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Files for the workshop in Bloomington July-August 2017

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

• Lecture	Python Code(s)
  lec1-intro.pptx	lec1.py
  lec2-branching-iteration.pptx	lec2.py
  lec3-strings-approximations.pptx	lec3.py
  lec4-basic-functions.pptx
  lec5-tuple-lists.pdf	lec5_tuples_lists.py
  lec6-dictionaries.pptx	lec6.py lec6_recursion_dictionaries.py
  lec7-adv-functions.pptx
  lec7-random-walk.pptx

• Sunday lectures Python ppt and python code.zip

Monday

AM

Prof. Glazier talk (pptx)

• Priyom's Verbal Model from Mark Alber Epithelial paper with annotations (docx) (Alber Article PDF).

PM

Reaction Kinetics Presentation (ppt)

• Zip file of COPASI, PDFs etc.

Tuesday

AM

PBPK modeling in SBML--COPASI (ppt)

• PK_simple_one_compartment.cps

PBPK model of Acetaminophen

• SBML format from BioModels (.xml) (or get it from directly from BioModels Database as model BIOMD0000000619)

• COPASI format (.cps)

• Human ADME data of Critchley et al. (.csv)

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.

• Defining ODEs in COPASI/SBML when they really don't look like chemical reactions (pptx)

A chaotic system implemented in COPASI/SBML.

• Chaotic Lorenz in COPASI.cps

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

• Holmes_sup_material.pdf

• Holmes et al. Noise Enhances...(pdf)

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

• Hirashima et al-2017-Development, Growth (pdf)