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  • 7ea87e646a Added DAG plot to gobrowser module and smokers workflow. einarr 2007-07-23 17:02:28 +00:00
  • 155dfada5c iups flatberg 2007-07-23 13:25:34 +00:00
  • 9db5991108 flatberg 2007-07-20 15:48:59 +00:00
  • 98f53d3448 updates flatberg 2007-07-20 12:32:54 +00:00
  • 7ee7aa968a Initial import flatberg 2007-07-20 09:36:26 +00:00
  • dd04e28a62 Query fix flatberg 2007-07-05 18:49:24 +00:00
  • 850deeec0d Renamed gene identifers to gene_id flatberg 2007-07-05 18:40:29 +00:00
  • 75c7c51708 DistanceToSelectionFunction einarr 2007-07-05 18:36:59 +00:00
  • 3f5d45d7af Renamed smalltest workflow to smokers. einarr 2007-07-05 18:24:45 +00:00
  • fae096afe4 Changed workflow name from smalltest to smokers, because it is heavily based on the smokers dataset. einarr 2007-07-05 13:20:52 +00:00
  • a503ffcdf8 Fixed linewidth in selection in scatter plots. einarr 2007-07-05 11:57:21 +00:00
  • d29013a863 T-test now works, and outputs a histogram as well as t-values and p-values. einarr 2007-07-03 16:25:38 +00:00
  • 99987999db Broke up a too long line. einarr 2007-07-02 09:54:56 +00:00
  • 884804c49a Added a dummy for the t-test function. Will be updated when I have access to my office computer tomorrow. einarr 2007-06-28 21:48:13 +00:00
  • b637a5badc Changed /usr/bin/python2.4 to /usr/bin/python, and hope that 2.5 will not have trouble running the app. einarr 2007-06-28 21:42:18 +00:00
  • 4eaea2fe59 Added empty lists as default values for all_data and all_plots in Options, so that subclasses of Options will work with the GUI without modifications. einarr 2007-06-28 21:33:09 +00:00
  • 7b20f44fef Added a GO similarity function that does not do anything useful yet. einarr 2007-06-22 15:37:59 +00:00
  • e5cd8a8077 Started on a function to enhance gene lists by using GO similarities. Not in a usable state. einarr 2007-06-22 15:37:22 +00:00
  • 68cc583d2c Added common_dimensions(ds) that lists common dimensions between two datasets. einarr 2007-06-22 15:35:45 +00:00
  • ff8833a22c Added read functions for the medium and large smokers sets. einarr 2007-06-21 10:28:10 +00:00
  • d6298a2d99 Ensures that the GO is only loaded once. einarr 2007-06-21 10:26:35 +00:00
  • ff2c42902f Commented out some log lines that just cluttered the log. einarr 2007-06-21 10:25:17 +00:00
  • 2eb3d71a5d Moved data/smokers-med to data/smokers-medium. einarr 2007-05-16 15:35:25 +00:00
  • 91032d729e Some more smoker data flatberg 2007-05-16 11:45:43 +00:00
  • 7bdfdea23b Added -d option to get all identifiers along a single dimension. einarr 2007-05-16 10:30:54 +00:00
  • c7bfefe358 Fixed resnik distances. einarr 2007-05-15 18:16:07 +00:00
  • 335efe231a go-gene-matrix takes a GO vs. GO distance matrix and a gene-go-mapping file and makes a gene vs. go distance matrix based on the shortest distances found between each gene and go term. einarr 2007-05-15 18:15:51 +00:00
  • 1ab558248c Piping information through dataset -i works. Added names of planned features to the dataset script. einarr 2007-05-09 21:52:59 +00:00
  • 7272eb63d2 Working on a script to query datasets without starting fluents. einarr 2007-05-09 17:41:50 +00:00
  • ebe7621817 some biocondoctur utilities flatberg 2007-05-06 13:51:06 +00:00
  • f1301be67a go-distance update. einarr 2007-04-26 18:54:34 +00:00
  • a0faed2614 Forgot some ... flatberg 2007-04-24 17:21:40 +00:00
  • 34ae426c86 Added correlation plot and moved colorbar to plots flatberg 2007-04-24 17:17:31 +00:00
  • 90bb25eb55 added default mappable to None flatberg 2007-04-24 17:16:34 +00:00
  • 31ac569c3e Added colorbar shortcut flatberg 2007-04-24 17:04:29 +00:00
  • fefaffb2e3 go-distance seems to be able to calculate resnik now. Not asserted with calculations by hand. einarr 2007-04-04 19:08:50 +00:00
  • 28f0f53e8a go-distance script soon calculating resnik distances. einarr 2007-04-03 13:08:48 +00:00
  • a5c3a1f154 A couple of extra lines of code in a script. einarr 2007-03-27 13:02:22 +00:00
  • 728c334e8a ontology distance script now accumulates annotations correctly. einarr 2007-03-26 23:15:14 +00:00
  • 11eb3306b9 Works a bit better. einarr 2007-03-26 17:18:26 +00:00
  • 947cf8385f Annotations on yeast from Stanford mdb. flatberg 2007-03-23 20:51:04 +00:00
  • 0904a59310 Gene ontolgy distance script in C. Will hopefully speed up calculations when finished. einarr 2007-03-23 13:25:07 +00:00
  • 6f19fe1b4b Resnick distance matrix flatberg 2007-03-16 17:05:46 +00:00
  • 0eff457910 Added biological process info to the small smokers example, and a README file to explain the dataset, at least the non-trivial parts. einarr 2007-03-15 23:57:35 +00:00
  • 3dc1867be4 Added entrez-go-mapping that maps entrez IDs to GO terms based on a file of the form: affy_id ::: geneid_1 /// geneid_2 ::: go(bp) ::: go(cc) ::: go(mf) einarr 2007-03-15 23:47:24 +00:00
  • 6fe4ff3c59 Added scripts folder for small but useful scripts. einarr 2007-03-15 12:46:41 +00:00
  • b02773b4e6 pls loading plot now have correct name flatberg 2007-03-15 10:38:52 +00:00
  • dbe49b366d added import of networkx flatberg 2007-03-15 10:38:05 +00:00
  • f6696dfacc Added gobrowser to smalltest workflow. einarr 2007-03-14 21:08:56 +00:00
  • 1c48315a0f Added debug output. einarr 2007-03-14 17:26:40 +00:00
  • 438a268b1d Inserted visible header sort flatberg 2007-03-14 16:34:50 +00:00
  • 3d2492578e whitespace flatberg 2007-03-14 16:33:54 +00:00
  • 3bd21ab089 metric support flatberg 2007-03-14 16:33:16 +00:00
  • 48047f1395 Moved lots of stuff back to sandbox flatberg 2007-03-14 16:32:49 +00:00
  • 7f1f639ee7 Updates on metric, whitespace flatberg 2007-03-14 16:31:25 +00:00
  • 22f6e3284c whitespace flatberg 2007-03-14 16:30:18 +00:00
  • 818dc0b2b0 added a logger for constructor calls flatberg 2007-03-14 16:27:23 +00:00
  • 212da78933 correct comp update flatberg 2007-03-14 16:17:21 +00:00
  • 00dd3e8d9d added validation on identifiers input flatberg 2007-03-14 16:06:16 +00:00
  • 51435d9fdc Fixed dataset type to network flatberg 2007-03-14 10:27:08 +00:00
  • ac447546a2 Annotation file for dim: gene_id flatberg 2007-03-14 10:26:11 +00:00
  • a9981779a6 network of articles flatberg 2007-03-14 10:25:35 +00:00
  • 9cbefb5705 in write_ftsv: adjusted so it splits specifically on tab, whitespace allowed in annotations flatberg 2007-03-14 10:24:49 +00:00
  • 6cbf6d0689 Initial commit of small example test workflow flatberg 2007-03-13 15:24:20 +00:00
  • 6b2737efb9 Added a line. einarr 2007-03-09 14:33:09 +00:00
  • f61bc353a9 Typofix einarr 2007-03-09 14:30:40 +00:00
  • 5be2f1faf6 Initial import of Iris data flatberg 2007-03-04 21:00:39 +00:00
  • ae9a207a71 Added a tag column in the GO browser to help link it to selections. einarr 2007-03-01 19:13:13 +00:00
  • 442b5fed5f Moved all files to the smokers-small subdirectory. einarr 2007-03-01 19:12:40 +00:00
  • f31795ac2a Corrected erroneous checkin. einarr 2007-03-01 15:27:50 +00:00
  • e01dd578cd Preserves PYTHONPATH einarr 2007-03-01 15:27:24 +00:00
  • ff070e5312 Preserves PYTHONPATH. einarr 2007-03-01 15:26:38 +00:00
  • 28e6c52f78 Fixed bug with hidden dimensions. einarr 2007-03-01 15:06:33 +00:00
  • d699afa6a5 fixed bu when trying to drag anything over an empty view flatberg 2007-03-01 15:03:53 +00:00
  • f8f3bd712e Smoker example data flatberg 2007-03-01 15:01:30 +00:00
  • 6101bf850c Changed CategoryDataset ftsv files to be written with 0 and 1 instead of True and False. einarr 2007-02-28 16:33:11 +00:00
  • 89636962a7 Added Workflow.get_data_file_name() which returns the full path to a given data file, or None if the file does not exist. This is tested in the test workflow. einarr 2007-02-28 14:56:24 +00:00
  • 934640ea62 Searches for /etc/fluentsrc and ~/.fluents configuration files. Adds the home configuration variable. einarr 2007-02-28 14:07:33 +00:00
  • 281337251d Added selection of lines in network plot flatberg 2007-02-27 21:19:24 +00:00
  • 78183df0e9 Alignment of function boxes flatberg 2007-02-27 18:14:58 +00:00
  • b754a5df44 Update from change of plots/view flatberg 2007-02-27 16:31:18 +00:00
  • 61cfd00558 Division of plots -> view/plots flatberg 2007-02-27 16:28:03 +00:00
  • 059cddbc16 Division of plots -> view/plots flatberg 2007-02-27 16:27:39 +00:00
  • bf1ad1be87 Removed old help function. einarr 2007-02-27 16:25:48 +00:00
  • 1ba4bf5f82 Initial config parser support. einarr 2007-02-27 16:08:22 +00:00
  • 686a1fdcd1 network/venn plot now maximizes the space available flatberg 2007-02-27 15:42:27 +00:00
  • d27278241c oops ... (broken code fixed) flatberg 2007-02-27 15:08:00 +00:00
  • 4de65f1085 Clean up flatberg 2007-02-27 15:05:21 +00:00
  • f73a6db0ee Added ctrl+arrows to navigate between plots. einarr 2007-02-26 23:00:25 +00:00
  • eacb44f32a Removed "Edit" menu. einarr 2007-02-26 22:12:32 +00:00
  • d040f11c2f Added identifier list update on selection changed. einarr 2007-02-26 18:02:34 +00:00
  • 537dc9f0ec Cleanup of selection browser module. Added comments, fixed some bits of code. einarr 2007-02-26 14:35:31 +00:00
  • c0bbe24c39 No selections in scatter marker now updates to no selection instead of last selection flatberg 2007-02-26 12:11:28 +00:00
  • a6fbef9cfa scatter plot selected markers are now on top (visible) flatberg 2007-02-26 11:20:02 +00:00
  • 2f60d0663d Clean up of import statements flatberg 2007-02-26 09:08:50 +00:00
  • 5ed602f355 Lots of changes .... (new selector, mode updates, histogram selection, ++) flatberg 2007-02-26 08:00:36 +00:00
  • 3ee8439e07 Added selection listeners to plots in context menu flatberg 2007-02-26 07:58:33 +00:00
  • a614908436 Size of current selection is now updated in details flatberg 2007-02-23 11:12:03 +00:00
  • 41e8ed511b Fixed dim_cursor_changed to to use the correct treemodel, and added show/hide on selection details flatberg 2007-02-23 10:46:04 +00:00
  • 0d8702bb71 added show/hide on dimensions flatberg 2007-02-21 19:57:27 +00:00