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2021-02-06brain.documentation/QUICKSTART.rst: specify the running environment.Hui Lan
2021-02-06update .gitignore such that it could track QUICKSTART.rst in ↵Hui Lan
brain.documentation (revision).
2021-02-06update .gitignore such that it could track QUICKSTART.rst in ↵Hui Lan
brain.documentation.
2021-02-06Move edge files in edge_pool to /disk1/edge_pool to save space in the workspace.Hui Lan
2020-12-13make_parameter_rnaseq.py: if a line in quant.sf is not complete, ignore this ↵Hui Lan
quant.sf.
2020-10-27buildRmatrix.py: use a string to store the max expression level from ↵Hui Lan
isoforms (revision).
2020-10-27buildRmatrix.py: use a string to store the max expression level from isoforms.Hui Lan
2020-10-21update_network.py: make TPM.txt.Hui Lan
2020-10-10buildRmatrix.py: use string instead of float to store TPM values. This ↵Hui Lan
script could run out of memory space (7GB) when there are more than 1000 RNA-seq samples.
2020-08-27buildRmatrix.py: get max value eariler.Hui Lan
2020-08-27buildRmatrix.py: remove a redundant line.Hui Lan
2020-08-16html_network.py: make URL for edge information such as ↵Hui Lan
AT3G09600_AT1G49720_0.html correct (revision 2).
2020-08-15html_network.py: make URL for edge information such as ↵Hui Lan
AT3G09600_AT1G49720_0.html correct (revision).
2020-08-14start_webapp.py and util_networkx.py: remove them (they are in ↵Hui Lan
/var/www/brain/brain).
2020-08-14html_network.py: make URL for edge information such as ↵Hui Lan
AT3G09600_AT1G49720_0.html correct.
2020-05-05update_netowrk_by_force.py: curl http://118.25.96.118/brain/before should be ↵Hui Lan
executed as a cron job.
2020-05-05update_netowrk_by_force.py: check why merge_edges.py does not fully work.Hui Lan
2020-05-04merge_edges.py: Remove 'May take a while.' Actually, after insertion speed ↵Hui Lan
improvement, writting one million rows to a sqlite db table is really fast.
2020-05-04merge_edges.py: Remove colon after [merge_edges.py].Hui Lan
2020-05-04merge_edges.py: rename make_new_edge2. Remove 2.Hui Lan
2020-05-04merge_edges.py: make sqlite insert really fast. Commit in the end instead ↵Hui Lan
of commit for each insertion.
2020-05-04merge_edges.py: string does not have isnumeric method.Hui Lan
2020-05-03download_and_map.py: when download_log.txt contains blank lines, this script ↵Hui Lan
will stop working. Make it work when the log file contains blank lines. These blank lines usually appear in the end of the log file.
2020-05-03configure.py: fewer daily downloadsHui Lan
2020-05-02download_and_map.py: lower the requirement of available disk space to make ↵Hui Lan
downloading and mapping proceed.
2020-04-04Modified .gitignoreHui Lan
2020-04-04Modified .gitignoreHui Lan
2020-03-27update_network_by_force.py: the number of %s should be the same as the ↵Hui Lan
number of arguments.
2020-03-27html_network.py: string like 'F3'H' will cause syntax error in JavaScript. ↵Hui Lan
json.dumps could not fix that.
2020-03-27html_network.py: string like 'F3'H' will cause syntax error in JavaScript.Hui Lan
2020-03-27update_network_by_force.py: code for build table of regulators and regulatees.Hui Lan
2020-03-26html_network.py: don't show intermediate resultHui Lan
2020-03-26html_network.py: remove many lines to make it simplerHui Lan
2020-02-15merge_edges.py: remove old function make_new_edge()Hui Lan
2020-02-15update_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
2020-02-15merge_edges.py: now db_fname has a place to printHui Lan
2020-02-15merge_edges.py: an integer in a list prevents the join method from workingHui Lan
2020-02-15update_network_by_force.py: disable visiting the web app each time when ↵Hui Lan
running update_network_by_force.py
2020-02-15merge_edges.py: a more memory efficient method to compute an edge's net strengthHui Lan
Compute an edge's strength on the fly instead of saving everything and then computing the net strength. The new function make_new_edge2 will replace make_new_edge.
2020-02-15merge_edges.py: do not show edge file names in network.logHui Lan
2020-02-15merge_edges.py: datetime.now() dose not work. Should be datetime.datetime.now()Hui Lan
2020-02-14merge_edges.py: write edge file names to network.logHui Lan
When merging many big edge files, the computer may run out of memory. Save the edge files that have been considered thus far and figure out where merging stopped.
2020-02-11merge_edges.py: use the most recent update date as the merged edge's date.Hui Lan
2020-02-11merge_edges.py: add a few comments for function make_new_edge.Hui Lan
2020-02-11merge_edges.py: log more information in network.log.Hui Lan
2020-02-11merge_edges.py: log number of edge files scanned.Hui Lan
2020-02-11merge_edges.py: what is the purpose of variable d.Hui Lan
2020-02-11merge_edges.py: make a better keyHui Lan
Use a combination of target gene ID and tf gene ID as a key. So if we having the following: Target: AT5G09445 AT5G09445 TF: AT1G53910 RAP2.12 Then the key will be "AT5G09445_AT1G53910". Before it was "AT5G09445 AT5G09445 AT1G53910 RAP2.12". This is OK in most cases, as long a gene ID's corresponding gene name is consistent. But if "AT1G53910" has a different gene name, then we will have a DIFFERENT key, which is not what we want.
2020-02-11merge_edges.py: why 10?Hui Lan
2020-02-11merge_edges.py: consider all files in directory EDGE_POOL whose file name ↵Hui Lan
starts with 'edegs'
generated by cgit v1.2.1 (git 2.18.0) at 2025-03-15 11:17:16 +0000