2024-07-22-24. VCell and COPASI teams run 25th Annual Workshop on Computational Cell Biology. Nine students (one could not attend due to flights being cancelled) from Arkansas, Connecticut, New York, Ohio, Texas and Viginia worked with instructors for 3 days, developing their computational models. Thanks to NIH for the funding!
2024-06-10. The team of researchers from Michigan State University used reaction-diffusion modeling with VCell to provide insights into biophysical carbon concentrating mechanisms in land plants.
Kaste, J. A., Walker, B. J., & Shachar-Hill, Y. (2024). Reaction-diffusion modeling provides insights into biophysical carbon concentrating mechanisms in land plants. Plant Physiology, kiae324.
https://pubmed.ncbi.nlm.nih.gov/38857179/
2024-05-14. The team of researchers from Australia and Johns Hopkins University used VCell to design and simulate a model explaining the formation of endocytic nanoclusters driven by distinct recruitment of Dynamin1 long- and short-tail isoforms.
Jiang, A., Kudo, K., Gormal, R.S., Ellis, S., Guo, S., Wallis, T.P., Longfield, S.F., Robinson, P.J., Johnson, M.E., Joensuu, M. and Meunier, F.A., 2024. Dynamin1 long-and short-tail isoforms exploit distinct recruitment and spatial patterns to form endocytic nanoclusters. Nature Communications, 15(1), p.4060.
https://pubmed.ncbi.nlm.nih.gov/38017688/ […]
2024-04-10. Michael Blinov and Ion Moraru presented VCell tutorial at HARMONY 2024 at University College London. Other topics discussed include interoperability of multiple standards like SBML, SED-ML and COMBINE archive supported by VCell.
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.
2024-02-12. Ingo Dreyer (U Talca, Chile) and Kai Konrad (U Wuerzburg, Germany) used VCell to design and simulate a model explaining the properties of transporter networks and the coupling of transport across the PM and VM. They demonstrated fundamental principles of coupled ion transport at membrane sandwiches to control H+ /K+ homeostasis and points to transceptor-like Ca2+ /H+ -based ion signaling in plant cells.
Kunkun Li, Christina Grauschopf, Rainer Hedrich, Ingo Dreyer, Kai R Konrad (2024). […]
Michael Blinov and Margaret Johnson from John Hopkins University were hosting the Special Interest Subgroup session on Biophysical Modeling of the Cell at Cell Bio 2023 – an ASCB/EMBO (https://www.ascb.org/cellbio2023/) meeting in Boston, MA, December 2-6. The speakers include Elizabeth Read (UCI), Margaret Johnson (JHU), Jason Haugh (NCSU), Graham Johnson (Allen Institute), and Ben O’Shaughnessy (Columbia U).
VCell was highlighted at the 22nd International Conference on Systems Biology (ICSB) that took place in Hartford October 8-12, 2023. The meeting was organized by CCAM faculty and co-chaired by Pedro Mendes and Ion Moraru. VCell team presented two tutorials (basic modeling by Ann Cowan and advanced features by Michael Blinov) and a poster.
2023-09-22. VCell collaborator Aurélie Carlier from Maastricht University published a manuscript where a computational model in VCell was used to represent the experimentally proven interactions between cadherin-11 and the two PDGFRs. The authors demonstrated the existence of a crosstalk between β-catenin (downstream to cadherin-11) and an ERK inhibitor protein (e.g. DUSP1).
Karagöz, Z., Passanha, F. R., Robeerst, L., van Griensven, M., LaPointe, V. L., & Carlier, A. (2023). Computational evidence for multi-layer crosstalk between the cadherin-11 and […]
2023-08-28. VCell collaborator Jason Haugh from North Carolina State University published a manuscript where experiments and VCell modeling demonstrated that G-actin diffusion is insufficient to achieve F-actin assembly in fast-treadmilling protrusions.
Appalabhotla, R., Butler, M.T., Bear, J.E. and Haugh, J.M. G-actin diffusion is insufficient to achieve F-actin assembly in fast-treadmilling protrusions. Biophys J. 2023 Aug 28;S0006-3495(23)00553-2. doi: 10.1016/j.bpj.2023.08.022. https://pubmed.ncbi.nlm.nih.gov/37644720/
See 5 biomodels and 14 mathmodels at https://vcell.org/appalabhotla-2023
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