Updated main README

.gitignore

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+__pycache__
+venv/
+.ipynb_checkpoints/

README.md

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-# arcade_emergent_behavior
+Supporting code for the article:
+
+> J Yu and N Bagheri. (2020). Agent-based models predict emergent behavior of heterogeneous cell populations in dynamic microenvironments. _Frontiers in Bioengineering and Biotechnology_. doi: [10.3389/fbioe.2020.00249](https://doi.org/10.3389/fbioe.2020.00249)
+
+## Setup files
+
+The `setups` directory contains all the setup files used for running simulations.
+Simulations were run using **[ARCADE v2.2](https://github.com/bagherilab/ARCADE/releases/tag/v2.2)**.
+
+The simulations `DEFAULT_random`, `MODULE_COMPLEXITY_both`, `MODULE_COMPLEXITY_metabolism`, and `MODULE_COMPLEXITY_signaling` use modified code; see supplementary materials for details.
+
+## Simulation data
+
+Raw simulation data and results are available on Mendeley Data:
+
+- `DEFAULT` . [http://dx.doi.org/10.17632/wzs7pxkgb9](http://dx.doi.org/10.17632/wzs7pxkgb9)
+- `MODULE COMPLEXITY` . [http://dx.doi.org/10.17632/7w2cdsrt87](http://dx.doi.org/10.17632/7w2cdsrt87)
+- `PARAMETER SENSITIVITY` . [http://dx.doi.org/10.17632/wpfycmb5sv](http://dx.doi.org/10.17632/wpfycmb5sv)
+- `GROWTH CONTEXT` . [http://dx.doi.org/10.17632/mmnh9hsv5y](http://dx.doi.org/10.17632/mmnh9hsv5y)
+- `CELL COMPETITION` (1/3) . [http://dx.doi.org/10.17632/5h6ng2y4fc](http://dx.doi.org/10.17632/5h6ng2y4fc)
+- `CELL COMPETITION` (2/3) . [http://dx.doi.org/10.17632/gzfwhgdtwz](http://dx.doi.org/10.17632/gzfwhgdtwz)
+- `CELL COMPETITION` (3/3) . [http://dx.doi.org/10.17632/dbj46mw6j9](http://dx.doi.org/10.17632/dbj46mw6j9)
+- `POPULATION HETEROGENEITY` (1/5) . [http://dx.doi.org/10.17632/bk9s769t3t](http://dx.doi.org/10.17632/bk9s769t3t)
+- `POPULATION HETEROGENEITY` (2/5) . [http://dx.doi.org/10.17632/mjpcm5my8z](http://dx.doi.org/10.17632/mjpcm5my8z)
+- `POPULATION HETEROGENEITY` (3/5) . [http://dx.doi.org/10.17632/hskf9mxbpw](http://dx.doi.org/10.17632/hskf9mxbpw)
+- `POPULATION HETEROGENEITY` (4/5) . [http://dx.doi.org/10.17632/ynzsfdswjz](http://dx.doi.org/10.17632/ynzsfdswjz)
+- `POPULATION HETEROGENEITY` (5/5) . [http://dx.doi.org/10.17632/p46dwfyvzg](http://dx.doi.org/10.17632/p46dwfyvzg)
+
+## Pipeline notebooks
+
+#### Parse simulation outputs
+
+The **[`parse_simulation_outputs`](parse_simulation_outputs.ipynb)** notebook provides the functions and scripts for parsing simulation files (`.json`) into pickled numpy arrays (`.pkl`).
+These parsed results are included with the raw simulation data.
+
+#### Analyze data & results
+
+The **[`analyze_data_results`](analyze_data_results.ipynb)** notebook provides functions and scripts for running basic analysis on simulation data and parsed results.
+All resulting `.json` and `.csv` files are provided in the `analysis` directory.
+
+#### Generate figure inputs
+
+The **[`generate_figure_inputs`](generate_figure_inputs.ipynb)** notebook walks through all the steps necessary to generate figure input files from raw data, parsed files, and basic analysis files.
+All resulting files are provided in the `analysis` directory.
+Refer to figure section in notebook for more details.
+
+To view figures, start a local HTTP server from the root folder, which can be done using Python or PHP:
+
+```bash
+$ python3 -m http.server
+$ php -S 127.0.0.1:8000
+```
+
+Note that the links in the notebook to figures assume the local port 8000; if your server is running on a different port, the links to the figures from the notebook will not work.
+Instead, you can navigate to `http://localhost:XXXX/` where `XXXX` is the port number and follow links to the figures.

requirements.txt

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+numpy
+scipy