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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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[Action Required] Meeting Times with Justin Lessler for MISM Webinar March 12
by Weyhmiller, Aubrie Anne 25 Feb '26

25 Feb '26

Hi MDSC team, Justin Lessler will be presenting at Duke on Thursday, March 12. Justin Lessler is a professor in the Department of Epidemiology researching the dynamics and control of infectious disease, with particular interest in SARS-CoV-2, influenza, cholera and dengue. Justin works on the development and application of statistics, dynamic models and novel study designs to better understand and control infectious disease. In particular, he is interested in creating synergies between infection control practice, data collection and infectious disease dynamics. You can read more about the presentation here.<https://immunescale.org/event/probing-immune-landscapes-across-scales-insig…> He is not a part of the RPs, but an external, relevant researcher. It would be great for folks from our team to at least attend the webinar. I think myself and/or Isma, Ashok, and Nrupen should meet with Justin. If you would like to meet with Justin in-person or virtually, please fill out this poll<https://doodle.com/group-poll/participate/ejgLYM4a> by Tuesday, March 3 so we can pick a time slot. I am asking @Krishnamurthy, Ashok Kumar<mailto:ashok@renci.org>, @Nrupen Bhavsar, Ph.D.<mailto:nrupen.bhavsar@duke.edu>, and @Gilani, Isma<mailto:igilani@renci.org> specifically to please fill out the poll. Kindly, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her

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FW: 1:1 Meetings with Dr. Justin Lessler (Thursday March 12, 2026)
by Weyhmiller, Aubrie Anne 20 Feb '26

20 Feb '26

Hi all, Flagging this for awareness! I know Nrupen has a connection to Justin. We should discuss in our next meeting if we want to meet with him. Best, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her From: Multiscale Immune System Modeling <MISM(a)duke.edu> Date: Thursday, February 19, 2026 at 11:39 To: Krishnamurthy, Ashok Kumar <ashok(a)renci.org>, Weyhmiller, Aubrie Anne <aubriew(a)renci.org>, Bobby Ni <bobby.ni(a)duke.edu>, Borsellino, Michael <borsellino(a)renci.org>, Bruce Rogers <bruce.rogers2(a)duke.edu>, Charles Nunn <clnunn(a)duke.edu>, cliburn.chan(a)duke.edu <cliburn.chan(a)duke.edu>, Dana Pasquale, Ph.D. <dana.pasquale(a)duke.edu>, Danielle Burner <danielle.burner(a)duke.edu>, sorelle <sorelle(a)umich.edu>, Georgia Tomaras, Ph.D. <gdt(a)duke.edu>, Gina-Maria Pomann, Ph.D. <gina-maria.pomann(a)duke.edu>, Peterson, Gabi <gpeterson(a)renci.org>, Grace McLaughlin <grace.mclaughlin(a)duke.edu>, Griffin Woolley <griffin.woolley(a)duke.edu>, Roupe, Griffin Riley <groupe(a)renci.org>, Huan Liang <huan.liang(a)duke.edu>, Gilani, Isma <igilani(a)renci.org>, Jake Burchard, Ph.D. <jake.burchard(a)duke.edu>, James Moody <james.moody(a)duke.edu>, Janice McCarthy, Ph.D. <janice.mccarthy(a)duke.edu>, Jason Ji, Ph.D. <zhicheng.ji(a)duke.edu>, Jason Xu <jqxu(a)g.ucla.edu>, Waller, Jeff <jeffw(a)renci.org>, Conway, Jessica Maral <jmc90(a)psu.edu>, Jianfeng Lu <jianfeng.lu(a)duke.edu>, Jiazheng Miao <jiazheng.miao(a)duke.edu>, Jichun.xie(a)duke.edu <Jichun.xie(a)duke.edu>, John Hickey <john.hickey(a)duke.edu>, Jonathan Li, Ph.D. <kan.li(a)duke.edu>, Jonathan Lin <jonathan.lin(a)duke.edu>, Judy Adkins <judy.adkins(a)duke.edu>, Judy Hall <judy.hall(a)duke.edu>, Justin Pollara, Ph.D. <jpollara(a)duke.edu>, kapil.devkota(a)duke.edu <kapil.devkota(a)duke.edu>, Kayla Kilpatrick, Ph.D. <kayla.kilpatrick(a)duke.edu>, Kevin Bryant Flores <kbflores(a)ncsu.edu>, Kristine Glauber <kristine.glauber(a)duke.edu>, Lacey Rende <lacey.rende(a)duke.edu>, Linh Do, Ph.D. <thuylinh.do(a)duke.edu>, Meghan Kwon <meghan.kwon(a)duke.edu>, Melanie Sadecki <msadeck(a)ncsu.edu>, Micah Luftig, Ph.D. <micah.luftig(a)duke.edu>, Mieke van der Mescht, Ph.D. <mieke.vandermescht(a)duke.edu>, Moses Sekaran, Ph.D. <moses.sekaran(a)duke.edu>, Nami Wada <nami.wada(a)duke.edu>, Nrupen Bhavsar, Ph.D. <nrupen.bhavsar(a)duke.edu>, R. Keith Reeves, Ph.D. <keith.reeves(a)duke.edu>, Rebecca North, Ph.D. <rebecca.thiem(a)duke.edu>, Richard Barfield <richard.barfield(a)duke.edu>, rohit.singh(a)duke.edu <rohit.singh(a)duke.edu>, Rory Henderson <rory.henderson(a)duke.edu>, Tyndall, Sarah <sarahtyndall(a)renci.org>, Shannon Clarke <shannon.clarke(a)duke.edu>, Shweta Dambal, Ph.D. <shweta.dambal(a)duke.edu>, Suchismita Roy <suchismita.roy(a)duke.edu>, Boeth, Ezra <eboeth(a)renci.org>, Umar Qureshi, Ph.D. <muhammad.qureshi(a)duke.edu>, Veronica Ciocanel, Ph.D. <veronica.ciocanel(a)duke.edu>, Zach Turner <zach.turner(a)duke.edu> Cc: MISM-Ops service <mism-ops(a)duke.edu> Subject: 1:1 Meetings with Dr. Justin Lessler (Thursday March 12, 2026) Some people who received this message don't often get email from mism(a)duke.edu. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification> Hello MISM Team Members, The seminar with Dr. Justin Lessler<https://sph.unc.edu/adv_profile/justin-lessler-phd/> is scheduled for Thursday March 12, 2026. He will be taking 1:1 meetings during his visit at Hock Plaza (9th floor, Room #9047). As MISM members, we are extending the opportunity for you to select a time to meet<https://prodduke.sharepoint.com/:w:/r/sites/U54CoE/Shared%20Documents/U54%2…> with him during his visit. If the time you want is already taken, please let us know and we will see if there is a way for to get you into the schedule. For ESIs (postdocs and graduate students) please considering signing up for the lunch discussion. Thank you, MISM Admin and CDEC Teams -- MISM(a)duke.edu<mailto:MISM@duke.edu> [cid:image001.png@01DCA192.3AFDA1F0]

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