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7ea87e646a Added DAG plot to gobrowser module and smokers workflow. Einar Ryeng 2007-07-23 17:02:28 +0000
155dfada5c iups Arnar Flatberg 2007-07-23 13:25:34 +0000
9db5991108 Arnar Flatberg 2007-07-20 15:48:59 +0000
98f53d3448 updates Arnar Flatberg 2007-07-20 12:32:54 +0000
7ee7aa968a Initial import Arnar Flatberg 2007-07-20 09:36:26 +0000
dd04e28a62 Query fix Arnar Flatberg 2007-07-05 18:49:24 +0000
850deeec0d Renamed gene identifers to gene_id Arnar Flatberg 2007-07-05 18:40:29 +0000
75c7c51708 DistanceToSelectionFunction Einar Ryeng 2007-07-05 18:36:59 +0000
3f5d45d7af Renamed smalltest workflow to smokers. Einar Ryeng 2007-07-05 18:24:45 +0000
fae096afe4 Changed workflow name from smalltest to smokers, because it is heavily based on the smokers dataset. Einar Ryeng 2007-07-05 13:20:52 +0000
a503ffcdf8 Fixed linewidth in selection in scatter plots. Einar Ryeng 2007-07-05 11:57:21 +0000
d29013a863 T-test now works, and outputs a histogram as well as t-values and p-values. Einar Ryeng 2007-07-03 16:25:38 +0000
99987999db Broke up a too long line. Einar Ryeng 2007-07-02 09:54:56 +0000
884804c49a Added a dummy for the t-test function. Will be updated when I have access to my office computer tomorrow. Einar Ryeng 2007-06-28 21:48:13 +0000
b637a5badc Changed /usr/bin/python2.4 to /usr/bin/python, and hope that 2.5 will not have trouble running the app. Einar Ryeng 2007-06-28 21:42:18 +0000
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. Einar Ryeng 2007-06-28 21:33:09 +0000
7b20f44fef Added a GO similarity function that does not do anything useful yet. Einar Ryeng 2007-06-22 15:37:59 +0000
e5cd8a8077 Started on a function to enhance gene lists by using GO similarities. Not in a usable state. Einar Ryeng 2007-06-22 15:37:22 +0000
68cc583d2c Added common_dimensions(ds) that lists common dimensions between two datasets. Einar Ryeng 2007-06-22 15:35:45 +0000
ff8833a22c Added read functions for the medium and large smokers sets. Einar Ryeng 2007-06-21 10:28:10 +0000
d6298a2d99 Ensures that the GO is only loaded once. Einar Ryeng 2007-06-21 10:26:35 +0000
ff2c42902f Commented out some log lines that just cluttered the log. Einar Ryeng 2007-06-21 10:25:17 +0000
2eb3d71a5d Moved data/smokers-med to data/smokers-medium. Einar Ryeng 2007-05-16 15:35:25 +0000
91032d729e Some more smoker data Arnar Flatberg 2007-05-16 11:45:43 +0000
7bdfdea23b Added -d option to get all identifiers along a single dimension. Einar Ryeng 2007-05-16 10:30:54 +0000
c7bfefe358 Fixed resnik distances. Einar Ryeng 2007-05-15 18:16:07 +0000
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. Einar Ryeng 2007-05-15 18:15:51 +0000
1ab558248c Piping information through dataset -i works. Added names of planned features to the dataset script. Einar Ryeng 2007-05-09 21:52:59 +0000
7272eb63d2 Working on a script to query datasets without starting fluents. Einar Ryeng 2007-05-09 17:41:50 +0000
ebe7621817 some biocondoctur utilities Arnar Flatberg 2007-05-06 13:51:06 +0000
f1301be67a go-distance update. Einar Ryeng 2007-04-26 18:54:34 +0000
a0faed2614 Forgot some ... Arnar Flatberg 2007-04-24 17:21:40 +0000
34ae426c86 Added correlation plot and moved colorbar to plots Arnar Flatberg 2007-04-24 17:17:31 +0000
90bb25eb55 added default mappable to None Arnar Flatberg 2007-04-24 17:16:34 +0000
31ac569c3e Added colorbar shortcut Arnar Flatberg 2007-04-24 17:04:29 +0000
fefaffb2e3 go-distance seems to be able to calculate resnik now. Not asserted with calculations by hand. Einar Ryeng 2007-04-04 19:08:50 +0000
28f0f53e8a go-distance script soon calculating resnik distances. Einar Ryeng 2007-04-03 13:08:48 +0000
a5c3a1f154 A couple of extra lines of code in a script. Einar Ryeng 2007-03-27 13:02:22 +0000
728c334e8a ontology distance script now accumulates annotations correctly. Einar Ryeng 2007-03-26 23:15:14 +0000
11eb3306b9 Works a bit better. Einar Ryeng 2007-03-26 17:18:26 +0000
947cf8385f Annotations on yeast from Stanford mdb. Arnar Flatberg 2007-03-23 20:51:04 +0000
0904a59310 Gene ontolgy distance script in C. Will hopefully speed up calculations when finished. Einar Ryeng 2007-03-23 13:25:07 +0000
6f19fe1b4b Resnick distance matrix Arnar Flatberg 2007-03-16 17:05:46 +0000
0eff457910 Added biological process info to the small smokers example, and a README file to explain the dataset, at least the non-trivial parts. Einar Ryeng 2007-03-15 23:57:35 +0000
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) Einar Ryeng 2007-03-15 23:47:24 +0000
6fe4ff3c59 Added scripts folder for small but useful scripts. Einar Ryeng 2007-03-15 12:46:41 +0000
b02773b4e6 pls loading plot now have correct name Arnar Flatberg 2007-03-15 10:38:52 +0000
dbe49b366d added import of networkx Arnar Flatberg 2007-03-15 10:38:05 +0000
f6696dfacc Added gobrowser to smalltest workflow. Einar Ryeng 2007-03-14 21:08:56 +0000
1c48315a0f Added debug output. Einar Ryeng 2007-03-14 17:26:40 +0000
438a268b1d Inserted visible header sort Arnar Flatberg 2007-03-14 16:34:50 +0000
3d2492578e whitespace Arnar Flatberg 2007-03-14 16:33:54 +0000
3bd21ab089 metric support Arnar Flatberg 2007-03-14 16:33:16 +0000
48047f1395 Moved lots of stuff back to sandbox Arnar Flatberg 2007-03-14 16:32:49 +0000
7f1f639ee7 Updates on metric, whitespace Arnar Flatberg 2007-03-14 16:31:25 +0000
22f6e3284c whitespace Arnar Flatberg 2007-03-14 16:30:18 +0000
818dc0b2b0 added a logger for constructor calls Arnar Flatberg 2007-03-14 16:27:23 +0000
212da78933 correct comp update Arnar Flatberg 2007-03-14 16:17:21 +0000
00dd3e8d9d added validation on identifiers input Arnar Flatberg 2007-03-14 16:06:16 +0000
51435d9fdc Fixed dataset type to network Arnar Flatberg 2007-03-14 10:27:08 +0000
ac447546a2 Annotation file for dim: gene_id Arnar Flatberg 2007-03-14 10:26:11 +0000
a9981779a6 network of articles Arnar Flatberg 2007-03-14 10:25:35 +0000
9cbefb5705 in write_ftsv: adjusted so it splits specifically on tab, whitespace allowed in annotations Arnar Flatberg 2007-03-14 10:24:49 +0000
6cbf6d0689 Initial commit of small example test workflow Arnar Flatberg 2007-03-13 15:24:20 +0000
6b2737efb9 Added a line. Einar Ryeng 2007-03-09 14:33:09 +0000
f61bc353a9 Typofix Einar Ryeng 2007-03-09 14:30:40 +0000
5be2f1faf6 Initial import of Iris data Arnar Flatberg 2007-03-04 21:00:39 +0000
ae9a207a71 Added a tag column in the GO browser to help link it to selections. Einar Ryeng 2007-03-01 19:13:13 +0000
442b5fed5f Moved all files to the smokers-small subdirectory. Einar Ryeng 2007-03-01 19:12:40 +0000
f31795ac2a Corrected erroneous checkin. Einar Ryeng 2007-03-01 15:27:50 +0000
e01dd578cd Preserves PYTHONPATH Einar Ryeng 2007-03-01 15:27:24 +0000
ff070e5312 Preserves PYTHONPATH. Einar Ryeng 2007-03-01 15:26:38 +0000
28e6c52f78 Fixed bug with hidden dimensions. Einar Ryeng 2007-03-01 15:06:33 +0000
d699afa6a5 fixed bu when trying to drag anything over an empty view Arnar Flatberg 2007-03-01 15:03:53 +0000
f8f3bd712e Smoker example data Arnar Flatberg 2007-03-01 15:01:30 +0000
6101bf850c Changed CategoryDataset ftsv files to be written with 0 and 1 instead of True and False. Einar Ryeng 2007-02-28 16:33:11 +0000
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. Einar Ryeng 2007-02-28 14:56:24 +0000
934640ea62 Searches for /etc/fluentsrc and ~/.fluents configuration files. Adds the home configuration variable. Einar Ryeng 2007-02-28 14:07:33 +0000
281337251d Added selection of lines in network plot Arnar Flatberg 2007-02-27 21:19:24 +0000
78183df0e9 Alignment of function boxes Arnar Flatberg 2007-02-27 18:14:58 +0000
b754a5df44 Update from change of plots/view Arnar Flatberg 2007-02-27 16:31:18 +0000
61cfd00558 Division of plots -> view/plots Arnar Flatberg 2007-02-27 16:28:03 +0000
059cddbc16 Division of plots -> view/plots Arnar Flatberg 2007-02-27 16:27:39 +0000
bf1ad1be87 Removed old help function. Einar Ryeng 2007-02-27 16:25:48 +0000
1ba4bf5f82 Initial config parser support. Einar Ryeng 2007-02-27 16:08:22 +0000
686a1fdcd1 network/venn plot now maximizes the space available Arnar Flatberg 2007-02-27 15:42:27 +0000
d27278241c oops ... (broken code fixed) Arnar Flatberg 2007-02-27 15:08:00 +0000
4de65f1085 Clean up Arnar Flatberg 2007-02-27 15:05:21 +0000
f73a6db0ee Added ctrl+arrows to navigate between plots. Einar Ryeng 2007-02-26 23:00:25 +0000
eacb44f32a Removed "Edit" menu. Einar Ryeng 2007-02-26 22:12:32 +0000
d040f11c2f Added identifier list update on selection changed. Einar Ryeng 2007-02-26 18:02:34 +0000
537dc9f0ec Cleanup of selection browser module. Added comments, fixed some bits of code. Einar Ryeng 2007-02-26 14:35:31 +0000
c0bbe24c39 No selections in scatter marker now updates to no selection instead of last selection Arnar Flatberg 2007-02-26 12:11:28 +0000
a6fbef9cfa scatter plot selected markers are now on top (visible) Arnar Flatberg 2007-02-26 11:20:02 +0000
2f60d0663d Clean up of import statements Arnar Flatberg 2007-02-26 09:08:50 +0000
5ed602f355 Lots of changes .... (new selector, mode updates, histogram selection, ++) Arnar Flatberg 2007-02-26 08:00:36 +0000
3ee8439e07 Added selection listeners to plots in context menu Arnar Flatberg 2007-02-26 07:58:33 +0000
a614908436 Size of current selection is now updated in details Arnar Flatberg 2007-02-23 11:12:03 +0000
41e8ed511b Fixed dim_cursor_changed to to use the correct treemodel, and added show/hide on selection details Arnar Flatberg 2007-02-23 10:46:04 +0000
0d8702bb71 added show/hide on dimensions Arnar Flatberg 2007-02-21 19:57:27 +0000

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