pops_lung

Web Portal for the Precision Oncology Probe Set (POPS) for Lung Cancer.

This is the implementation for the data portal associated with the following publication:

McMillan, E. A., Ryu, M.-J., Diep, C. H., Mendiratta, S., Clemenceau, J. R., Vaden, R. M., Kim, J.-H., Motoyaji, T., Covington, K. R., Peyton, M., Huffman, K., Wu, X., Girard, L., Sung, Y., Chen, P.-H., Mallipeddi, P. L., Lee, J. Y., Hanson, J., Voruganti, S., … White, M. A. (2018). Chemistry-first approach for nomination of personalized treatment in lung cancer. Cell, 173(4). https://doi.org/10.1016/j.cell.2018.03.028

The portal can be currently acccessed here: https://pops.biohpc.swmed.edu/pops/

Setup

This website is built based on a LAMP stack (Linux, Apache, MySQL, PHP). In order to set it up in your server environment, please install the following:

1. Apache: version 2.4+
2. MySQL: version 5.1+
3. PHP: version 5.5+

Once dependencies are intalled do the following:

1. Clone the pops/ directory to your server

2. Contact @jeanrclemenceau for access to the data files

3. Replace the placeholder.txt file with the corresponding content for the following directories:

   • pops/curves/
   • pops/gsea/
   • pops/pegplots/
   • pops/roc-curves/
   • pops/scanningks/
   • pops/elasticnet/
   • pops/images/compounds/

4. Build the MySQL POPS database using the given dump file (POPS_LUNG_DB_<version>.sql)

5. Copy the contents of SecuritySettings.php and replace line 10 of `pops/pops_conf.php'

6. Update any relevant email addresses and passwords in pops/pops_conf.php

7. Setup your server for sending STMP emails

8. Point your httpd apache server to the code directory

9. Start your httpd server