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lingutln [Wed, 23 Nov 2011 21:02:47 +0000 (21:02 +0000)]
Save functionality. Done by Nikhil.
svn path=/; revision=219
elserj [Sat, 19 Nov 2011 00:06:37 +0000 (00:06 +0000)]
Added Venn diagram creation script, to be used with supercluster database
svn path=/; revision=218
lingutln [Thu, 17 Nov 2011 00:06:58 +0000 (00:06 +0000)]
Added some Modification to annotate box. Done by Nikhil.
svn path=/; revision=217
preecej [Tue, 15 Nov 2011 00:59:17 +0000 (00:59 +0000)]
Changed "term_name" to "is_synonym_of" in PO_term_search_response
svn path=/; revision=216
preecej [Mon, 14 Nov 2011 21:23:17 +0000 (21:23 +0000)]
Added more querystring options
svn path=/; revision=215
preecej [Mon, 14 Nov 2011 20:22:05 +0000 (20:22 +0000)]
Revised to make generically available via plantontology.org, also to add
synonym searching functionality
svn path=/; revision=214
lingutln [Mon, 14 Nov 2011 19:21:05 +0000 (19:21 +0000)]
Adding a label functionality. Done by Nikhil.
svn path=/; revision=213
lingutln [Mon, 7 Nov 2011 19:52:57 +0000 (19:52 +0000)]
Uploaded initial version of image annotation project
svn path=/; revision=212
rajar [Wed, 2 Nov 2011 21:46:59 +0000 (21:46 +0000)]
removed one file
svn path=/; revision=211
rajar [Wed, 2 Nov 2011 21:42:55 +0000 (21:42 +0000)]
Script to run TMHMM application
svn path=/; revision=210
rajar [Wed, 2 Nov 2011 21:41:32 +0000 (21:41 +0000)]
deleted
svn path=/; revision=209
rajar [Wed, 2 Nov 2011 21:39:40 +0000 (21:39 +0000)]
COMMAND TO RUN PREDOTAR
svn path=/; revision=208
rajar [Wed, 2 Nov 2011 21:33:03 +0000 (21:33 +0000)]
Script to run TMHMM application
svn path=/; revision=207
rajar [Wed, 2 Nov 2011 21:14:26 +0000 (21:14 +0000)]
Script to run TARGETP Aplication
svn path=/; revision=206
rajar [Wed, 2 Nov 2011 21:06:45 +0000 (21:06 +0000)]
svn path=/; revision=205
rajar [Wed, 2 Nov 2011 20:54:43 +0000 (20:54 +0000)]
Script to run TMHMM Application
svn path=/; revision=204
rajar [Wed, 2 Nov 2011 20:53:06 +0000 (20:53 +0000)]
File removed
svn path=/; revision=203
rajar [Wed, 2 Nov 2011 20:14:25 +0000 (20:14 +0000)]
Script to run Targetp application
svn path=/; revision=202
rajar [Tue, 1 Nov 2011 20:24:46 +0000 (20:24 +0000)]
Script to run TMMHMM
svn path=/; revision=201
preecej [Wed, 26 Oct 2011 21:45:53 +0000 (21:45 +0000)]
Cleanup...
svn path=/; revision=200
preecej [Wed, 26 Oct 2011 21:45:24 +0000 (21:45 +0000)]
Cleanup...
svn path=/; revision=199
preecej [Wed, 26 Oct 2011 21:33:46 +0000 (21:33 +0000)]
Cleanup time...
svn path=/; revision=198
lingutln [Tue, 25 Oct 2011 22:29:29 +0000 (22:29 +0000)]
test
svn path=/; revision=197
elserj [Tue, 25 Oct 2011 22:14:52 +0000 (22:14 +0000)]
restructuring of the jaiswal lab svn repo
svn path=/; revision=196
foxsa [Tue, 25 Oct 2011 20:24:16 +0000 (20:24 +0000)]
test file added 13:24
svn path=/; revision=195
foxsa [Tue, 25 Oct 2011 20:21:48 +0000 (20:21 +0000)]
test file added
svn path=/; revision=194
foxsa [Tue, 25 Oct 2011 20:20:26 +0000 (20:20 +0000)]
svn path=/; revision=193
foxsa [Tue, 25 Oct 2011 20:19:38 +0000 (20:19 +0000)]
svn path=/; revision=192
foxsa [Tue, 25 Oct 2011 20:15:50 +0000 (20:15 +0000)]
modified by sam fox
svn path=/; revision=191
preecej [Wed, 19 Oct 2011 00:11:18 +0000 (00:11 +0000)]
Mod'd the heat map "temperature" to apply evenly to all grouped paralogs that
map to a single original gene. This is clearer for the user.
svn path=/; revision=190
preecej [Tue, 18 Oct 2011 19:01:19 +0000 (19:01 +0000)]
update doc
svn path=/; revision=189
preecej [Tue, 18 Oct 2011 00:31:22 +0000 (00:31 +0000)]
Heat map feature complete.
svn path=/; revision=188
preecej [Mon, 17 Oct 2011 23:25:12 +0000 (23:25 +0000)]
More gradient heat map progress...
svn path=/; revision=187
preecej [Mon, 17 Oct 2011 22:10:01 +0000 (22:10 +0000)]
Adding gradient heat-map feature. In progress...
svn path=/; revision=186
preecej [Sat, 15 Oct 2011 01:14:27 +0000 (01:14 +0000)]
Completed gene symbol feature; working on heat map feature
svn path=/; revision=185
preecej [Fri, 14 Oct 2011 20:22:14 +0000 (20:22 +0000)]
minor adjustments to maize script; in progress: adding gene symbol
feature to gene swapper
svn path=/; revision=184
preecej [Wed, 5 Oct 2011 00:19:18 +0000 (00:19 +0000)]
Added maize classical gene name and symbol mapping script for POC
svn path=/; revision=183
elserj [Sat, 24 Sep 2011 00:26:26 +0000 (00:26 +0000)]
Added potato
svn path=/; revision=182
rajar [Wed, 14 Sep 2011 21:11:03 +0000 (21:11 +0000)]
initial import of Rajani's repo
svn path=/; revision=181
preecej [Thu, 8 Sep 2011 01:32:48 +0000 (01:32 +0000)]
fixed non-PMID: ref pub strip at line 291
svn path=/; revision=180
preecej [Wed, 7 Sep 2011 23:01:12 +0000 (23:01 +0000)]
paw_...: backed out the max file size option
Local...: added GO web service autocomplete reference
svn path=/; revision=179
preecej [Wed, 7 Sep 2011 22:30:23 +0000 (22:30 +0000)]
Updated test.TermSearch_JSON.php to use Test env vars
svn path=/; revision=178
preecej [Wed, 7 Sep 2011 22:27:22 +0000 (22:27 +0000)]
Making this file env-specific
svn path=/; revision=177
preecej [Wed, 7 Sep 2011 18:07:41 +0000 (18:07 +0000)]
Publication adjustments
svn path=/; revision=176
preecej [Sat, 3 Sep 2011 00:19:57 +0000 (00:19 +0000)]
Tweaked for oryza (refined multi-species handling)
svn path=/; revision=175
preecej [Fri, 2 Sep 2011 21:51:09 +0000 (21:51 +0000)]
Added Reference Publication page generation; modified ontology
provenance format
svn path=/; revision=174
preecej [Fri, 2 Sep 2011 01:32:04 +0000 (01:32 +0000)]
Added provenance for Gene Synonyms, Ontologies
svn path=/; revision=173
preecej [Sat, 27 Aug 2011 00:12:47 +0000 (00:12 +0000)]
Added more Evidence Code and Evidence functionality, GO web services,
and GO/PO web service term id lookup capabilities
svn path=/; revision=172
preecej [Fri, 26 Aug 2011 00:32:15 +0000 (00:32 +0000)]
Added GO web services in TermSearch_JSON. More XML doc output revisions
on paw_TranformForImport.
svn path=/; revision=171
preecej [Thu, 25 Aug 2011 00:23:16 +0000 (00:23 +0000)]
In progress; Revised ontology info, ontology references, evidence, evidence codes,
and gene synonyms. Generated XML pages for all except Publications.
That's next.
svn path=/; revision=170
preecej [Wed, 24 Aug 2011 01:29:34 +0000 (01:29 +0000)]
In progress; added handling for grouped ont term ids in gaf import, inc multiple gene
synonyms, evidence codes, evidence data (with_or_from), and publication
ids (db:reference PMID's). Need to complete by building corresponding wiki XML pages
and properties.
svn path=/; revision=169
preecej [Mon, 22 Aug 2011 23:47:25 +0000 (23:47 +0000)]
Changed Has_Evidence_Code to array; now allows multiple values per
ontological reference; also added to Annotation formand template display
svn path=/; revision=168
preecej [Mon, 22 Aug 2011 22:57:27 +0000 (22:57 +0000)]
whoops, don't want this one in there
svn path=/; revision=167
preecej [Mon, 22 Aug 2011 22:56:00 +0000 (22:56 +0000)]
Moved wiki config files and pruned all old versions in one fell swoop
svn path=/; revision=166
preecej [Mon, 22 Aug 2011 22:29:11 +0000 (22:29 +0000)]
holds proper db connex string for command-line PHP scripts like
flushJobs and refreshLinks
svn path=/; revision=165
preecej [Wed, 17 Aug 2011 23:57:05 +0000 (23:57 +0000)]
Includes indirect listing of db conection info
svn path=/; revision=164
preecej [Wed, 17 Aug 2011 23:51:23 +0000 (23:51 +0000)]
updates related to moving db connection strings to .conf files
svn path=/; revision=163
preecej [Wed, 17 Aug 2011 19:52:37 +0000 (19:52 +0000)]
Updated web service URLs
svn path=/; revision=162
preecej [Wed, 17 Aug 2011 19:48:35 +0000 (19:48 +0000)]
List of species used to drive data in an autocompletion list
svn path=/; revision=161
preecej [Wed, 17 Aug 2011 19:30:25 +0000 (19:30 +0000)]
Updated web service URLs
svn path=/; revision=160
preecej [Wed, 17 Aug 2011 19:03:08 +0000 (19:03 +0000)]
Official development copies of internal web services used by the wiki
svn path=/; revision=159
preecej [Wed, 17 Aug 2011 18:57:44 +0000 (18:57 +0000)]
svn path=/; revision=158
preecej [Wed, 17 Aug 2011 18:47:30 +0000 (18:47 +0000)]
Version of semantic_wiki/prototyping/TermSearch_JSON.php generalized for
broader use (outside the plant annotation wiki)
svn path=/; revision=157
preecej [Wed, 17 Aug 2011 17:48:52 +0000 (17:48 +0000)]
removed Gene Synonym Pair SIO and related properties
svn path=/; revision=156
preecej [Mon, 15 Aug 2011 20:32:48 +0000 (20:32 +0000)]
Added comments for future version of script; added verbose display of
original file's gene nodes (textlabel and xref id)
svn path=/; revision=155
preecej [Fri, 12 Aug 2011 23:23:28 +0000 (23:23 +0000)]
Added ability to map to multiple original gene boxes; added verbose
display and count of unmapped original genes
svn path=/; revision=154
preecej [Fri, 12 Aug 2011 20:03:53 +0000 (20:03 +0000)]
added commentary
svn path=/; revision=153
preecej [Fri, 12 Aug 2011 18:04:22 +0000 (18:04 +0000)]
perldoc edits
svn path=/; revision=152
preecej [Fri, 12 Aug 2011 17:44:05 +0000 (17:44 +0000)]
Changed refs from "paralog" to "homolog"; edited perldoc
svn path=/; revision=151
preecej [Thu, 11 Aug 2011 19:20:23 +0000 (19:20 +0000)]
Added options, set config defaults, hardened the code
svn path=/; revision=150
preecej [Thu, 11 Aug 2011 00:08:27 +0000 (00:08 +0000)]
Added creation of new groups when needed.
svn path=/; revision=149
preecej [Wed, 10 Aug 2011 22:26:37 +0000 (22:26 +0000)]
Added multiple paralog gene box illustration, coloring, and unique hexid
generation
svn path=/; revision=148
preecej [Wed, 10 Aug 2011 18:58:38 +0000 (18:58 +0000)]
Added more node attribute changes
svn path=/; revision=147
preecej [Wed, 10 Aug 2011 00:25:14 +0000 (00:25 +0000)]
added TODOs
svn path=/; revision=146
preecej [Wed, 10 Aug 2011 00:17:11 +0000 (00:17 +0000)]
Began modifying DataNodes for 1-to-1: added label prefix, added Comment
svn path=/; revision=145
preecej [Tue, 9 Aug 2011 19:59:58 +0000 (19:59 +0000)]
Testing...
svn path=/; revision=144
preecej [Tue, 9 Aug 2011 00:10:22 +0000 (00:10 +0000)]
Added GPML hex id hash, nodes_by_gene_id hash, and new nodes array. Revised gene swapping
algorithm and successfully tested node-swapping DOM approach all the way to file.
svn path=/; revision=143
preecej [Mon, 8 Aug 2011 20:07:56 +0000 (20:07 +0000)]
Removes pubs and pub refs from doc.
svn path=/; revision=142
preecej [Fri, 5 Aug 2011 23:14:12 +0000 (23:14 +0000)]
Added MH's gene counting code, changed gene hash tp accept 1-to-many
mappings, removed Biopax publication nodes in output file using XML:DOM
svn path=/; revision=141
preecej [Fri, 5 Aug 2011 19:33:44 +0000 (19:33 +0000)]
Separated locus and accession id vars; made each more flexible.
svn path=/; revision=140
preecej [Wed, 3 Aug 2011 22:24:36 +0000 (22:24 +0000)]
Set seed values for fresh import.
svn path=/; revision=139
preecej [Wed, 3 Aug 2011 21:10:35 +0000 (21:10 +0000)]
Just keeping the wiki code current
svn path=/; revision=138
preecej [Wed, 3 Aug 2011 19:06:06 +0000 (19:06 +0000)]
added folder to hold "static" wiki content pages, such as the Main Page
svn path=/; revision=137
preecej [Mon, 1 Aug 2011 20:31:23 +0000 (20:31 +0000)]
Added GPML read-in, STDOUT/file out/manipulation tests.
svn path=/; revision=136
preecej [Sat, 30 Jul 2011 00:42:34 +0000 (00:42 +0000)]
Adds simple read-in of csv gene-swapping file
svn path=/; revision=135
preecej [Fri, 29 Jul 2011 23:54:56 +0000 (23:54 +0000)]
Updated just before migration to Test.
svn path=/; revision=134
preecej [Fri, 29 Jul 2011 23:52:30 +0000 (23:52 +0000)]
Added before migrating to Test.
svn path=/; revision=133
preecej [Fri, 29 Jul 2011 23:41:31 +0000 (23:41 +0000)]
Added the planteome skin, built from the vector skin
svn path=/; revision=132
preecej [Fri, 29 Jul 2011 23:32:24 +0000 (23:32 +0000)]
Latest version of paw forms, just before migration to Test env.
svn path=/; revision=131
preecej [Fri, 29 Jul 2011 22:36:33 +0000 (22:36 +0000)]
Completed GAF import transformation script for scale testing.
svn path=/; revision=130
preecej [Fri, 29 Jul 2011 01:42:52 +0000 (01:42 +0000)]
Began XML doc write using XML::Writer
svn path=/; revision=129
preecej [Thu, 28 Jul 2011 21:37:04 +0000 (21:37 +0000)]
Added commentary amd config file read-in
svn path=/; revision=128
preecej [Thu, 28 Jul 2011 18:39:11 +0000 (18:39 +0000)]
Includes Mamatha's first updates to opt args
svn path=/; revision=127
preecej [Thu, 28 Jul 2011 18:36:18 +0000 (18:36 +0000)]
Completed data read-in of GAF file (paw_TransformForImport.pl)
svn path=/; revision=126
preecej [Tue, 26 Jul 2011 17:39:25 +0000 (17:39 +0000)]
New script for directly modifying PathVisio GPML files - swaps one
species' genes for another (after projection)
svn path=/; revision=125
preecej [Mon, 25 Jul 2011 23:46:47 +0000 (23:46 +0000)]
Began breaking out GAF from generic CSV, tab format.
svn path=/; revision=124
preecej [Sat, 23 Jul 2011 00:47:37 +0000 (00:47 +0000)]
Started adding GAF format input option to Rev 0.2
svn path=/; revision=123
preecej [Tue, 19 Jul 2011 22:42:53 +0000 (22:42 +0000)]
Minor query updates to better handle obsolete terms
svn path=/; revision=122
preecej [Fri, 15 Jul 2011 18:24:00 +0000 (18:24 +0000)]
Added a max return count of 50, filtered out OBSOLETE terms and any
terms not affiliated with the two branches of the PO (anatomy, and
growth & development stages).
svn path=/; revision=121
preecej [Fri, 15 Jul 2011 18:11:15 +0000 (18:11 +0000)]
Modified queries to provide more fields from the AmiGO db.
svn path=/; revision=120
projects / old-jaiswallab-svn / .git / log