- Mism-external - lists.renci.org

Upcoming Journal Clubs
by Weyhmiller, Aubrie Anne 21 Aug '26

21 Aug '26

Hi all, Below is some information about our upcoming journal clubs. Looking forward to seeing you all soon! * August 25, 2026 (In-person and online, 1.5 hours) * 11 - 11:30 AM: POC2 Demo to Cliburn, Keith, and Bobby * 11:30 - 12:30 PM: MDSC Roadmap Planning * Goals, deliverables, and milestones for Y2-Y5 * September 8, 2026 (In-person and online, 1.5 hours) * Eran Agmon will join us again. * Demo what we have so far and get feedback * Discussion questions for Eran * All, please add any questions you have for Eran into this document<https://docs.google.com/document/d/1izRKkW9reSsaeo8R58FT5aPCRpdgQ6gWFKo2ewb…> by Friday, 8/28. I will share the list of questions with him then so he has time to prepare answers, which we can discuss during the meeting. Have a great weekend, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her

1 0

Lunch After Ramya Final Presentation on Thursday 8/13
by Weyhmiller, Aubrie Anne 12 Aug '26

12 Aug '26

Hi all, As you know, Ramya will be giving her final presentation in-person at RENCI (and on Zoom) on Thursday August 13 from 1 - 1:30 PM. It would be wonderful if folks could attend in-person if possible. We will be catering Chipotle for lunch after to celebration her. Please let me know if you plan to attend in-person and for lunch by end of day Tuesday, August 11. Best, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her

1 2

Meeting in September
by Weyhmiller, Aubrie Anne 11 Aug '26

11 Aug '26

Hi Eran, Hope you had a good week! Our team would love to connect with you again in September to potentially demo our platform so far and how we have implemented Vivarium, and continue collaboration discussions. We have the following journal club times in September. Do either of these work for you? If not, I’ll work to find some other times. * Tuesday September 8, 11 - 12 ET * Tuesday September 22, 11 - 12 ET Best, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her

2 2

Virtual Journal Club Tomorrow
by Weyhmiller, Aubrie Anne 10 Aug '26

10 Aug '26

Hi all, Looking forward to our virtual journal club tomorrow. Please check your calendar invite and confirm you have an invite that says Special Virtual Edition. The RENCI team will present our understanding of POC3 scope and features for review and discussion with the team. Best, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her

1 0

Invitation to MDSC Demo on August 25 11 - 11:30 AM
by Weyhmiller, Aubrie Anne 10 Aug '26

10 Aug '26

Hi Bobby, MDSC would like to invite you to an internal demo with Cliburn and Keith on August 25 11 - 11:30 AM. We will show a brief demo of upload, annotation, and execution of a vivarium chemotaxis model. Cliburn suggested you might have good feedback for us given your experience with Vivarium. Let me know if you are interested and I will send you the zoom invite! Best, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her

2 2

Journal Club Tomorrow 11 AM
by Weyhmiller, Aubrie Anne 31 Jul '26

31 Jul '26

Hi Eran, We are looking forward to chatting with you tomorrow at 11 AM ET! I see you accepted the calendar invite. Please let me know if you have any questions. Best, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her

2 2

Submit Your Questions For Eran by EOD
by Weyhmiller, Aubrie Anne 28 Jul '26

28 Jul '26

Hi all, Please put your questions for Eran in this google doc<https://docs.google.com/document/d/1vna-YLe6unyU9vHtRrfOeoyn-IlkF0LR0MnTosg…> by end of the day today. I will be sending him the questions and a thank you email tomorrow morning. Best, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her

1 0

7/28 Journal Club Preparation: Vivarium 2 Presentation from Eran Agmon
by Weyhmiller, Aubrie Anne 27 Jul '26

27 Jul '26

Hi all, Looking forward to our next journal club on Tuesday, 7/28 from 11 - 12. Eran Agmon, PI of the Vivarium lab, will join us to talk about Vivarium 2 and his vision for his October seminar and tutorial. This session will be hybrid due to the in-person/hybrid demo of POC2 from 1 - 2 PM. Folks should have an hour between meetings to grab lunch or whatever else you need! Below are relevant papers and resources to review prior to journal club to facilitate a strong discussion. Please use this document<https://docs.google.com/document/d/1vna-YLe6unyU9vHtRrfOeoyn-IlkF0LR0MnTosg…> to capture questions for Eran. Eran is also an author on papers evaluating model repositories for reproducibility, creating FAIR standards for mechanistic models, and other model standardization and reproducibility work, so our questions for him can venture into those areas as well. * Vivarium chemotaxis paper (2020)<https://www.mdpi.com/1099-4300/22/10/1101> * Vivarium 1 paper (2022)<https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinfo…> <https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinfo…> * Paper with John Hickey, RP2 investigator<https://www.cell.com/cell-systems/fulltext/S2405-4712(24)00089-9> <https://www.cell.com/cell-systems/fulltext/S2405-4712(24)00089-9> * Vivarium 2 paper (2025)<https://arxiv.org/abs/2512.23754> * Vivarium lab homepage<https://vivariumlab.com/> <https://vivariumlab.com/> (has resources, people, publications list) TLDR; Vivarium person is coming to journal club. You don’t have to read every paper linked above, but please think of a good question and record it here<https://docs.google.com/document/d/1vna-YLe6unyU9vHtRrfOeoyn-IlkF0LR0MnTosg…>. Best, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her

1 1

7/14 MISM Journal Club Summary
by Weyhmiller, Aubrie Anne 14 Jul '26

14 Jul '26

Hi all, Thanks for another great discussion today! Below is a recap of key items. Summary Items/Decisions * We will continue discussing Vivarium with Eran Agmon at our 7/28 journal club. Please be prepared with questions. I will send another email chain with relevant resources to review and a link to a document to capture questions for Eran. * We will also move this journal club instance to hybrid, see the bullet below. * We will meet 1 - 2 PM on 7/28 for an in-person demo of POC2. This will give folks an hour to grab lunch and settle in between journal club and the demo. I will send a calendar invite. * The RENCI dev team will review Vivarium 2 and estimate a level of effort and rough timeline for implementation. This was in response to the ask from Ashok on if MDSC could support Vivarium 2 by Eran’s October seminar/tutorial. Best, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her

1 0

MDSC July Journal Club Topics
by Weyhmiller, Aubrie Anne 13 Jul '26

13 Jul '26

Hi all, I’m happy to announce the topics for our July journal clubs. This month we will focus on Vivarium. Tuesday, July 14, 11 - 12 PM (In-person/hybrid): We will focus on the Viviarium chemotaxis paper we are using for POC-2 work (linked here<https://drive.google.com/file/d/1Yx6AuiD3cjWvbeB9af1R14iQgC5gd3_O/view?usp=…>, and attached). Please read the paper and be prepared to discuss their Multi-Scale Design Principles and how they break multiscale processes into components. Tuesday, July 28, 11 - 12 PM (virtual): Eran Agnon will join us to talk about Viviarium 2 and to have a discussion on his vision for the October MISM Vivarium tutorial. Best, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her

1 1