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FW: [EXTERNAL] Re: Computational model repository
by Weyhmiller, Aubrie Anne 23 Apr '26

23 Apr '26

Hi MDSC folks, See this email chain for information about a connection Ashok and Nrupen recently made to Herbert Sauro, the Director of the NIH Center for Model Reproducibility<https://reproduciblebiomodels.org/>. Sounds like Ashok and Nrupen will meet with Herbet soon to discuss collaboration opportunities. I highly recommend checking out their website<https://reproduciblebiomodels.org/>, including their page on model and simulation annotation<https://reproduciblebiomodels.org/research/annotation/>. Best, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her From: Krishnamurthy, Ashok Kumar <ashok(a)renci.org> Date: Wednesday, April 22, 2026 at 11:58 To: Weyhmiller, Aubrie Anne <aubriew(a)renci.org>, Gilani, Isma <igilani(a)renci.org>, Todd, Bryttany <btodd(a)renci.org> Subject: FW: [EXTERNAL] Re: Computational model repository Please forward to others on RENCI team. Ashok From: Krishnamurthy, Ashok Kumar <ashok(a)renci.org> Date: Wednesday, April 22, 2026 at 11:57 AM To: Nrupen Bhavsar, Ph.D. <nrupen.bhavsar(a)duke.edu>, penggr(a)mail.nih.gov <penggr(a)mail.nih.gov>, Herbert M Sauro <hsauro(a)uw.edu>, Hunter Robbins <robbinsh(a)uw.edu> Cc: NIAID Data Sharing <NIAID_datasharing(a)niaid.nih.gov> Subject: Re: [EXTERNAL] Re: Computational model repository Thank you for connecting us, Grace. Wonderful to meet you, Herbert and Hunter. I have filled out the scheduling grid. Look forward to our discussions. Ashok -- Ashok Krishnamurthy, PhD Director, RENCI<http://www.renci.org/> Professor, SDSS<https://sdss.unc.edu/> Research Professor, Computer Science<https://cs.unc.edu/> Co-Director, Informatics and Data Science, TraCS<https://tracs.unc.edu/> University of North Carolina, Chapel Hill<http://www.unc.edu/> From: Nrupen Bhavsar, Ph.D. <nrupen.bhavsar(a)duke.edu> Date: Wednesday, April 22, 2026 at 6:03 AM To: penggr(a)mail.nih.gov <penggr(a)mail.nih.gov>, Herbert M Sauro <hsauro(a)uw.edu>, Hunter Robbins <robbinsh(a)uw.edu> Cc: Krishnamurthy, Ashok Kumar <ashok(a)renci.org>, NIAID Data Sharing <NIAID_datasharing(a)niaid.nih.gov> Subject: Re: [EXTERNAL] Re: Computational model repository Thank you for connecting us, Grace. We look forward to learning more about the exciting work Herbert and his team are doing. Thank you, Nrupen From: Peng, Grace (NIH/NIBIB) [E] <penggr(a)mail.nih.gov> Date: Tuesday, April 21, 2026 at 11:29 AM To: Herbert M Sauro <hsauro(a)uw.edu>; Hunter Robbins <robbinsh(a)uw.edu> Cc: Krishnamurthy, Ashok Kumar <ashok(a)renci.org>; NIAID Data Sharing <NIAID_datasharing(a)niaid.nih.gov>; Nrupen Bhavsar, Ph.D. <nrupen.bhavsar(a)duke.edu> Subject: RE: [EXTERNAL] Re: Computational model repository Thanks Herbert! From: Herbert M Sauro <hsauro(a)uw.edu> Sent: Tuesday, April 21, 2026 11:08 AM To: Hunter Robbins <robbinsh(a)uw.edu>; Peng, Grace (NIH/NIBIB) [E] <penggr(a)mail.nih.gov> Cc: Ashok Krishnamurthy <ashok(a)renci.org>; NIAID Data Sharing <NIAID_datasharing(a)niaid.nih.gov>; Nrupen Bhavsar, Ph.D. <nrupen.bhavsar(a)duke.edu> Subject: [EXTERNAL] Re: Computational model repository I would be happy to set up a conversation. We’ve been working with models and model repositories for many years. We recently recurated the entire biomodels repositories so it’s probably the most reproducible database of models in any scientific domain. Hunter, could you help set up a zoom meeting with Ashok and Nrupen. Herbert Sauro Herbert Sauro, Professor Director: NIH Center for model reproducibility University of Washington, Bioengineering 206-685-2119, www.sys-bio.org<http://www.sys-bio.org/>, http://reproduciblebiomodels.org/ Mobile: 206-880-8093 hsauro(a)uw.edu<mailto:hsauro@uw.edu> Books: http://books.analogmachine.org/ On Tue, Apr 21, 2026 at 6:59 AM Peng, Grace (NIH/NIBIB) [E] <penggr(a)mail.nih.gov<mailto:penggr@mail.nih.gov>> wrote: Dear Ashok and Nrupen, It was a pleasure meeting you last week. I’m using this email to introduce you to Dr. Herbert Sauro, who is the contact PI for the NIBIB P41 Center for Reproducible Biomedical Modeling, https://reproduciblebiomodels.org/<https://urldefense.com/v3/__https:/reproduciblebiomodels.org/__;!!K-Hz7m0Vt…>. Hi Herbert, Ashok and Nrupen are the leaders of the Model and Data Core for the NIAID MISM Center, https://immunescale.org/<https://urldefense.com/v3/__https:/immunescale.org/__;!!K-Hz7m0Vt54!kiq9FYu…>. In their core, they are curating models to make them reproducible. I think they would benefit from learning about your center and the tools you are developing for the MSM Community. Best wishes, Grace From: Krishnamurthy, Ashok Kumar <ashok(a)renci.org<mailto:ashok@renci.org>> Sent: Wednesday, April 15, 2026 1:34 PM To: Peng, Grace (NIH/NIBIB) [E] <penggr(a)mail.nih.gov<mailto:penggr@mail.nih.gov>> Cc: Nrupen Bhavsar, Ph.D. <nrupen.bhavsar(a)duke.edu<mailto:nrupen.bhavsar@duke.edu>> Subject: [EXTERNAL] Computational model repository Dear Grace, It was a pleasure to talk to you!!! It feels like the work being done from NIBIB is very relevant to what we are doing in the Model and Data Sharing Core of MISM. Please connect us with the researchers and any other material you can provide to help us evaluate the fit to what we are doing. Thank you for bringing up this connection! With best regards, Ashok -- Ashok Krishnamurthy Director, RENCI<https://urldefense.com/v3/__http:/www.renci.org/__;!!K-Hz7m0Vt54!kiq9FYuWCY…> Professor, SDSS<https://urldefense.com/v3/__http:/sdss.unc.edu/__;!!K-Hz7m0Vt54!kiq9FYuWCYT…> Co-Director, NC TraCS<https://urldefense.com/v3/__https:/tracs.unc.edu/__;!!K-Hz7m0Vt54!kiq9FYuWC…> Informatics and Data Science University of North Carolina, Chapel Hill<https://urldefense.com/v3/__http:/www.unc.edu/__;!!K-Hz7m0Vt54!kiq9FYuWCYTi…> CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe. CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and are confident the content is safe.

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Journal Club Recap and Monday Leadership Meeting
by Weyhmiller, Aubrie Anne 21 Apr '26

21 Apr '26

Hi all, Thanks for a great discussion at journal club today! It was lovely to see (mostly) everyone in person 😊 And thanks Ashok for lunch! I unfortunately forgot to turn on AI companion and record the meeting. Here are Andrew’s slides<https://docs.google.com/presentation/d/1ZW-ZRUzyDQpgRaKyBPAG0cj_sergOB8XnSR…> and Ashok’s slide<https://docs.google.com/presentation/d/1L26BAQdFNHpQXoN87hqQNk7KhOYgT4M2/ed…>. At the Monday leadership meeting, Isma, Nrupen, Jason, Ashok, Yaphet, myself, and Bryttany will discuss next steps and report back to the team. The Monday agenda is packed with meeting report outs from the FARR workhsop and NIAID meeting, an update from me on the MISM internship program, and a large block for disucssing today’s presentation and next steps. Thanks all, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her

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FW: MDSC Lecture for MISM Internship
by Weyhmiller, Aubrie Anne 20 Apr '26

20 Apr '26

Hi all, I had an excellent conversation with Kayla today, who is working on the MISM internship program. She explained the program is hosting 6 interns (graduate students, 5 PhD and 1 Masters) for 10 weeks from May 18 to ~July 24. Each RP will have 2 interns, and the research projects are outlined in the attached document. During the program, MISM will host various presentations/workshops (see the other attached doc). I think it would be great for MDSC to host an introduction to model and data sharing presentation during the first week (orientation). This could introduce the FAIR principles and existing resources such as the great model, data, code, and workflow guidelines<https://imageomics.github.io/Imageomics-guide/wiki-guide/FAIR-Guide/> from the Imageomics group we met at the FARR conference. There is room in the schedule for a later presentation in July. This could focus on more detailed FAIR components like ontologies, exchange formats like SBML, and Croissant for ML workflows. I’m happy to lead this effort. Ashok, we could also bring in other RENCI folks that are experts or at least consult with them. I know we have some folks who work with Croissant. Happy to talk more about this before/after journal club on Tuesday. I wanted to start a conversation here since we don’t have another meeting (aside from journal club) until April 27. If this sounds good to folks, I’d like to nail down a time slot for orientation week and start outlining a presentation before April 27. Best, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her From: Weyhmiller, Aubrie Anne <aubriew(a)renci.org> Date: Thursday, April 16, 2026 at 17:49 To: Kayla Kilpatrick, Ph.D. <kayla.kilpatrick(a)duke.edu> Subject: Re: MDSC Lecture for MISM Internship Hi Kayla, Ditto, it was a great conversation! Thanks for sharing those documents. I’ll check in with the MDSC team and get back to you. Best, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her From: Kayla Kilpatrick, Ph.D. <kayla.kilpatrick(a)duke.edu> Date: Thursday, April 16, 2026 at 13:55 To: Weyhmiller, Aubrie Anne <aubriew(a)renci.org> Subject: MDSC Lecture for MISM Internship Hi Aubrie, It was great chatting with you today! I've attached the project descriptions, along with the draft curriculum here. For the intro lecture/workshop during orientation week, here are some times that would work for scheduling if any of these work for you/the MDSC: -May 21: 10-11, 1-2 -May 22: 10-11, 11-12, 1-2 For a second talk, I think we might be able to squeeze something in July 1 or July 8 (maybe 11-12 or 1-2 those days). Let me know if there's anything else I can provide that would be helpful! Thanks! Kayla -- Kayla Kilpatrick, PhD (she/her) Biostatistician III BERD Methods Core Department of Biostatistics and Bioinformatics Duke University School of Medicine

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In-Person Journal Club this Tuesday, April 21 from 11 - 12
by Weyhmiller, Aubrie Anne 17 Apr '26

17 Apr '26

Hi MDSC folks, We have our second in-person strategic journal club this Tuesday, April 21 from 11 - 12 in the Franklin Conference room at RENCI. Andrew Su from the NIAID Data Portal team will be joining virtually to present their work on connecting the NIAID data ecosystem metadata to the open knowledge network, and how that can be wrapped in MCPs and used to access and analyze immune-system related data. This should be an interesting presentation and a great discussion on how we can collaborate. Andrew is planning to present for 20 - 25 minutes, and the remaining time will be open for discussion. I don’t think there are lunch plans, so bring your own lunch! Best, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her

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Andrew Su from NIAID Data Portal Presenting to MDSC on 4/21
by Weyhmiller, Aubrie Anne 14 Apr '26

14 Apr '26

Hi Cliburn, On Tuesday, 4/21 from 11 - 12 ET, Andrew Su from the NIAID Data Portal team will be joining our MDSC journal club meeting. He will present their work on connecting the NIAID data ecosystem metadata to the open knowledge network, and how that can be wrapped in MCPs and used to access and analyze immune-system related data. This should be an interesting presentation and a great discussion on how we can collaborate. It would be great if you are available and can attend. Best, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her

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Notes from FARR Workshop
by Weyhmiller, Aubrie Anne 14 Apr '26

14 Apr '26

Hi all, Here is a notes doc<https://docs.google.com/document/d/1Wrnl5vSJ9DPNyMxUFXg_peFZyjHJJKPQ4mrHU3p…> <https://docs.google.com/document/d/1Wrnl5vSJ9DPNyMxUFXg_peFZyjHJJKPQ4mrHU3p…> from the FARR workshop Nrupen, Isma, and I attended last week. A few discussion points for our next meetings: * Should we develop an AI-agent to assess FAIRness of models? * Strong theme of moving past FAIR for humans and move towards AI readiness * ❗MISM should require SKILL.md<http://skill.md/> file (Isma and Nrupen agree) so agent can run workflow * https://workflowhub.eu/ * Internship program: coordinate with CDEC to implement FAIR requirements * Training to get interns familiar with FAIR and expectations * Implement FAIR checklist for output products (good way to test run our standards) * 🥐Croissant is an open, community-built, standardized metadata vocabulary for ML datasets, including key attributes and properties of datasets, as well as information required to load them into ML tools. Croissant enables data interoperability across ML frameworks and beyond, making ML easier to reproduce and replicate. By building the vocabulary as an extension to schema.org, a machine-readable standard to describe structured data, Croissant also makes ML datasets discoverable beyond the scope of the repository where they have been published. https://mlcommons.org/working-groups/data/croissant/ Thanks, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her

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Re: CDEC notes and conference planning
by Weyhmiller, Aubrie Anne 06 Apr '26

06 Apr '26

Hey all, Thanks again for letting me join your meeting last week. The MDSC team discussed and we love the idea of implementing AbMAP in the platform and creating a resource and training for users. We are early in the development process, so it may be a couple months before we have something user-friendly up and running. While we build out a development plan for this, I will be sure to note any questions our team has around community needs and bring them back to the CDEC. Once we have something up and running, we can schedule a more in-depth meeting to demo what we have and talk about how to collaborate to make a useful resource for the community. Happy to hear any thoughts! Best, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her From: Gina-Maria Pomann, Ph.D. <gina-maria.pomann(a)duke.edu> Date: Tuesday, March 31, 2026 at 16:22 To: Lacey Rende <lacey.rende(a)duke.edu> Cc: Lauren Anderson, Ph.D. <lauren.g.anderson(a)duke.edu>, R. Keith Reeves, Ph.D. <keith.reeves(a)duke.edu>, Weyhmiller, Aubrie Anne <aubriew(a)renci.org>, Griffin Woolley <griffin.woolley(a)duke.edu>, Justin Pollara, Ph.D. <jpollara(a)duke.edu>, Kayla Kilpatrick, Ph.D. <kayla.kilpatrick(a)duke.edu> Subject: CDEC notes and conference planning Hi Everyone, Thanks for meeting today. I am attaching the updated conference planning document for review and thoughts that we can discuss next week. Here are the notes from the meeting with Aubrie: * Aubrie will meet Kayla to talk about internship * Aubrie will let us know when they need help developing the training . We need to develop guidance on how to use it and then also details about model details and attributes. * Aubrie will circle back with us after speaking with MDSC leads. Best, Gina-Maria Pomann Associate Professor, Duke Department of Biostatistics and Bioinformatics Director, Duke Biostatistics, Epidemiology and Research Design (BERD) Core: https://biostat.duke.edu/biostatistics-core Phone: 919-684-3135 (forwards to cell) I work flexibly during hours that are best for me. Respecting the working patterns of others, I do not expect replies outside of traditional working hours.

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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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