code for analyzing mosquito and drosophila data collected in a wind tunnel
Download and compile the relevant database from the Dryad Digital Repository: https://doi.org/10.5061/dryad.n0b8m .
To view and access the data:
Install MySQL database (e.g., through https://www.mamp.info/en/) (Note: to access phpMyAdmin (database GUI) through the MAMP start page, on MAMP window click Preferences, and change PHP version to 7.0.x)
Make new empty database called “wind_tunnel_db”.
Import database file using: /path/to/mysql -uusername -ppassword wind_tunnel_db < /path/to/wind_tunnel_db.sql
E.g., on a mac with MAMP using root user:
/Applications/MAMP/Library/bin/mysql -uroot -proot wind_tunnel_db < /Users/me/Downloads/wind_tunnel_db.sql
It’s a large database so it will take some time. If using phpMyAdmin, you can view the database and watch the tables being populated if you want.
Next you will need to create an environment variable containing the connection URI. This should be called WIND_TUNNEL_TEST_DB_CXN_URL and should look like “mysql+mysqldb://username:[email protected]:8889/wind_tunnel_db”
Do the same for infotaxis db, calling the empty database “infotaxis_db” and populating with the file infotaxis_db.sql . Its environment variable should be called INFOTAXIS_DB_CXN_URL and should look like "mysql+mysqldb://username:[email protected]:8889/infotaxis_db"
Getting code to run using Anaconda and Python 2.7:
Download Anaconda for Python 2.7 (https://www.anaconda.com/download/#macos).
Create new environment using Python 2.7 and Anaconda: conda create --name wind_tunnel_env python=2.7 anaconda
Activate new environment: source activate wind_tunnel_env
Note: if using MAMP, need to add MAMB binaries to path. In .bash_profile in home directory, add line: export PATH=”/Applications/MAMP/Library/bin:$PATH” so that when mysql-python connector is installed it knows where to look for mysql_config
Then when env is active install mysql-python (MySQLdb):
pip install mysql-python
Navigate to repository where code lives (or a parent directory).
Run:
jupyter notebook
To open the notebook files. All figures in the manuscript are contained in _paper_draft.ipynb. Plots involving infotaxis simulations require you to first run and save the infotaxis results, which can be done using the code cells in _paper_auxiliary_code.ipynb.