Agenda: Cell Modeling Workshop 2021
Agenda: Cell Modeling Workshop 2021
Apply | Home | Agenda | Instructors
Presentations from prior workshops are available on the MMBioS YouTube channel.
Agenda
This agenda is tentative and subject to change.
| Monday, July 12 | |
|---|---|
| BioNetGen / RuleBender | |
| 7:30-8:00 | Icebreaker |
| 8:00-8:30 | Introduction to 2021 Cell Modeling Workshop |
| 8:30-10:15 | Introduction to Reaction Network Modeling with BioNetGen (interactive presentation and hands-on demo) |
| 10:15-10:30 | Break |
| 10:30-12:00 |
Introduction to Rule-Based Modeling with BioNetGen: (interactive presentation and hands-on demo) |
| 12:00-1:00 | Lunch / Dinner Break |
| 1:00-2:30 |
Compartmental models; other advanced models |
| 2:30-3:00 | Break |
| 3:00-4:00 |
PyBioNetGen |
| *Note that schedule is in Pacific Time (PDT) | |
| Tuesday, July 13 | |
| MCell / CellBlender | |
| 7:30-8:00 | Icebreaker |
| 8:00-9:30 |
Particle-based Spatial Reaction/Diffusion Modeling with MCell (Interactive Presentation followed by Q&A) |
| 9:30-9:45 | Introduction to Blender User Interface |
| 9:45-10:30 | CellBlender Workflow and tour of built-in examples |
| 10:30-10:45 | Break |
| 10:45-12:00 | Building a complete spatial model of intracellular, inter-organelle transport |
| 12:00-1:00 |
Lunch / Dinner Break |
| 1:00-2:30 | Model building (continued) with visualization and analysis |
| 2:30-3:00 | Break |
| 3:00-4:00 |
Model import and export full circle between CellBlender and RuleBender |
| *Note that schedule is in Pacific Time (PDT) | |
| Wednesday, July 14 | |
| CellOrganizer | |
| 7:30-8:30 | Icebreaker |
| 8:00-9:30 |
Overview of approaches to learning and using generative models of cell organization (lecture followed by Q&A) |
| 9:30-10:00 | Cellorganizer paradigms overview |
| 10:00-10:15 |
Break |
| 10:15-10:45 | Analysis and Modeling of Cell and Organelle Shape |
| 10:45-11:15 | Automating cell simulations through CellOrganizer |
| 11:15-12:00 |
Tutorial session 1 (participants do modules of their own choice and staff available to help) |
| 12:00-1:00 | Lunch / Dinner Break |
| 1:00-2:45 | Tutorial session 2 (participants do modules of their own choice and staff available to help) |
| 2:45-3:00 |
Wrap-up Questions |
| *Note that schedule is in Pacific Time (PDT) | |
| Thursday, July 15 | |
| Advanced Topics | |
| 7:30-9:30 | CellOrganizer - Advanced Topics |
| 9:30-10:00 |
Break |
| 10:00-12:00 | BioNetGen/RuleBender - Advanced Topics |
| 12:00-12:30 |
Break |
| 12:30-2:30 | MCell/CellBlender - MCell4 Python API |
| 2:30- | Open discussions. Contact individual teams on Slack to arrange. |
| *Note that schedule is in Pacific Time (PDT) | |
| Friday, July 16 | |
| Advanced Topics and Projects | |
| 7:30-9:30 | MCell/CellBlender - Advanced Topics |
| 9:30-10:00 |
Break |
| 10:00-12:00 | CellOrganizer - Advanced Topics |
| 12:00-12:30 |
Break |
| 12:30-2:30 | BioNetGen/RuleBender - Advanced Topics |
| 2:30- | Open discussions. Contact individual teams on Slack to arrange. |
| *Note that schedule is in Pacific Time (PDT) | |