a manuscript evaluating existing FAIR (Findability, Accessibility, Interoperability, and Reproducibility) principles for models, specifically in terms of IID models. We would like to collect feedback from the RPs on how (or how not) Findability, Accessibility, Interoperability, and Reproducibility show up in their domains for mechanistic models, ABMs, and ML/AI models. Would you be able to help circulate this to the RPs and request a response by Friday, March 20? A couple paragraphs from each RP would be great. I’ve included some example questions and resources below to stimulate thoughts. * How easy or difficult is it to find, access, and run models from other researchers? * Are there certain repositories used to store and share models and datasets? * How/where do you typically find relevant models and datasets? * Are there certain formats used to increase interoperability and reusability such that models can be reused and integrated in other models/systems? * Machine-readable formats including SBML, CellML, etc * Modular code or resources * Containerization * Is annotation typically included for understandability and interoperability? * Using ontologies (EDAM, SBO, etc) * Are there differences in the FAIRness of sharing mechanistic models versus agent-based models versus ML/AI models? Relevant resources: * read more about the FAIR principles for research software<https://www.nature.com/articles/s41597-022-01710-x> * This paper<https://pmc.ncbi.nlm.nih.gov/articles/PMC11875277/> discusses further FAIR guidelines for mechanistic models. Best, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her

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[For Review] Justin Lessler Discussion Doc
by Weyhmiller, Aubrie Anne 04 Mar '26

04 Mar '26

Hi all, Here is a document<https://docs.google.com/document/d/1LCOrKwtu1D6JRSNiyQ6WCtSVZYTy7iXC_-H4zpn…> for capturing discussion questions for Justin Lessler during our March 12 meeting. Please populate prior to March 12 (particularly @Nrupen Bhavsar, Ph.D.<mailto:nrupen.bhavsar@duke.edu> and @Krishnamurthy, Ashok Kumar<mailto:ashok@renci.org>). Best, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her

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MISM Model & Data Sharing Commons MVP SOW – For Today’s Discussion
by Peterson, Gabi 02 Mar '26

02 Mar '26

Hi All, Nrupen, Cliburn, and Jason – during our meeting later today, Isma will present our MISM Model and Data Sharing Commons MVP SOW.<https://docs.google.com/document/d/1-g66tGVs1uaiX6P2k8_biOlcHuTuLjnwW22mS5a…> This document outlines the scope and deliverables for the MVP phase. If you have a few minutes (10-15) ahead of the call, a quick review would be helpful to inform the discussion. Please let me know if you have any trouble accessing the document. Looking forward to connecting this afternoon. Best, Gabi Gabi Peterson, PMP (she/her/hers) Research Project Manager Renaissance Computing Institute University of North Carolina at Chapel Hill 100 Europa Drive, Suite 540 Chapel Hill, NC 27517-7583

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