Workshop 18 files:

• Week's Schedule (.docx) (updated Monday 3PM)

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Sunday Aug. 5, 2018

• Intro To Programming_Somogyi.zip

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Monday Aug. 6, 2018

• SauroFiles2018CC3D.zip

• Introductory Network Modeling Slides_Glazier.zip (not covered in class but may be useful)

• Introduction to Biology For Modeling - James Glazier (ppt)

We have a reservation for tonight for the workshop group at;

Anystsang's Little Tibet Restaurant
415 E 4th St,
Bloomington, IN 47408
It's just a few blocks from Woodburn Hall. Directions

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Tuesday Aug. 7, 2018

• Morning: Herbert Sauro (tbd)

• Afternoon: James Sluka (PBPK_Sluka.zip)

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Wednesday Aug. 8, 2018

Presentations

• Short Intro to CompuCell3D - James Glazier

• Intro to CompuCell3D - Maciej Swat

• Intro to CompuCell3D - example simulations - James Glazier

• Intro to CompuCell3D - James Glazier, Maciej Swat

Simulations

• my_first_simulation

• cell_motion

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Thursday Aug. 9, 2018

Presentations

• Cell Lineage - Priyom Adhyapok

Simulation

• Cell Lineage Simulation - intro

• Cell Lineage - Complete Simulation

• diffusion_intro

• chemotaxis intro

• bacterium_macrophage

• Chemotaxis With Parameter Scan - Lambda Volume

• Chemotaxis With Parameter Scan - Lambda Chemo

• epithelial sheet - Priyom Adhyapok

• convergent extension - Priyom Adhyapok

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Friday Aug. 10, 2018

Presentations

• Friday Intro Slides: CC3D Introduction to Compartments & Links

• CC3D and SBML (Cyclin cell cycle in SBML)

Demos

• vascular demo

• simplified vascular tumor demo

• Final cyclin cell cycle SBML model

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