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Rev Chgset Date Author Log Message
(edit) @318 [318] 07/14/10 20:37:54 t updated download site to lyorn
(edit) @317 [317] 02/14/10 22:35:05 t fixed gcc compilation errors by adding stdlib.h include
(edit) @316 [316] 05/21/09 19:30:59 t updated for latest Python
(edit) @315 [315] 02/16/09 08:49:59 t whoops, fixed to use eq 4, Stormo, 2000.
(edit) @314 [314] 02/16/09 07:50:40 t an example of how to correct for bg nts
(edit) @313 [313] 08/25/08 08:45:12 t updated for MSU course
(edit) @312 [312] 07/01/08 08:03:05 t updated with video link & paper ref
(edit) @311 [311] 05/05/08 10:57:51 t added some motif stuff
(edit) @310 [310] 05/05/08 10:08:06 t added motif searching, better zoom/translation
(edit) @309 [309] 05/05/08 03:00:08 t initial user interface
(edit) @308 [308] 05/04/08 00:37:34 t some initial useful scripts to load in the data
(edit) @307 [307] 05/03/08 20:36:24 t added vertex/ working space
(edit) @306 [306] 03/09/08 22:46:57 t more
(edit) @305 [305] 03/09/08 22:40:07 t another class project/hw
(edit) @303 [303] 02/05/08 09:19:57 t fixed motif scoring bug, rearranged deck chairs
(edit) @301 [301] 02/05/08 09:03:17 t reverse merge (why is this necessary !?)
(edit) @299 [299] 02/05/08 01:40:05 t fixed some size stuff; misc docstring updates.
(edit) @298 [298] 02/01/08 13:27:21 t fixed details for RawPWMMotifs
(edit) @297 [297] 02/01/08 01:39:40 t changed simple_key to consensus, simplified library display. am I done …
(edit) @296 [296] 02/01/08 01:25:30 t display consensus for imported motifs, too
(edit) @295 [295] 02/01/08 01:22:17 t fixed stupid searching NotImplementedError?
(edit) @294 [294] 02/01/08 01:20:00 t fixed batch export; commented out batch import.
(edit) @293 [293] 02/01/08 01:12:31 t JASPAR format parsing now works.
(edit) @292 [292] 02/01/08 01:11:55 t uncommon dup session error now just logs you out
(edit) @291 [291] 02/01/08 00:08:14 t added 'palindromic' flag.
(edit) @290 [290] 01/31/08 23:22:09 t a bit of sequence cleanup
(edit) @289 [289] 01/31/08 18:43:05 t added simple site soring system.
(edit) @288 [288] 01/31/08 03:30:31 t added in uniform statistics calculation, allowed user to set preferred A/T …
(edit) @287 [287] 01/31/08 02:09:37 t cleaned up the motif dir a bit
(edit) @286 [286] 01/30/08 02:09:41 t miscellaneous cleanup; added "Raw PWM Motif" for imported motif types; …
(edit) @285 [285] 01/30/08 02:08:46 t changed assert to a (more informative) Exception
(edit) @284 [284] 01/30/08 01:25:59 t stopped doing the database drop & sped up tests dramatically. may cause …
(edit) @283 [283] 01/28/08 01:14:05 t added notes, color field (still unused), and 'combine' selectbox.
(edit) @282 [282] 01/28/08 00:43:11 t redirect to login page (with 'follow' URL) if session expires. w00t.
(edit) @281 [281] 01/26/08 23:02:35 t - added /style CSS; - gussied up the canal.templates functions, added …
(edit) @280 [280] 01/22/08 22:32:01 t added batch export
(edit) @279 [279] 01/21/08 23:59:50 t a number of minor fixes to the motif searching stuff, courtesy of erich.
(edit) @278 [278] 01/21/08 00:11:02 t minor HTML changes; simple test(s) of the edit forms.
(edit) @277 [277] 01/20/08 23:58:11 t finished adding edit capabilities.
(edit) @276 [276] 01/20/08 22:38:34 t added start/stop arguments to detail views
(edit) @275 [275] 01/20/08 02:14:50 t minor cleanup & test fix
(edit) @274 [274] 01/20/08 02:09:51 t added svn ignore on *.pyc
(edit) @273 [273] 01/20/08 02:03:59 t fixed get_motifs; added PDF download.
(edit) @272 [272] 01/20/08 01:49:16 t added bitmap display of motifs
(edit) @271 [271] 01/19/08 03:21:05 t fixed e-mail fn test
(edit) @270 [270] 01/19/08 03:15:45 t display/export PWM matches
(edit) @269 [269] 01/19/08 02:51:20 t interface to build PWM from list of input sites
(edit) @268 [268] 01/19/08 01:39:59 t some more tests
(edit) @267 [267] 01/19/08 01:34:45 t some fixes, some tests.
(edit) @266 [266] 01/19/08 01:09:31 t added simple motif search of a sequence
(edit) @265 [265] 01/18/08 23:21:27 t basic motif library; right now, only IUPAC motifs
(edit) @264 [264] 01/18/08 23:18:29 t quixote imports
(edit) @263 [263] 01/18/08 23:15:42 t updated mailserver, e-mail addy
(edit) @262 [262] 01/03/08 19:21:22 t length fix, I think
(edit) @261 [261] 12/19/07 02:57:38 t start of a server-side motif library/searching interface
(edit) @259 [259] 12/19/07 00:10:52 t added 'make_pfm', changed 'make_PWM' to 'make_pwm', switched to …
(edit) @258 [258] 12/12/07 14:01:12 t some code for profiling
(edit) @257 [257] 12/12/07 12:50:26 t doc renaming, updating a bit
(edit) @256 [256] 12/12/07 12:37:42 t fixed find_exact and find_iupac examples
(edit) @255 [255] 12/12/07 03:04:47 t removed debugging prints
(edit) @254 [254] 12/12/07 03:00:51 t Added offsets into the mess; miscellaneous threading cleanup
(edit) @253 [253] 12/12/07 01:51:26 t fixed a newly introduced memory leak & made tests work
(edit) @252 [252] 12/12/07 01:35:18 t added a calc_score function to the python EnergyOperator?, + test; added …
(edit) @251 [251] 12/11/07 23:10:53 t added doctest intro, updated index
(edit) @250 [250] 12/11/07 23:08:56 t removed requirement for setuptools
(edit) @247 [247] 12/09/07 22:26:10 t updated test version requirement
(edit) @246 [246] 12/09/07 22:22:50 t fixed? -fPIC requirement, courtesy of Humberto Ortiz-Zuazaga
(edit) @245 [245] 12/09/07 22:17:21 t updated copyright notice
(edit) @244 [244] 12/09/07 22:11:29 t added TODO item about running doctests; added a str function to both PWMs …
(edit) @243 [243] 12/09/07 17:09:42 t added build functions
(edit) @242 [242] 12/09/07 15:55:37 t bumped version # to 0.8.1
(edit) @241 [241] 12/09/07 15:38:44 t added _motility.find_exact, fixed minimum value calculation to properly …
(edit) @240 [240] 11/12/07 00:21:17 t fixed by Humberto Ortiz Zuazaga for compiling just motility.
(edit) @239 [239] 09/25/07 23:41:50 t fixed README typo; fixed variable rename in test-queue; included test for …
(edit) @237 [237] 07/16/07 11:51:53 t Web site updated
(edit) @235 [235] 05/28/07 13:14:16 t removed biopython 'require', quixote 'require'.
(edit) @233 [233] 05/28/07 12:52:30 t added thirdparty tag to some new tests that require external binaries
(edit) @232 [232] 05/28/07 12:48:20 t bumped version number
(edit) @231 [231] 05/28/07 11:28:22 t debugged nasty object manager bug; refactored some test code; added in …
(edit) @230 [230] 05/28/07 11:25:46 t ignore build stuff
(edit) @229 [229] 05/28/07 11:25:03 t added documentation, build file ignore
(edit) @228 [228] 05/27/07 16:14:04 t switched over to using my own blastparser, instead of BioPython?'s. …
(edit) @227 [227] 05/27/07 13:40:50 t simplified BLAST analysis page a bit; added in a 'dump' debugging …
(edit) @226 [226] 05/27/07 12:36:09 t EditBlast?.init now properly calls BaseEditHandler?.init; added in a …
(edit) @225 [225] 05/27/07 12:34:01 t added 'force' option to 'hide folder' function, for test purposes
(edit) @224 [224] 05/27/07 12:33:39 t generalized ConfigParser? error handler
(edit) @223 [223] 05/27/07 12:00:40 t added show_command option
(edit) @222 [222] 05/26/07 16:12:14 t added a few more tests for the seqcomp export functionality.
(edit) @221 [221] 05/26/07 15:56:03 t initial seqcomp analysis export code.
(edit) @220 [220] 05/26/07 15:55:25 t added (and then commented out) 'exit_after_requests' parameter.
(edit) @219 [219] 05/26/07 15:45:45 t some basic dependency/version tests; included paircomp.
(edit) @218 [218] 05/25/07 16:47:56 t added an iterator interface to Comparison, and added slots to …
(edit) @217 [217] 05/23/07 21:00:46 t added generic Publisher/FCGI cleanup hook; maybe SCGI will even pay …
(edit) @215 [215] 05/23/07 14:10:50 t added a more informative message than "it failed" when trying to add an …
(edit) @214 [214] 04/04/07 10:44:14 t Fixed an exception-handling problem & cleaned up some free->delete issues.
(edit) @212 [212] 03/30/07 17:34:53 t updated cygwin1.dll to match that of the compile server
(edit) @211 [211] 03/30/07 16:58:12 t fixed EOL problem in dist-making script.
(edit) @209 [209] 03/30/07 10:56:44 t added in some assertion checking for dna sequence type
(edit) @208 [208] 03/29/07 17:31:51 t removed vista analysis; fixed problem with non-empty queue in …
(edit) @207 [207] 03/29/07 16:55:48 t added in size display hack, with (some) tests for pairwise analysis views.
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