17 April 2024. Dr. Agmon and his collaborators from Stanford published a Cell Systems paper “Integrating multiplexed imaging and multiscale modeling identifies tumor phenotype conversion as a critical component of therapeutic T cell efficacy” utilizing the software Vivarium to simulate tumor/T cell interactions https://www.sciencedirect.com/science/article/pii/S2405471224000899   Congratulations to Eran Agmon as the co-first author of a paper in the very prestigious Cell Systems journal!

 

CCAM welcomes the new Assistant Professor Dr. Sarvenaz Sarabipour! Dr. Sarabipour received her PhD in Engineering from Johns Hopkins University and performed her postdoctoral work at Johns Hopkins Institute for Computational Medicine and Department of Biomedical Engineering. Sarvenaz’s research in computational systems biology focuses on developing experimental and computational methods to study mechanisms of signal transduction in cells and tissue. The Sarabipour lab is accepting students!

VCell and COPASI were presented at HARMONY 2024 (https://co.mbine.org/author/harmony-2024/) at University College London. Michael Blinov gave a tutorial on VCell, while Frank Bergman (one of COPASI developers) talked about the web version of COPASI running through JavaScript.  Other topics discussed include interoperability of multiple standards like SBML, SED-ML and COMBINE archive supported by both VCell and COPASI.

VCell, COPASI and SpringSalad were taught and used for projects at the  25th Annual Computational Cell Biology (CCB) workshop that took place online February 26-28th.  The invited talks were given by Yulia Timofeeva (University of Warwick), James P Sluka (Indiana University) and Kevin Janes (University of Virginia). Sixteen participants were selected to work with VCell and COPASI instructors on their projects, and eight gave presentations on their projects at the Modeling Symposium.

Congratulations to Dr. Agmon and his collaborators from Stanford for publishing an article in Cell Reports on T cell-mediated curation and restructuring of tumor tissue coordinates an effective immune response. https://www.sciencedirect.com/science/article/pii/S2211124723015061