VCell Open Discussion Forum

Contact owners and managers

1–30 of 292

Welcome to the open discussion forum for users and developers of the Virtual Cell, a unique computational environment for modeling and simulation of cell biology. The VCell has been specifically designed to be a tool for a wide range of scientists, from experimental cell biologists to theoretical biophysicists. The creation of biological or mathematical models can range from the simple, to evaluate hypotheses or to interpret experimental data, to complex multi-layered models used to probe the predicted behavior of complex, highly non-linear systems. Such models can be based on both experimental data and purely theoretical assumptions. Feel free to contribute your ideas, questions and suggestions.

0 selected

Abdulrahman Almutairi, les...@gmail.com4

Mar 24

Using Logical Operators (AND OR)

Hi Les, Thank you! I was not using that syntax. It works now. Best, Abdul On Tuesday, March 12, 2024

unread,

Using Logical Operators (AND OR)

Hi Les, Thank you! I was not using that syntax. It works now. Best, Abdul On Tuesday, March 12, 2024

Mar 24

Mar 13

25th CCB workshop - YouTube and in-person!

*** Attention: This is an external email. Use caution responding, opening attachments or clicking on

unread,

25th CCB workshop - YouTube and in-person!

*** Attention: This is an external email. Use caution responding, opening attachments or clicking on

Mar 13

Adam Hoppe, … Jim Schaff4

Mar 7

Thank you for the excellent workshop!

Thanks Jim for the speedy response. I will aim to work on the model later this week/weekend. I too am

unread,

Thank you for the excellent workshop!

Thanks Jim for the speedy response. I will aim to work on the model later this week/weekend. I too am

Mar 7

Carole Dowds, Les Loew3

Feb 20

Missing Catalytic dashed-line option

Thank you Les, I got it to work, much appreciated. C. On Monday, February 19, 2024 at 2:10:04 PM UTC

unread,

Missing Catalytic dashed-line option

Thank you Les, I got it to work, much appreciated. C. On Monday, February 19, 2024 at 2:10:04 PM UTC

Feb 20

Carole Dowds, Blinov,Michael3

Feb 13

Parameter Estimation Tutorial

Dear Michael, Apologies its in a COPSIA tutorial link sent out in the CCB Online 2024, I will email

unread,

Parameter Estimation Tutorial

Dear Michael, Apologies its in a COPSIA tutorial link sent out in the CCB Online 2024, I will email

Feb 13

Jan 8

DEADLINE APPROACHING: Computational Cell Biology Workshop

ONLY 5 DAYS TILL THE APPLICATION DEADLINE. Details on how to apply are below. Apply to blinov@uchc.

unread,

DEADLINE APPROACHING: Computational Cell Biology Workshop

ONLY 5 DAYS TILL THE APPLICATION DEADLINE. Details on how to apply are below. Apply to blinov@uchc.

Jan 8

12/5/23

Computational Cell Biology Workshop Online Feb. 26-28, 2024 - PLEASE SPREAD THE WORD

The workshop is free. However, to be admitted please email the following information to l...@uchc.edu

unread,

Computational Cell Biology Workshop Online Feb. 26-28, 2024 - PLEASE SPREAD THE WORD

The workshop is free. However, to be admitted please email the following information to l...@uchc.edu

12/5/23

11/28/23

Group Moderation policy change.

Dear Virtual Cell community, We changed the Google Group moderation rules to prevent spam. New

unread,

Group Moderation policy change.

Dear Virtual Cell community, We changed the Google Group moderation rules to prevent spam. New

11/28/23

11/15/23

you've submitted 5323 jobs, only 40 run at a time

Hi Joshua, Just an FYI, it is likely that you do not realize that you have over 5000 vcell simulation

unread,

you've submitted 5323 jobs, only 40 run at a time

Hi Joshua, Just an FYI, it is likely that you do not realize that you have over 5000 vcell simulation

11/15/23

Ethan John, Blinov,Michael2

11/7/23

VCell Node Rate Constants

Hello, There are several methods to find appropriate rate constants, but there are no best approaches

unread,

VCell Node Rate Constants

Hello, There are several methods to find appropriate rate constants, but there are no best approaches

11/7/23

Aravind Chandrasekaran, … James Schaff5

11/6/23

Hi Avarind, Sorry for the inconvenience, VCell is back up after restarting one of our services. We

unread,

Hi Avarind, Sorry for the inconvenience, VCell is back up after restarting one of our services. We

11/6/23

Kun, Blinov,Michael3

10/18/23

What determines the time step of rule based simulation

Got it! Thanks for the explanations! Best, Xikun 在2023年10月18日星期三 UTC+11 01:33:14<Blinov,Michael

unread,

What determines the time step of rule based simulation

Got it! Thanks for the explanations! Best, Xikun 在2023年10月18日星期三 UTC+11 01:33:14<Blinov,Michael

10/18/23

Kun, Blinov,Michael2

10/17/23

How to specify the reaction rates in batch simulations with rule based model

Hello, In my previous email I explained the meaning of DirectHalf and InverseHalf. Batch file

unread,

How to specify the reaction rates in batch simulations with rule based model

Hello, In my previous email I explained the meaning of DirectHalf and InverseHalf. Batch file

10/17/23

Kun, … Blinov,Michael14

10/17/23

How to run similations in batch

Hello, Sorry for a delayed answer - everyone in the team was at COMBINE and ICSB meetings. Rates in

unread,

How to run similations in batch

Hello, Sorry for a delayed answer - everyone in the team was at COMBINE and ICSB meetings. Rates in

10/17/23

Aravind Chandrasekaran, Jim F2

10/10/23

VCell GUI issues.

I'm not sure if this applies to you but I can tell you if you see the Ajax spinner I would then

unread,

VCell GUI issues.

I'm not sure if this applies to you but I can tell you if you see the Ajax spinner I would then

10/10/23

Chi Wut WONG, … Les Loew3

9/22/23

Stoichiometry in the mass action kinetic type

Yes, select the reaction connector with the arrow and enter the stoichiometry below. The software

unread,

Stoichiometry in the mass action kinetic type

Yes, select the reaction connector with the arrow and enter the stoichiometry below. The software

9/22/23

Chi Wut WONG, … Blinov,Michael7

9/21/23

Does VCell capable to simulation cell division and cell population?

Thanks, Michael! On Thursday, September 21, 2023 at 6:31:05 PM UTC-5 Blinov,Michael wrote: Yes, under

unread,

Does VCell capable to simulation cell division and cell population?

Thanks, Michael! On Thursday, September 21, 2023 at 6:31:05 PM UTC-5 Blinov,Michael wrote: Yes, under

9/21/23

mefaz amjad, Blinov,Michael2

9/21/23

Parameter Guide

Hello, VCell has an extensive searchable Help available under menu Help -> VCelll Help. If your

unread,

Parameter Guide

Hello, VCell has an extensive searchable Help available under menu Help -> VCelll Help. If your

9/21/23

Kun, Blinov,Michael3

9/19/23

Some species missing in the exported batch simulation results & export generated network

Thank you for the instructions! That perfectly solves the problem. On Mon, Sep 18, 2023 at 11:57 PM

unread,

Some species missing in the exported batch simulation results & export generated network

Thank you for the instructions! That perfectly solves the problem. On Mon, Sep 18, 2023 at 11:57 PM

9/19/23

VCell Open Discussion Forum, Schaff,Jim3

9/19/23

Multiple simulations fail at 0% completion.

Thanks a lot for these suggestions. Will use these to debug. On Monday, September 18, 2023 at 11:18:

unread,

Multiple simulations fail at 0% completion.

Thanks a lot for these suggestions. Will use these to debug. On Monday, September 18, 2023 at 11:18:

9/19/23

Aravind Chandrasekaran, Schaff,Jim4

9/18/23

Thanks a lot. On Monday, September 18, 2023 at 4:26:59 PM UTC-4 Schaff,Jim wrote: VCell service has

unread,

Thanks a lot. On Monday, September 18, 2023 at 4:26:59 PM UTC-4 Schaff,Jim wrote: VCell service has

9/18/23

9/18/23

Re: [VCell] Query to Modelling a Pore in Plant

Himefaz, I'm not familiar with plant biology, but it seems that a pore (stomata?) is made up of

unread,

Re: [VCell] Query to Modelling a Pore in Plant

Himefaz, I'm not familiar with plant biology, but it seems that a pore (stomata?) is made up of

9/18/23

9/18/23

It has recovered itself. 在2023年9月17日星期日 UTC+10 23:46:02<Kun> 写道： Everything works well in the

unread,

It has recovered itself. 在2023年9月17日星期日 UTC+10 23:46:02<Kun> 写道： Everything works well in the

9/18/23

9/12/23

COMBINE 2023 update

Hello, fellow SBMLers, SBGNers, BioPAXers, BNGLers, and other modelers and developers, COMBINE in

unread,

COMBINE 2023 update

Hello, fellow SBMLers, SBGNers, BioPAXers, BNGLers, and other modelers and developers, COMBINE in

9/12/23

Aravind Chandrasekaran, Les Loew4

9/3/23

VCell simulation export fails to download.

Thanks, Les, I am having this issue again today. The requests submitted for download this morning

unread,

VCell simulation export fails to download.

Thanks, Les, I am having this issue again today. The requests submitted for download this morning

9/3/23

Aravind Chandrasekaran

9/3/23

Simulation status not accurate since morning

Since Sunday morning, I have not been able to track progress of the simulations. The simulations that

unread,

Simulation status not accurate since morning

Since Sunday morning, I have not been able to track progress of the simulations. The simulations that

9/3/23

Aravind Chandrasekaran, Blinov,Michael3

8/30/23

Issues Downloading batch simulation data.

Thanks a lot. This protocol worked. On Tuesday, August 29, 2023 at 1:58:41 PM UTC-4 Blinov,Michael

unread,

Issues Downloading batch simulation data.

Thanks a lot. This protocol worked. On Tuesday, August 29, 2023 at 1:58:41 PM UTC-4 Blinov,Michael

8/30/23

8/29/23

COMBINE/ICSB tutorials and workshops, COMBINE financial aid

Dear colleagues, Time is running out for tutorials/workshop proposals and financial aid applications!

unread,

COMBINE/ICSB tutorials and workshops, COMBINE financial aid

Dear colleagues, Time is running out for tutorials/workshop proposals and financial aid applications!

8/29/23

8/14/23

COMBINE 2023: October 5-8th, Farmington, CT

Dear Computational Biologists, The "Computational Modeling in Biology" Network (COMBINE,

unread,

COMBINE 2023: October 5-8th, Farmington, CT

Dear Computational Biologists, The "Computational Modeling in Biology" Network (COMBINE,

8/14/23

Shiv Shukla, Schaff,Jim2

8/10/23

VCell currently does not have a general Python API for modeling, simulation and analysis. You may

unread,

VCell currently does not have a general Python API for modeling, simulation and analysis. You may

8/10/23

Search

Clear search

Close search

Google apps

Main menu