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Welcome Sri Navulri to the MDSC Team!
by Weyhmiller, Aubrie Anne 09 Jul '26

09 Jul '26

Dear MDSC team, We are pleased to introduce Sri Navuluri is joining our team. Sri is a program manager in Nrupen’s lab and will be spending some time on this project working with me to move forward specific initiatives. To start, he will join our journal clubs and biweekly leadership meetings to get up to speed. Please join me in welcoming Sri! Best, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her

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Virtual Journal Club Tomorrow
by Weyhmiller, Aubrie Anne 30 Jun '26

30 Jun '26

Hi all, Looking forward to seeing everyone at our virtual journal club tomorrow! During the CAIRNS demo two weeks ago, there was a discuss about capturing/distributing/leveraging AI sourced team knowledge. Michael Stealy from RENCI has been working on TeamBrain, a tool that essentially does what we are interested in. Michael will be joining us and giving a brief overview of TeamBrain, a demo, and then we will have an open discussion about how this could potentially fit into CAIRNS/our platform. See you tomorrow, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her

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Upcoming Journal Clubs
by Weyhmiller, Aubrie Anne 22 Jun '26

22 Jun '26

Hi all, I updated the calendar invites for our journal club series. For clarity, below are our upcoming journal club dates. * Tuesday June 30 - virtual * Tuesday July 14 - hybrid * Tuesday July 28 - virtual Please let me know if you have any questions. Best, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her

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Journal Club Tomorrow
by Weyhmiller, Aubrie Anne 15 Jun '26

15 Jun '26

Hi all, A reminder that our hybrid journal club is tomorrow from 11 - 12 PM. Jason and Huimin will be giving a demo of CAIRNS. You can join via zoom, or in-person at the Europa Center in the Franklin conference room. We have Chipotle build you own bowls again for lunch. I had something come up and will not be able to attend tomorrow. Sarah Tyndall will help get the Zoom and lunch set up (thank you @Tyndall, Sarah<mailto:sarahtyndall@renci.org>!!!). Please record the zoom meeting. I will schedule an automatic slack reminder to start the recording at 11:05. Best, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her

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MDSC Leadership Meeting Starting 30 Minutes Late Today
by Weyhmiller, Aubrie Anne 08 Jun '26

08 Jun '26

Hi all, Due to a conflict, we will move our meeting to start at 4:30 today. I think it should only take us 15 minutes to get through the agenda items. Nrupen, I can stay until 5 if you and Ashok can so we can discuss the manuscript. If not let me know and I will find another time for us to meet. Best, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her

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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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[For Review] MISM Internship Program Asking for Data Quality Presenter
by Weyhmiller, Aubrie Anne 28 Apr '26

28 Apr '26

Hi all, I let Kayla know MDSC will be presenting to the MISM interns for 1 hour on May 21 on FAIR model and data sharing. Please see her additional question for MDSC: "Do you think anyone in the MDSC would be able to present on data types and quality in this area of research? Or at least know of someone I can reach out to? The person I had been thinking of is unfortunately unable to give this talk. My thought here was to talk about common data types the interns might encounter, as well as common issues/things to look out for. I'll ask around as well but figured the MDSC might be a good place to try!” Does anyone feel this is a topic they can present on this topic, or know someone that could? Please let me know by end of day Friday if this is something you could present on, or if you know someone who could. Best, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her

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