VCell News & Events 2023-09-12T18:32:55+00:00

Events

News

VCell at ICSB 2023

October 12th, 2023|

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.

A model of the cadherin-11 and PDGFR pathways crosstalk

September 22nd, 2023|

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 PDGFR pathways. Scientific Reports13(1), 15804. https://pubmed.ncbi.nlm.nih.gov/37737289/
VCell biomodels is available at https://vcell.org/karagoz-2023

19 new VCell models on G-actin diffusion are published by Haugh group

August 28th, 2023|

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

Biophysical Modeling of the Cell special interests group at ASCB

July 17th, 2023|

Prof Margaret Johnson from John Hopkins University and Michael Blinov are 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 session will take place on Wednesday, December 6, 8:30 AM – 11:00 AM (https://www.ascb.org/cellbio2023/program/subgroups/).

24th Annual Computational Cell Biology (CCB) workshop

June 28th, 2023|

2023-06-28. The  24th Annual Computational Cell Biology (CCB) workshop took place at the Center for Cell Analysis and Modeling (CCAM) on June 26-28th. 11 participants from all over the US (from Maryland to Illinois) came to Farmington to work on developing their modeling projects using VCell and COPASI software tools, designed and maintained at CCAM. The students were helped by a CCAM team consisting of Michael Blinov, Ann Cowan, Leslie Loew, Pedro Mendes, Ion Moraru, Kelvin Peterson, Jim Schaff, Nathan Schaumburger, and Boris Slepchenko.

VCell is used in a research on aging

May 4th, 2023|

2023-05-04. The interdisciplinary team consisting of CCAM modelers Drs. Blinov and Moraru and researchers from the Center on Aging Drs. Kuchel and Kositsawat, together with former undergrad students Schaumburger and Pally published a manuscript theoretically explaining the bistability of clinical outcomes: the likelihood of an individual remaining mobile over time either increases to almost 100% or decreases to almost zero. The VCell software was extensively used for parameter scans and fitting.

Schaumburger, N., Pally, J., Moraru, I. I., Kositsawat, J., Kuchel, G. A., & Blinov, M. L. (2023). Dynamic model assuming mutually inhibitory biomarkers of frailty suggests bistability with contrasting mobility phenotypes. Frontiers in Network Physiology, 3, 1079070.

https://www.frontiersin.org/articles/10.3389/fnetp.2023.1079070/full

VCell 7.5 Release

May 1st, 2023|

2023-05-01. VCell 7.5 has been released. It features parameter estimation from the latest version of COPASI; model exchange via multiple standards, including, SBML, SEDML and OMEX; parameter scans in local client simulations; and hardening of unit handling including automatic unit transformations. Full specs available https://vcell.org/run-vcell-software.

VCell model of wild-type Bacillus subtilis spores

March 1st, 2023|

2023-03-01.VCell was used to demonstrate that expression of the 2Duf protein in wild-type Bacillus subtilis spores stabilizes inner membrane proteins and increases spore resistance to wet heat and hydrogen peroxide. Find links to the paper on our published models page.

VCell poster at BPS 2023 in San Diego

February 20th, 2023|

2023-02-20. The VCell team presented a poster at the Biophysical Society Annual Meeting in San Diego (https://www.biophysics.org/2023meeting#/).

2023 Computational Cell Biology workshop

February 13th, 2023|

2023-02-13. The 24th Annual Computational Cell Biology workshop was sponsored by Cell Analysis and Modeling Center at the UConn Health on February 13-15th. It was an intense online event designed to enable cell biologists and biphysicists to develop mathematical models of their experimental systems.Keynote speakers included Jason Haugh, Pablo Iglesias and Ursula Kummer.

SpringSaLaD used for Coarse-Grained Molecular Modeling

November 16th, 2022|

SpringSaLaD software was used to model contractility kits, complexes in the cytoplasm of Dictyostelium cells consisting of myosin II and cortexillin I in the publication, Particle-based model of mechanosensory contractility kit assembly.

VCell and COPASI are used to study antibiotic biosynthesis

October 3rd, 2022|

2022-09-28.VCell and COPASI were used together to study the kinetic behavior of antibiotic biosynthesis. The paper describes the same model designed in both COPASI (for parameter estimations) and VCell (for simulation reaction curves). Find links to the paper on our published models page.

VCell tutorial at ICSB 2022 in Berlin

September 13th, 2022|

2022-09-12. The VCell team will give a tutorial at the 21st International Conference on Systems Biology – the premier meeting on systems studies in biology, human evolution disease and planetary health. The meeting will take place in Berlin, Germany on October 8th-12th. The tutorial will be on October 9th at 12:30pm local time (https://www.icsb2022.berlin/satellite-events).

VCell is used for computational investigation of the dynamic control of cAMP signaling by PDE4 isoform types

July 18th, 2022|

2022-06-18. VCell collaborator Aurélie Carlier from Maastricht University published a manuscript on computational investigation of the dynamic control of cAMP signaling by PDE4 isoform types. The authors demonstrated that cAMP signaling is distinctly regulated by different PDE4 isoform types andthat this isoform-specificity should be considered in both computational and experimental follow-up studies to better define PDE4 enzymes as therapeutic targets in diseases in which cAMP signaling is aberrant.
Paes, D., Hermans, S., van den Hove, D., Vanmierlo, T., Prickaerts, J., Carlier, A. (2022). Biophys J., 121(14):2693-2711. doi: 10.1016/j.bpj.2022.06.019. Epub 2022 Jun 18.
https://pubmed.ncbi.nlm.nih.gov/35717559/
VCell biomodels are available at https://vcell.org/paes-2022

The 23rd Annual Workshop on Computational Cell Biology

June 24th, 2022|

2022-05-25. The 23rd Computational Cell Biology workshop took place at R. D. Berlin Center for Cell Analysis and Modeling (CCAM) on May 23-25th. For 3 days more than 40 online participants learnt how to use VCell, COPASI and SpringSalad software tools for modeling of cell biology systems. 16 participants participated in the “project track”, working individually with CCAM staff on developing their modeling projects.

New VCell Model of nutrients transporter network in plants

June 24th, 2022|

2022-04-14. A new compartmental VCell Model was used to explore nutrients transporter network in plants. Find links to the paper and BioModel on our published models page.

VCell is used in Nature biosynthesis paper

June 24th, 2022|

2022-02-10. VCell was used to analyze structure of a B12-dependent radical SAM enzyme in carbapenem biosynthesis in a new Nature paper (available on our published models page).

Teaching with VCell MathModels

December 8th, 2021|

2021-12-8. A discussion of how to use a VCell MathModel to teach mathematical modeling in cellular systems has been published by the Carlier lab with contributions from Cowan and Loew. Find links to the paper and public VCell models on our published models page.

New VCell Model of Nucleocytoplasmic Actin Dynamics

November 24th, 2021|

2021-11-24. A new VCell Model of actin dynamics was used to explore how phsophorylation of cofilin is involved in transmission of signals to the transcriptional machinery by depleting of nuclear G-actin. Find links to the paper on our published models page.

VCell Model of LINE-1 RNA lifecycle

October 5th, 2021|

2021-10-05. A new publication by Martin et al. describes a VCell model of the lifecyle of LINE-1 RNA elements in order to understand their activation and propagation. Find links to the paper and public VCell models on our published models page.