VCell
National Resource for Cell
Analysis and Modeling
Service, Outreach, Training and
Dissemination
Ann Cowan
VCell
National Resource for Cell
Analysis and Modeling
Service
In one month (Oct) there were:
176 different users logged in
439 applications (within 375 Biomodels) and 15 Mathmodels saved
425 simulation runs saved
In the past 6 months there have been:
997 different users logged in
2,810 applications (within 1,437 Biomodels) and 103 Mathmodels saved
4,226 simulation runs saved
VCell
National Resource for Cell
Analysis and Modeling
Service
Nov 2015 Dec 2014
Total Registered VCell Users
Users Who Ran Simulations
Currently Stored Models
Currently Stored Simulations
Publicly Available Models
Publicly Available Simulations
18,833
5,051
69,647
420,802
849
6,166
18,038
4,651
65,412
390,835
791
5,799
diff
795
400
4,235
29,967
58
367
%
increase
4
9
6
8
7
6
VCell
National Resource for Cell
Analysis and Modeling
Service
VCell
National Resource for Cell
Analysis and Modeling
Service
VCell
Published VCell Models (2012 – 2015):
National Resource for Cell
Analysis and Modeling
39
Published VCell Models 2015
1.
2.
3.
4.
5.
6.
7.
8.
9.
10.
11.
12.
Boras, B.W., S.P. Hirakis, L.W. Votapka, R.D. Malmstrom, R.E. Amaro, and A.D. McCulloch. 2015. Bridging scales through multiscale
modeling: a case study on protein kinase A. Front Physiol. 6:250 PMC4563169.
Ibrahim, B. 2015. In silico spatial simulations reveal that MCC formation and excess BubR1 are required for tight inhibition of the
anaphase-promoting complex. Mol Biosyst. 11:2867-2877.
Ibrahim, B. 2015. Spindle assembly checkpoint is sufficient for complete Cdc20 sequestering in mitotic control. Comput Struct
Biotechnol J. 13:320-328 PMC4430708.
Rezgui, A., M. Madec, C. Lallement, and J. Haiech. 2015. Integration of SBML models for the description of biological system in a lab-onchip. In Mixed Design of Integrated Circuits & Systems (MIXDES), 2015 22nd International Conference. IEEE. 165-170.
Wu, F., B.G. van Schie, J.E. Keymer, and C. Dekker. 2015. Symmetry and scale orient Min protein patterns in shaped bacterial sculptures.
Nat Nanotechnol. 10:719-726.Brown,
S.A., L.D. McCullough, and L.M. Loew. 2015. Computational neurobiology is a useful tool in translational neurology: the example of
ataxia. Frontiers in neuroscience. 9:1 PMC 4300942.
Karttunen, J., S. Mantynen, T.O. Ihalainen, J.K. Bamford, and H.M. Oksanen. 2015. Non-structural proteins P17 and P33 are involved in
the assembly of the internal membrane-containing virus PRD1. Virology. 482:225-233.
Li, L., N. Gervasi, and J.A. Girault. 2015. Dendritic geometry shapes neuronal cAMP signalling to the nucleus. Nature Communications.
6:6319.
Rigatti, M., A.V. Le, C. Gerber, Moraru, II, and K.L. Dodge-Kafka. 2015. Phosphorylation state-dependent interaction between
AKAP7delta/gamma and phospholamban increases phospholamban phosphorylation. Cellular Signalling. 27:1807-1815.
Timofeeva, Y., and K.E. Volynski. 2015. Calmodulin as a major calcium buffer shaping vesicular release and short-term synaptic
plasticity: facilitation through buffer dislocation. Frontiers in cellular neuroscience. 9:239 PMC 4486835.
Wragg, R.T., G. Gouzer, J. Bai, G. Arianna, T.A. Ryan, and J.S. Dittman. 2015. Synaptic activity regulates the abundance and binding of
complexin. Biophys J. 108:1318-1329 PMC 4375453.
Zakharova, N.V., E.O. Artemenko, N.A. Podoplelova, A.N. Sveshnikova, I.A. Demina, F.I. Ataullakhanov, and M.A. Panteleev. 2015.
Platelet Surface-Associated Activation and Secretion-Mediated Inhibition of Coagulation Factor XII. PLoS One. 10:e0116665 PMC
4331558.
VCell
National Resource for Cell
Analysis and Modeling
Service
VCell Software Releases
• VCell 5.3 deployed to release site. - June 6, 2015
– New topology with relaxed constraints
– New units (each model has own unit system – for SBML import)
– Improved data analysis in spatial models
• VCell 6.0 alpha – releasing soon to beta site
VCell
National Resource for Cell
Analysis and Modeling
Service
VCell Software Releases
• VCell 5.3 deployed to release site. - June 6, 2015
• VCell 6.0 alpha – releasing soon to beta
–
–
–
–
–
–
New Rule-Based integration/GUI for model development
Nfsim non-spatial stochastic network-free solver
EBChombo solver for local mesh refinement, with parallel capabilities
VisIt-based visualization for viewing results
Event description simplified in BioModel interface
VCellAPI (allows plugins)
VCell
National Resource for Cell
Analysis and Modeling
Outreach
VCell Website Redesign
VCell
National Resource for Cell
Analysis and Modeling
Outreach
User Outreach/Feedback
VCell
National Resource for Cell
Analysis and Modeling
Training
New tutorial format
VCell
National Resource for Cell
Analysis and Modeling
Training
VCellEducation on YouTube
VCell
National Resource for Cell
Analysis and Modeling
Training
Courses and Workshops
2015 VCell Short Course June 22-24;
11 participants from 9 institutions.
2015 VCell course
VCell
National Resource for Cell
Analysis and Modeling
Training
Courses and Workshops
•
•
2015 Q-Bio (Blinov)
2015 CSHL meeting: Cellular dynamics & Models (former CCB) March 3-6; ½ day Tutorial
(Moraru, Blinov, Loew)
VCell
National Resource for Cell
Analysis and Modeling
Training
New Developments
•
NSF REU grant to Laubenbacher
— provides undergraduate experiences that include VCell
•
Applied to host 2017 Q-Bio workshop
•
Collaboration with Wendell Lim and Bruce Mayer to develop VCell models to
accompany second edition of their Cell Signaling textbook.
VCell
National Resource for Cell
Analysis and Modeling
Dissemination
NRCAM Publications (2012-2015): 34
NRCAM Publications 2015:
1. Brown, S.A., L.D. McCullough, and L.M. Loew. 2015. Computational neurobiology is a
useful tool in translational neurology: the example of ataxia. Frontiers in neuroscience.
9:1 PMC 4300942.
2. Hucka, M., F.T. Bergmann, A. Drager, S. Hoops, S.M. Keating, N. Le Novere, C.J.
Myers, B.G. Olivier, S. Sahle, J.C. Schaff, L.P. Smith, D. Waltemath, and D.J.
Wilkinson. 2015. Systems Biology Markup Language (SBML) Level 2 Version 5:
Structures and Facilities for Model Definitions. J Integr Bioinform. 12:271.
3. Hucka, M., F.T. Bergmann, S. Hoops, S.M. Keating, S. Sahle, J.C. Schaff, L.P. Smith,
and D.J. Wilkinson. 2015. The Systems Biology Markup Language (SBML): Language
Specification for Level 3 Version 1 Core. J Integr Bioinform. 12:266.
VCell
National Resource for Cell
Analysis and Modeling
Dissemination
Undergraduate/graduate courses that use VCell:
Colgate University: Biol 334/Math334 Systems Biology - Ahmet Ay
Carnegie Melon:Robert Murphy (and online with CourseHero.com)
Fred Hutchinson Cancer Research Center: Introduction to Biological Modeling - Steve Andrews
Mount Sinai: Dynamical Modeling Methods for Systems Biology -Eric Sobie (and online with
Coursera)
Univeristy of Illinois: BioE 201 Conservation Principles on Bioengineering - Imoukhuede
UC Davis: Biological Sciences 20Q - Modeling in Biology – Mogilner
UCSD: BENG/CHEM/PHARM 276 Numerical Analysis for Multi-Scale Biology - McCulloch,
McCammon
Cornell University minicourse: Molecular Switches in Signaling and Disease (2013)
University of Leiden: Mathematical Biology: the Virtual Cell
Universitat Duisburg-Essen Introduction to systems biology: modeling and simulation
IIT Madras : Online course
BE306: don’t know where, public models in VCell
UCHC courses: Introduction to Systems Biology, Cell Biology, Biochem II, Practical Microscopy and
Modeling