VCell News & Events 2022-11-16T21:20:40+00:00

Events

News

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).

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.

VCell Used to Validate new cAMP Model

October 4th, 2021|

2021-10-04. VCell was used to validate a new model for cAMP metabolism used to explore cAMP signaling in pulmonary microvascular endothelial cells. Find links to the paper and on our published models page.

VCell Model of ion transport in Kidney

September 22nd, 2021|

2021-09-22. A new VCell model from the Carlier lab is combined with experiments to explore regulation of ion transport in the kidney proximal tubule. Find links to the paper and public VCell models on our published models page.

New model of FAK influence on YAP-TAZ

September 10th, 2021|

2021-09-10. VCell MathModels were used to explore how FAK activation influences YAP/TAZ translocation in a new publication by Eroume et al. in Biophysical Journal. Find links to the paper and public VCell models on our published models page.

New model of actin filament nucleation

September 9th, 2021|

2021-09-9. VCell models and COPASI parameter estimation tools were used to test molecular mechanisms for actin filament nucleation in a paper from the Loew and Pollard labs. Find links to the paper and public VCell models on our published models page.

New model of Sperm Calcium

July 28th, 2021|

2021-7-27. A new VCell model by Korobkin et al, explores calcium oscillations in mammalian sperm. COPASI software was also utilized for parameter estimation to fit the models.   Find links to the paper and public VCell models on our published models page.

2021 Computational Cell Biology Workshop held June 21-23.

June 24th, 2021|

2021-6-24  CCAM’s annual Computational Cell Biology Workshop was again held online June 21-23, 2021.  The workshop provided instruction to over 50 individuals from around the world on mathematical modeling techniques using VCell, COPASI and SpringSaLaD software. Fifteen of the participants worked closely with CCAM researchers to develop their own models related to their research projects. Another successful year for the modeling workshop! a combined workshop for VCell, COPASI, and SpringSaLaD modeling software. Thanks to all for a very successful course!  Videos of the classes and presentations can be found on the CompCellBiol YouTube channel.

VCell model of YAP/TAZ

May 8th, 2021|

2021-5-08. A new VCell model from the Rangamani lab explores how YAP/TAZ signaling integrates inputs from different biophysical properties of the cell. Find links to the paper and public VCell models on our published models page.

VCell model of Axon Initial Segment

April 5th, 2021|

2021-4-05. A VCell model was used to assess the role of casein kinase 2 and ankyrin-G on sodium channel recruitment to the axon initial segment. Find links the citation on our published models page.

VCell model of Mitochondrial ATP production

April 1st, 2021|

2021-4-1. A new VCell model by Afzal et al, from the Lederer and Jafri labs explores how cristae geometry affects energy production in mitochondria Find links to the paper and public VCell models on our published models page.

VCell model of Mad signaling

March 30th, 2021|

2021-3-30. A new paper from the Inaba lab uses a VCell model to explore how pMad is asymmetrically partitioned to forming daughter nuclei during division of stem cells in the Drosophila ovary.  Find links to the model and citation on our published models page.

VCell 7.4 released

March 23rd, 2021|

2021-03-23.VCell 7.4 has been released.  New in VCell 7.4 is the ability to preview geometries from the VCell database, vastly accelerated multiple trajectory stochastic simulations using the Gibson-Bruck solver, extension of unit display and automatic conversion to rate and assignment rules, support for external access to containerized versions of some VCell solvers with command line execution, as well as numerous additional improvements and bug fixes.