| Age | Commit message (Collapse) | Author | |
|---|---|---|---|
| 2024-08-05 | update_network_by_force.py: improve code speed | Hui Lan | |
| 2024-08-05 | update_network_by_force.py: fix runtime error | Hui Lan | |
| 2024-08-05 | update_network_by_force.py: review and make updates | Hui Lan | |
| 2024-08-05 | Update write_log_file() so that it put the most recent message on the top; ↵ | Hui Lan | |
| remove duplicate write_log_file() | |||
| 2024-08-04 | Do not record duplicate edges (to save space). May take longer to run. | Hui Lan | |
| 2022-11-07 | update_network_by_force.py: back up the edge file once a month. | Hui Lan | |
| 2021-07-20 | update_network_by_force.py: get the difference in edges (yesterday vs. today). | Hui Lan | |
| 2021-02-09 | update_network_by_force.py: move the position of the 'update done' log. | Hui Lan | |
| 2021-02-09 | update_network_by_force.py: compute overlap with AtRegNet.20210208.csv. | Hui Lan | |
| 2020-05-05 | update_netowrk_by_force.py: curl http://118.25.96.118/brain/before should be ↵ | Hui Lan | |
| executed as a cron job. | |||
| 2020-05-05 | update_netowrk_by_force.py: check why merge_edges.py does not fully work. | Hui Lan | |
| 2020-03-27 | update_network_by_force.py: the number of %s should be the same as the ↵ | Hui Lan | |
| number of arguments. | |||
| 2020-03-27 | update_network_by_force.py: code for build table of regulators and regulatees. | Hui Lan | |
| 2020-02-15 | update_network_by_force.py: enable visiting the web app each time the ↵ | Hui Lan | |
| network is updated The Apache web server will be restarted daily to free memory. sudo service apache2 restart | |||
| 2020-02-15 | update_network_by_force.py: disable visiting the web app each time when ↵ | Hui Lan | |
| running update_network_by_force.py | |||
| 2020-01-21 | update_network_by_force.py: update G.pickle and SOURCE_NODES.pickle with ↵ | Hui Lan | |
| edges.txt Visit the following link to update two pickle files used the Webapp, G.pickle and SOURCE_NODES.pickle. http://118.25.96.118/brain/before The visit could be done using the command line tool curl, as follows: curl http://118.25.96.118/brain/before -Hui | |||
| 2020-01-21 | merge_edges.py: write all edge information to an SQLite database file called ↵ | Hui Lan | |
| edges.sqlite When I saved a static html page for each edge (e.g., http://118.25.96.118/static/edges/AT1G20910_AT1G30100_0.html), it took 5GB disk space for saving 1 million html pages. Not very disk space efficient. An alternative is to save all edge information in a database table (i.e., edge), and query this database table for a particular edge. The database file edges.sqlite takes less than 200MB for 1 million edges, requiring 10 times smaller space than the static approach. The reason is that we do not have a lot of HTML tags in the database. Quite happy about that, though it seems that filling a database is a bit slower (2 hours??? for 1 million rows). Also updated two files that were affected: update_network.py and update_network_by_force.py. Now instead of copying 1 million static html page to the Webapp, I just need to copy edges.sqlite to static/edges/. Faster. In the Webapp, I updated start_webapp.py and added a file templates/edge.html for handling dynamic page generation. -Hui | |||
| 2019-12-12 | update_network_by_force.py: summarize the association strength in the edge file | Hui Lan | |
| It would be interesting to see how edges' association strengths change over time, as time is an input variable for the function that computes the association strength. | |||
| 2019-12-07 | create backup_files.py for backing up files | Hui Lan | |
| Define a function copy_and_backup_file(src_file, dest_dir) to do backup and compression work. The function copy_and_backup_file is used in update_network_by_force.py. -Hui | |||
| 2019-12-04 | brain: add python and R code to local repository. | Hui Lan | |
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index : BRAINCL | |
| Unnamed repository; edit this file 'description' to name the repository. | Git |
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