--- a
+++ b/EXPERIMENTS.md
@@ -0,0 +1,53 @@
+# Recreate the initial experiments
+We will recreate the experiments from "Genome-wide association study of behavioral, physiological and gene expression traits in outbred CFW mice". The command below will download the datasets used in the mouse genome paper into a local directory called `mice_data_set` for processing.
+
+## Set up a Jupyter notebook with the R Kernel
+Next, use the Conda package manager to set up a virtual environment to run the Jupyter notebooks that recreate the original experiments on the datasets.
+
+```
+conda create -n r-kernel
+conda activate r-kernel
+conda install r-recommended r-irkernel
+conda install jupyter
+```
+
+
+Add the R-kernel spec to Jupyter and install required packages.
+```
+R -e 'IRkernel::installspec()'
+R -e 'install.packages("qtl", repos = "http://cran.us.r-project.org")'
+R -e 'install.packages("qqman", repos = "http://cran.us.r-project.org")'
+R -e 'install.packages("data.table", repos = "http://cran.us.r-project.org")'
+R -e 'install.packages("stringr", repos = "http://cran.us.r-project.org")'
+R -e 'install.packages("qqman", repos = "http://cran.us.r-project.org")'
+R -e 'install.packages("devtools", repos = "http://cran.us.r-project.org")'
+```
+
+Run Jupyter notebook
+
+```
+jupyter notebook
+```
+
+## Run Map.ipynb
+Running this notebook before synthesizing data is optional as the original `abBMD` analysis was downloaded in the steps above. Map.ipynb can be run to optinally recreate the original experiment results. To run the notebook, open `./research_paper_code/notebooks/map.ipynb` in Jupyter notebook, and choose Kernel->Run All. This will run through the R-studio code in this repository that recreates the results from the original paper. As data is generated, you will see plots and data files generated in the following formats:
+
+```
+(base) redlined@redlined-980:~/GitHub/synthetic-data-genomics/mice_data_set/out$ head lm_abBMD_1_79646.csv
+"","snp","chr","pos","p"
+"1","rs29477109",11,95292217,5.05231663641996e-14
+"2","rs27071351",11,96114911,7.07418067212828e-14
+"3","rs27024162",11,96918116,7.17058199722633e-14
+"4","rs49423067",11,96918212,7.19866140655625e-14
+"5","rs29470802",11,95263588,8.04984862217419e-14
+"6","rs29459746",11,95987376,1.03725122425739e-13
+"7","rs50417410",11,97011284,1.04333530152468e-13
+"8","rs29473466",11,96920033,1.33866242959213e-13
+"9","rs221074340",11,96018255,1.35574083178291e-13
+```
+
+![image](https://user-images.githubusercontent.com/6510818/136842534-32ed43ac-e80f-47b2-9788-2f5f7149d257.png)
+
+
+
+