<commit_before>##tcseg

Source code for the Tribolium casteneum (Tc) segmentation modeling project on the CompuCell platform.

This project manages the Python source code for a CompuCell modeling project. CompuCell3D is an open-source simulation environment for multi-cell, single-cell-based modeling of tissues, organs and organisms.  It uses Cellular Potts Model to model cell behavior.  This CompuCell project is funded by the NIH and EPA.  Compucell3D is led by <NAME> (IU), <NAME>(IU) and <NAME> (U.Wisc. Milwaukee)

The Tribolium c. modeling project is funded by a grant from the National Science Foundation. It is led by <NAME> and <NAME> (Trinity College) and <NAME> (Unversity of Arizona).  Student research assistants include:

* <NAME>, Trinity
* <NAME>, Trinity
* <NAME> 

The focus of the project is to create a Monte-Carlo cellular-level model of the process of segmentation in an arthropod. 

There are three main source files that make up the Simulation.  These are typically found in the /Simulation folder of a ComputCell project.
These are the files that will typically be edited and revised during development.

*  Simulation/ElongationModel.py -- initialization file
*  Simulation/ElongationModelSteppable.py -- scripts that define the steps that are performed on each Monte Carlo step.

There are also two main simulation (.cc3d) files.  These rarely need editing:

* tcseg.cc3d
* tcseg_batch.cc3d

# To sync with upstream ram8647/tcseg
1. $ git fetch upstream
2. $ git checkout master
3. $ git merge upstream/master

# Standard work flow in Terminal Window
=====================================
1. Sync with upstream repo
1. $ git fetch upstream
2. $ git checkout master<commit_msg>Further update readme.md<commit_after>##tcseg

Source code for the Tribolium casteneum (Tc) segmentation modeling project on the CompuCell platform.

This project manages the Python source code for a CompuCell modeling project. CompuCell3D is an open-source simulation environment for multi-cell, single-cell-based modeling of tissues, organs and organisms.  It uses Cellular Potts Model to model cell behavior.  This CompuCell project is funded by the NIH and EPA.  Compucell3D is led by <NAME> (IU), <NAME>(IU) and <NAME> (U.Wisc. Milwaukee)

The Tribolium c. modeling project is funded by a grant from the National Science Foundation. It is led by <NAME> and <NAME> (Trinity College) and <NAME> (Unversity of Arizona).  Student research assistants include:

* Yuxuan (Effie) Li, Trinity
* <NAME>, Trinity
* <NAME>, Carleton College

The focus of the project is to create a Monte-Carlo cellular-level model of the process of segmentation in an arthropod. 

There are three main source files that make up the Simulation.  These are typically found in the /Simulation folder of a ComputCell project.
These are the files that will typically be edited and revised during development.

*  Simulation/ElongationModel.py -- initialization file
*  Simulation/ElongationModelSteppable.py -- scripts that define the steps that are performed on each Monte Carlo step.

There are also two main simulation (.cc3d) files.  These rarely need editing:

* tcseg.cc3d
* tcseg_batch.cc3d

# To sync with upstream ram8647/tcseg
1. $ git fetch upstream
2. $ git checkout master
3. $ git merge upstream/master

# Standard work flow in Terminal Window

1. Sync with upstream repo
1. $ git fetch upstream
2. $ git checkout master
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