National Resource for Cell Analysis and Modeling VCell Service, Outreach, Training and Dissemination Ann Cowan

National Resource for Cell Analysis and ModelingVCell

Service, Outreach, Training and Dissemination

Ann Cowan


In one month (Oct) there were:

176 different users logged in

439 applications (within 375 Biomodels) and 15 Mathmodels saved

425 simulation runs saved

Service

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


ServiceNov 2015 Dec 2014 diff

% increase

Total Registered VCell Users 18,833 18,038 795 4Users Who Ran Simulations 5,051 4,651 400 9Currently Stored Models 69,647 65,412 4,235 6Currently Stored Simulations 420,802 390,835 29,967 8Publicly Available Models 849 791 58 7Publicly Available Simulations 6,166 5,799 367 6


Service


Service


Published VCell Models (2012 – 2015): 39

1. 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.

2. 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.

3. Ibrahim, B. 2015. Spindle assembly checkpoint is sufficient for complete Cdc20 sequestering in mitotic control. Comput Struct Biotechnol J. 13:320-328 PMC4430708.

4. Rezgui, A., M. Madec, C. Lallement, and J. Haiech. 2015. Integration of SBML models for the description of biological system in a lab-on-chip. In Mixed Design of Integrated Circuits & Systems (MIXDES), 2015 22nd International Conference. IEEE. 165-170.

5. 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,

6. 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.

7. 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.

8. Li, L., N. Gervasi, and J.A. Girault. 2015. Dendritic geometry shapes neuronal cAMP signalling to the nucleus. Nature Communications. 6:6319.

9. 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.

10. 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.

11. 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.

12. 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.

Published VCell Models 2015


Service

• 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 Software Releases


Service

• 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 Software Releases


Outreach

VCell Website Redesign

http://cgsb-web.cam.uchc.edu/

http://cgsb-web.cam.uchc.edu/


OutreachUser Outreach/Feedback


TrainingNew tutorial format


TrainingVCellEducation on YouTube


Training

2015 VCell Short Course June 22-24; 11 participants from 9 institutions.

2015 VCell course

Courses and Workshops


TrainingCourses and Workshops • 2015 Q-Bio (Blinov)• 2015 CSHL meeting: Cellular dynamics & Models (former CCB) March 3-6; ½ day Tutorial

(Moraru, Blinov, Loew)


Training

• 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.

New Developments


DisseminationNRCAM Publications (2012-2015): 34

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.

NRCAM Publications 2015:


Colgate University: Biol 334/Math334 Systems Biology - Ahmet AyCarnegie Melon:Robert Murphy (and online with CourseHero.com)Fred Hutchinson Cancer Research Center: Introduction to Biological Modeling - Steve AndrewsMount Sinai: Dynamical Modeling Methods for Systems Biology -Eric Sobie (and online with

Coursera)Univeristy of Illinois: BioE 201 Conservation Principles on Bioengineering - ImoukhuedeUC Davis: Biological Sciences 20Q - Modeling in Biology – MogilnerUCSD: BENG/CHEM/PHARM 276 Numerical Analysis for Multi-Scale Biology - McCulloch,

McCammonCornell University minicourse: Molecular Switches in Signaling and Disease (2013)University of Leiden: Mathematical Biology: the Virtual CellUniversitat Duisburg-Essen Introduction to systems biology: modeling and simulationIIT Madras : Online courseBE306: don’t know where, public models in VCell

UCHC courses: Introduction to Systems Biology, Cell Biology, Biochem II, Practical Microscopy and Modeling

Undergraduate/graduate courses that use VCell:

Dissemination

Documents

National Resource for Cell Analysis and Modeling VCell Service, Outreach, Training and Dissemination Ann Cowan