Files for the workshop in Bloomington July-August 2017

class snapshot 1 class snapshot 2 Class group shot

Photos

Sunday, July 30th

Monday, July 31st

Tuesday, August 1st

Wednesday, August 2nd

Thursday, August 3rd

Friday, August 4th


Maps

{*} Bloomington and Woodburn Hall (pdf) {*} Detailed IU map (png) {*} Google Map


Schedules

{*} Week's Schedule (.docx) {*} Week's Schedule (.pdf)


Quick reference cards

  1. Single page Python reference card (pdf)

  2. An 8 page, more comprehensive Python reference card (pdf)

  3. CompuCell3D quick reference card (pdf)


Presentation Slides

Sunday

Monday

AM

Prof. Glazier talk (pptx)

PM

Reaction Kinetics Presentation (ppt)

Tuesday

AM

PBPK modeling in SBML--COPASI (ppt)

PBPK model of Acetaminophen

PM

CC3D Intro (.pptx)

The biophysical nature of cells: potential cell behaviours revealed by analytical and computational studies of cell surface mechanics. R. Magno et al. (pdf)

Wednesday

MultiScale Modeling With CC3D-SBML (.pptx)

delta-notch slides (.pptx)

delta-notch in COPASI (.cps)

Thursday

Priyom Adhyapok's

CC3D Gradient 1 (zip)

CC3D Gradient 2 (zip)

CC3D Gradient 3 (zip)

Julio Belmonte's

cellcycle_DN (zip)

Friday

Julio Belmonte's

Directed Movement files (zip)

Cell Compartments and Links (pptx)

Epithelial Sheet files (zip)

Juliano Gianlupi

Parameter Scanning (pdf)

Gilberto Thomas

Heikos Model (zip)

Heiko's Cancer Model 2
(click to download the full size image)


Models, Files, Papers and ''how to ...''

Doing ODEs in COPASI/SBML as "Global Variables" that are of type "ODE" instead of defining chemical reactions.

A chaotic system implemented in COPASI/SBML.

Holmes et al., Gene Expression Noise Enhances Robust Organization of the Early Mammalian Blastocyst

Hirashima et al., "Cellular Potts modeling of complex multicellular behaviors in tissue morphogenesis"

Workshops/Workshop17/Files (last edited 2017-08-14 18:20:40 by thielmax)