algorithm
8 years agoJava Main function master
Andreas Maunz [Fri, 28 Sep 2012 10:54:46 +0000 (12:54 +0200)]
Java Main function

8 years agoJava doc
Andreas Maunz [Thu, 20 Sep 2012 08:20:59 +0000 (10:20 +0200)]
Java doc

8 years agoCDK
Andreas Maunz [Wed, 19 Sep 2012 13:56:00 +0000 (15:56 +0200)]
CDK

8 years agoJava
Andreas Maunz [Wed, 19 Sep 2012 13:55:37 +0000 (15:55 +0200)]
Java

8 years agoJava
Andreas Maunz [Wed, 19 Sep 2012 09:57:02 +0000 (11:57 +0200)]
Java

8 years agoAdded cache switch for bbrc-sample WS
Andreas Maunz [Fri, 10 Aug 2012 09:20:23 +0000 (11:20 +0200)]
Added cache switch for bbrc-sample WS

8 years agoMerge branch 'release/v3.2.0' v4.0.0
rautenberg [Fri, 13 Jul 2012 07:36:44 +0000 (09:36 +0200)]
Merge branch 'release/v3.2.0'

8 years agoswitch to opentox-ruby 4.0.0, add to ChangeLog release/v3.2.0
rautenberg [Thu, 12 Jul 2012 11:38:08 +0000 (13:38 +0200)]
switch to opentox-ruby 4.0.0, add to ChangeLog

8 years agoswitch to opentox-ruby 4.0.0, add to ChangeLog
rautenberg [Thu, 12 Jul 2012 11:36:51 +0000 (13:36 +0200)]
switch to opentox-ruby 4.0.0, add to ChangeLog

8 years agoAdded subjectids.
David Vorgrimmler [Wed, 20 Jun 2012 12:35:48 +0000 (14:35 +0200)]
Added subjectids.

8 years agoAdded subjectid for A&A.
David Vorgrimmler [Tue, 19 Jun 2012 12:12:58 +0000 (14:12 +0200)]
Added subjectid for A&A.

8 years agoAdded missing subjectid.
David Vorgrimmler [Tue, 19 Jun 2012 07:37:12 +0000 (09:37 +0200)]
Added missing subjectid.

8 years agoChanged feature uri and p_value in match.
David Vorgrimmler [Mon, 11 Jun 2012 10:20:03 +0000 (12:20 +0200)]
Changed feature uri and p_value in match.

8 years agoMerge branch 'bbrc-sample' into development
David Vorgrimmler [Tue, 5 Jun 2012 14:04:32 +0000 (16:04 +0200)]
Merge branch 'bbrc-sample' into development

8 years agoAdded GET for match bbrc-sample
Andreas Maunz [Thu, 24 May 2012 06:36:45 +0000 (08:36 +0200)]
Added GET for match

8 years agoUsing OOB estimated p-Values for feature metadata
Andreas Maunz [Wed, 23 May 2012 09:00:23 +0000 (11:00 +0200)]
Using OOB estimated p-Values for feature metadata

8 years agoCorrected LAST effect calculation
Andreas Maunz [Mon, 21 May 2012 13:21:46 +0000 (15:21 +0200)]
Corrected LAST effect calculation

8 years agoBBRC service: simplified effect calculation
Andreas Maunz [Mon, 21 May 2012 13:10:08 +0000 (15:10 +0200)]
BBRC service: simplified effect calculation

8 years agoChisq estimation for /match
Andreas Maunz [Mon, 21 May 2012 11:58:32 +0000 (13:58 +0200)]
Chisq estimation for /match

8 years agoSupport for Chisq estimation method
Andreas Maunz [Mon, 21 May 2012 06:56:14 +0000 (08:56 +0200)]
Support for Chisq estimation method

8 years agorenaming
Andreas Maunz [Wed, 16 May 2012 14:39:00 +0000 (16:39 +0200)]
renaming

8 years agoAdded support for backbone-false
Andreas Maunz [Wed, 16 May 2012 12:32:58 +0000 (14:32 +0200)]
Added support for backbone-false

8 years agomatching service uses last-utils
Andreas Maunz [Mon, 14 May 2012 11:46:24 +0000 (13:46 +0200)]
matching service uses last-utils

8 years agoAdded random seed to bbrc sample.
David Vorgrimmler [Wed, 9 May 2012 15:08:18 +0000 (17:08 +0200)]
Added random seed to bbrc sample.

8 years agoEmitting stripped patterns
Andreas Maunz [Wed, 9 May 2012 11:18:17 +0000 (13:18 +0200)]
Emitting stripped patterns

8 years agoSupporting merge time in metadata
Andreas Maunz [Tue, 8 May 2012 14:42:35 +0000 (16:42 +0200)]
Supporting merge time in metadata

8 years agoAdded metadata: minfreq and nr_hits
Andreas Maunz [Tue, 8 May 2012 12:48:20 +0000 (14:48 +0200)]
Added metadata: minfreq and nr_hits

8 years agoMerge branch 'bbrc-sample' of github.com:opentox/algorithm into bbrc-sample
David Vorgrimmler [Tue, 8 May 2012 09:27:29 +0000 (11:27 +0200)]
Merge branch 'bbrc-sample' of github.com:opentox/algorithm into bbrc-sample

Conflicts:
fminer.rb

8 years agoAdded parameters to dataset metadata.
David Vorgrimmler [Tue, 8 May 2012 09:24:40 +0000 (11:24 +0200)]
Added parameters to dataset metadata.

8 years agoFixed r quit
Andreas Maunz [Tue, 8 May 2012 06:28:28 +0000 (08:28 +0200)]
Fixed r quit

8 years agoRemoved debug
Andreas Maunz [Tue, 8 May 2012 06:18:04 +0000 (08:18 +0200)]
Removed debug

8 years agoBetter comments
Andreas Maunz [Mon, 7 May 2012 13:31:22 +0000 (15:31 +0200)]
Better comments

8 years agoEmbedded R code
Andreas Maunz [Mon, 7 May 2012 06:36:18 +0000 (08:36 +0200)]
Embedded R code

8 years agoAdded bbrc-sample as a submodule
Andreas Maunz [Fri, 4 May 2012 12:12:37 +0000 (14:12 +0200)]
Added bbrc-sample as a submodule

8 years agoReverted gitmodules
Andreas Maunz [Fri, 4 May 2012 12:10:21 +0000 (14:10 +0200)]
Reverted gitmodules

8 years agoCleaner parameter handling for sampling
Andreas Maunz [Fri, 4 May 2012 11:58:53 +0000 (13:58 +0200)]
Cleaner parameter handling for sampling

8 years agoAdded bbrc-sample as submodule
Andreas Maunz [Fri, 4 May 2012 11:57:44 +0000 (13:57 +0200)]
Added bbrc-sample as submodule

8 years agoInitial commit
Andreas Maunz [Thu, 3 May 2012 14:33:32 +0000 (16:33 +0200)]
Initial commit

8 years agoBugfix. Missing ":" for add_uri param.
davor [Thu, 26 Apr 2012 11:00:20 +0000 (13:00 +0200)]
Bugfix. Missing ":" for add_uri param.

8 years agoRemoved URI.escape
David Vorgrimmler [Mon, 23 Apr 2012 13:12:12 +0000 (15:12 +0200)]
Removed URI.escape

8 years agoUndo changes (wrong branch).
davor [Fri, 20 Apr 2012 10:14:53 +0000 (13:14 +0300)]
Undo changes (wrong branch).

8 years agoAdded pc / jl changes.
davor [Fri, 20 Apr 2012 10:14:15 +0000 (13:14 +0300)]
Added pc / jl changes.

8 years agoAdded pc/jl entry.
davor [Fri, 20 Apr 2012 10:09:12 +0000 (13:09 +0300)]
Added pc/jl entry.

8 years agoURI encoding of prediction feature removed again
David Vorgrimmler [Fri, 20 Apr 2012 09:09:02 +0000 (11:09 +0200)]
URI encoding of prediction feature removed again

Conflicts:

README.md

8 years agoMerge branch 'pc_unified_from_jl' into development
David Vorgrimmler [Wed, 18 Apr 2012 14:13:37 +0000 (16:13 +0200)]
Merge branch 'pc_unified_from_jl' into development

8 years agoNow fingerprints, activities, compounds have the same keys and order pc_unified_from_jl
David Vorgrimmler [Wed, 18 Apr 2012 09:14:43 +0000 (11:14 +0200)]
Now fingerprints, activities, compounds have the same keys and order

8 years agoNow fixes are more readable.
David Vorgrimmler [Tue, 17 Apr 2012 14:03:22 +0000 (16:03 +0200)]
Now fixes are more readable.

8 years agoBugfixes: Handling lib and pc_type
David Vorgrimmler [Tue, 17 Apr 2012 13:53:04 +0000 (15:53 +0200)]
Bugfixes: Handling lib and pc_type

8 years agoImproved debug out
Andreas Maunz [Tue, 17 Apr 2012 12:46:41 +0000 (14:46 +0200)]
Improved debug out

8 years agoAdded min_sim transform to cosine space
Andreas Maunz [Fri, 13 Apr 2012 14:10:23 +0000 (16:10 +0200)]
Added min_sim transform to cosine space

8 years agoMerge branch 'jl' into pc_unified_from_jl
Andreas Maunz [Fri, 13 Apr 2012 13:09:02 +0000 (15:09 +0200)]
Merge branch 'jl' into pc_unified_from_jl

Conflicts:
lazar.rb

8 years agoUpdated README
Andreas Maunz [Fri, 13 Apr 2012 08:14:34 +0000 (10:14 +0200)]
Updated README

8 years agoURI encoding of prediction feature removed again
Andreas Maunz [Fri, 13 Apr 2012 07:33:33 +0000 (09:33 +0200)]
URI encoding of prediction feature removed again

8 years agoMerge branch 'hotfix/metadata_fix' into development
rautenberg [Thu, 12 Apr 2012 09:58:53 +0000 (11:58 +0200)]
Merge branch 'hotfix/metadata_fix' into development

8 years agoMerge branch 'hotfix/metadata_fix' metadata_fix
rautenberg [Thu, 12 Apr 2012 09:58:28 +0000 (11:58 +0200)]
Merge branch 'hotfix/metadata_fix'

8 years agoMajor bug fixed: order of compounds was unsure in transform.rb jl
Andreas Maunz [Thu, 12 Apr 2012 09:52:27 +0000 (11:52 +0200)]
Major bug fixed: order of compounds was unsure in transform.rb

8 years agoFixed params to feature_type
Andreas Maunz [Thu, 12 Apr 2012 08:12:56 +0000 (10:12 +0200)]
Fixed params to feature_type

8 years agoFix in Metadata generation
rautenberg [Thu, 12 Apr 2012 07:56:23 +0000 (09:56 +0200)]
Fix in Metadata generation

8 years agoFixed param name to prediction_feature
Andreas Maunz [Thu, 12 Apr 2012 07:49:44 +0000 (09:49 +0200)]
Fixed param name to prediction_feature

8 years agoFixed POST dest to /fs/rfe
Andreas Maunz [Thu, 12 Apr 2012 07:48:41 +0000 (09:48 +0200)]
Fixed POST dest to /fs/rfe

8 years agoRelaxed YAML check
Andreas Maunz [Thu, 12 Apr 2012 07:47:34 +0000 (09:47 +0200)]
Relaxed YAML check

8 years agoChecking training compounds exceed features
Andreas Maunz [Thu, 12 Apr 2012 07:21:24 +0000 (09:21 +0200)]
Checking training compounds exceed features

8 years agoUpdate doc
Andreas Maunz [Wed, 11 Apr 2012 14:59:02 +0000 (16:59 +0200)]
Update doc

8 years agoMerge branch 'jl' into pc_unified_from_jl
Andreas Maunz [Wed, 11 Apr 2012 11:32:36 +0000 (13:32 +0200)]
Merge branch 'jl' into pc_unified_from_jl

8 years agopc_type and lib autodetection from feature dataset
Andreas Maunz [Wed, 11 Apr 2012 11:26:46 +0000 (13:26 +0200)]
pc_type and lib autodetection from feature dataset

8 years agoAdded common value_map routine to wrapper
Andreas Maunz [Tue, 10 Apr 2012 12:05:40 +0000 (14:05 +0200)]
Added common value_map routine to wrapper

8 years agoRemoved value_map from params
Andreas Maunz [Tue, 10 Apr 2012 11:32:57 +0000 (13:32 +0200)]
Removed value_map from params

8 years agoMerge branch 'development' into jl
davor [Tue, 10 Apr 2012 07:45:33 +0000 (09:45 +0200)]
Merge branch 'development' into jl

8 years agoMerge commit 'd243f8e9bebff49899cd510e83be15abe8741cc8' into development
davor [Tue, 10 Apr 2012 07:36:07 +0000 (09:36 +0200)]
Merge commit 'd243f8e9bebff49899cd510e83be15abe8741cc8' into development

8 years agoBugfix. Escaping prediction feature title in rfe POST.
davor [Tue, 10 Apr 2012 07:34:16 +0000 (10:34 +0300)]
Bugfix. Escaping prediction feature title in rfe POST.

Prediction feature title has to be escaped to find it in further calculations (e.g. define y-column in R calculations).

8 years agotransferring feature metadata to result of rfe
Andreas Maunz [Tue, 10 Apr 2012 07:15:46 +0000 (09:15 +0200)]
transferring feature metadata to result of rfe

8 years agoPOST target for all descriptors changed to /pc/AllDescriptors
Andreas Maunz [Thu, 5 Apr 2012 08:40:53 +0000 (10:40 +0200)]
POST target for all descriptors changed to /pc/AllDescriptors

8 years agoSupporting lookup
Andreas Maunz [Wed, 4 Apr 2012 12:55:08 +0000 (14:55 +0200)]
Supporting lookup

8 years agoFixed feature meta data
Andreas Maunz [Wed, 4 Apr 2012 11:40:10 +0000 (13:40 +0200)]
Fixed feature meta data

8 years agoFixed documentation
Andreas Maunz [Tue, 3 Apr 2012 14:54:30 +0000 (16:54 +0200)]
Fixed documentation

8 years agoAdded openbabel
Andreas Maunz [Tue, 3 Apr 2012 14:26:50 +0000 (16:26 +0200)]
Added openbabel

8 years agoUnified interface to PC descriptors
Andreas Maunz [Mon, 2 Apr 2012 14:51:21 +0000 (16:51 +0200)]
Unified interface to PC descriptors

8 years agoAdded Java
Andreas Maunz [Mon, 2 Apr 2012 07:29:06 +0000 (09:29 +0200)]
Added Java

8 years agoRemoved del_nominal (60f306947f01bbc8).
davor [Tue, 20 Mar 2012 12:57:40 +0000 (13:57 +0100)]
Removed del_nominal (60f306947f01bbc8).

8 years agoMerge branch 'release/v3.1.0' into development
rautenberg [Tue, 13 Mar 2012 11:11:31 +0000 (12:11 +0100)]
Merge branch 'release/v3.1.0' into development

8 years agoMerge branch 'release/v3.1.0' v3.1.0
rautenberg [Tue, 13 Mar 2012 11:11:11 +0000 (12:11 +0100)]
Merge branch 'release/v3.1.0'

8 years agoEnabled del_nominal for rfe.
davor [Wed, 7 Mar 2012 16:12:03 +0000 (17:12 +0100)]
Enabled del_nominal for rfe.

8 years agoSet all feature types as numeric for rfe results.
davor [Mon, 5 Mar 2012 11:16:42 +0000 (12:16 +0100)]
Set all feature types as numeric for rfe results.

8 years agoAdded Changelog
Andreas Maunz [Fri, 24 Feb 2012 07:57:35 +0000 (08:57 +0100)]
Added Changelog

8 years agoMerge branch 'development' of github.com:opentox/algorithm into development
Andreas Maunz [Tue, 21 Feb 2012 15:24:33 +0000 (16:24 +0100)]
Merge branch 'development' of github.com:opentox/algorithm into development

8 years agoRegression: 'paths' as features merely by default.
Andreas Maunz [Thu, 16 Feb 2012 13:43:26 +0000 (14:43 +0100)]
Regression: 'paths' as features merely by default.

May be overwritten by user via params[:feature_type]=trees

8 years agoMerge branch 'development' of github.com:opentox/algorithm into development
davor [Wed, 15 Feb 2012 15:13:20 +0000 (16:13 +0100)]
Merge branch 'development' of github.com:opentox/algorithm into development

8 years agoCommented out metadata information BO.instanceOf because BO ontology is
davor [Wed, 15 Feb 2012 15:06:47 +0000 (16:06 +0100)]
Commented out metadata information BO.instanceOf because BO ontology is
not available

8 years agoFixed parameter name in metadata (minfreq)
Andreas Maunz [Wed, 15 Feb 2012 14:04:40 +0000 (15:04 +0100)]
Fixed parameter name in metadata (minfreq)

8 years agoMerge branch 'pc_new_1' into development
Andreas Maunz [Thu, 9 Feb 2012 14:40:00 +0000 (15:40 +0100)]
Merge branch 'pc_new_1' into development

8 years agoMerge branch 'development' into pc_new_1 pc_new_1
Andreas Maunz [Thu, 9 Feb 2012 14:31:01 +0000 (15:31 +0100)]
Merge branch 'development' into pc_new_1

8 years agoFixed tempfile deletion
Andreas Maunz [Thu, 9 Feb 2012 09:26:16 +0000 (10:26 +0100)]
Fixed tempfile deletion

8 years agoUpdated README
Andreas Maunz [Wed, 8 Feb 2012 13:50:04 +0000 (14:50 +0100)]
Updated README

8 years agoFixed minor bugs
Andreas Maunz [Wed, 8 Feb 2012 13:40:09 +0000 (14:40 +0100)]
Fixed minor bugs

8 years agoAdjusted rfe
Andreas Maunz [Wed, 8 Feb 2012 13:15:30 +0000 (14:15 +0100)]
Adjusted rfe

8 years agoAdded rfe
Andreas Maunz [Tue, 7 Feb 2012 16:14:45 +0000 (17:14 +0100)]
Added rfe

8 years agofixing a&a in fminer match
mguetlein [Tue, 31 Jan 2012 10:58:46 +0000 (11:58 +0100)]
fixing a&a in fminer match

8 years agoextend matching to 'nr_hits'
mguetlein [Tue, 31 Jan 2012 10:54:14 +0000 (11:54 +0100)]
extend matching to 'nr_hits'

8 years agofeature match functionallity for fminer
mguetlein [Tue, 31 Jan 2012 10:27:31 +0000 (11:27 +0100)]
feature match functionallity for fminer

8 years agoMerge branch 'caret' into pc_new_1
Andreas Maunz [Tue, 31 Jan 2012 09:25:05 +0000 (10:25 +0100)]
Merge branch 'caret' into pc_new_1