Hi all, This is a reminder for our journal club tomorrow from 11 - 12 and to come with at least one question for Eran. Please see my email from 7/20 for more information. As a note, we will have a hybrid demo of POC2 from 1 - 2 PM. Folks will have an hour between journal club and the POC-2 demo to grab lunch or whatever else you may need. Best, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her From: Weyhmiller, Aubrie Anne via Mism-external <mism-external@lists.renci.org> Date: Monday, July 20, 2026 at 11:00 To: Weyhmiller, Aubrie Anne via Mism-external <mism-external@lists.renci.org> Subject: [Mism-external] 7/28 Journal Club Preparation: Vivarium 2 Presentation from Eran Agmon 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-IlkF0LR0MnTosg0qao/edit?tab=t.0> 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/bioinformatics/btac049/6522109?login=true> <https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btac049/6522109?login=true> * 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-IlkF0LR0MnTosg0qao/edit?tab=t.0>. Best, Aubrie Aubrie Weyhmiller Research Scientist Renaissance Computing Institute (RENCI) Pronouns: she/her