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

Tuesday 6/2 Virtual Journal Club
by Weyhmiller, Aubrie Anne 02 Jun '26

02 Jun '26

Hi all, I am looking forward to seeing you all at our next virtual journal club on Tuesday, June 2. We’ll take a few minutes at the beginning to catch up and report out on the MISM annual retreat. Then, we will discuss implementing Vivarium in the MDSC Platform. There are two relevant papers folks should review prior to our meeting: * The Viviarium paper (2022): Vivarium: an interface and engine for integrative<https://drive.google.com/file/d/1w-aiTsTr1VO7LdideV7u6CvFDgszM3qT/view?usp=…> multiscale modeling in computational biology<https://drive.google.com/file/d/1w-aiTsTr1VO7LdideV7u6CvFDgszM3qT/view?usp=…> * A multiscale model utilizing Vivarium (2020): A Multi-Scale Approach to Modeling E. coli Chemotaxis<https://drive.google.com/file/d/1Yx6AuiD3cjWvbeB9af1R14iQgC5gd3_O/view?usp=…> Best, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her

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Vivarium papers for us to replicate
by Krishnamurthy, Ashok Kumar 27 May '26

27 May '26

Discuss at next journal club and consider implementing in our vivarium instance. Ashok

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Re: connecting for summer vivarium workshop
by Krishnamurthy, Ashok Kumar 27 May '26

27 May '26

From: Kevin Flores <kbflores(a)ncsu.edu> Date: Wednesday, May 27, 2026 at 9:45 AM To: Krishnamurthy, Ashok Kumar <ashok(a)renci.org> Cc: John Hickey <john.hickey(a)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

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[For Review by May 18] MISM Internship Presentation on FAIR Modeling
by Weyhmiller, Aubrie Anne 13 May '26

13 May '26

Hi all, I have developed draft slides<https://docs.google.com/presentation/d/1sMiCo43wyM5D94PUEWB_7vqPsJfwNCcF/ed…> for the May 21 presentation to the MISM intern cohort. I will be presenting a basic introduction to the FAIR principles, how FAIR is relevant to MISM and their work, and how they can take small steps to make their work this summer FAIR. The presentation is scheduled for 1 hour, I plan to have 30 - 40 minutes of content to leave room for discussion and transition time. I ask that @Nrupen Bhavsar, Ph.D.<mailto:nrupen.bhavsar@duke.edu> and @Krishnamurthy, Ashok Kumar<mailto:ashok@renci.org> specifically review, and I would greatly appreciate review from all others if possible. Notes about providing feedback: * Please provide feedback by Monday, May 18. * I will be OOO today - May 19 but may have time to look at and incorporate feedback starting May 18. I should have feedback by the time I return so I can turn the slides around as quickly as possible (presentation is May 21). * Please provide actionable feedback. I will not have time to make large changes. The clearer and more actionable your feedback is, the better. * Please feel free to go into the slides and make small edits. * I am particularly looking for help finding an example model to review as a final activity. If someone could find an example multi scale model and outline an activity with it, that would be incredibly helpful. Best, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her

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