opentox-ruby
7 years agoFixed row parsing master
Andreas Maunz [Mon, 1 Oct 2012 15:35:21 +0000 (17:35 +0200)]
Fixed row parsing

7 years agoSupport for missing data entries in CSV download
Andreas Maunz [Fri, 28 Sep 2012 10:10:00 +0000 (12:10 +0200)]
Support for missing data entries in CSV download

8 years agoCorrected nr cols log
Andreas Maunz [Thu, 20 Sep 2012 08:13:05 +0000 (10:13 +0200)]
Corrected nr cols log

8 years agoFixed creator
Andreas Maunz [Thu, 20 Sep 2012 06:34:44 +0000 (08:34 +0200)]
Fixed creator

8 years agoSwitched CDK from Ambit to rjb
Andreas Maunz [Wed, 19 Sep 2012 13:58:07 +0000 (15:58 +0200)]
Switched CDK from Ambit to rjb

8 years agoImproved WMV Classification prediction duration.
davor [Fri, 14 Sep 2012 12:18:10 +0000 (14:18 +0200)]
Improved WMV Classification prediction duration.

8 years agoFixed confidence for cosine similarity
Andreas Maunz [Wed, 12 Sep 2012 13:41:18 +0000 (16:41 +0300)]
Fixed confidence for cosine similarity

8 years agoRemoved debug
Andreas Maunz [Wed, 15 Aug 2012 14:42:24 +0000 (16:42 +0200)]
Removed debug

8 years agoBugfix: sorting CSV columns and appending line break to CSV
Andreas Maunz [Wed, 15 Aug 2012 13:34:20 +0000 (15:34 +0200)]
Bugfix: sorting CSV columns and appending line break to CSV

8 years agoBugfix: using normal '"' to quote SMARTS
Andreas Maunz [Wed, 15 Aug 2012 11:58:21 +0000 (13:58 +0200)]
Bugfix: using normal '"' to quote SMARTS

8 years agoRegenerate gemspec for version 4.0.0
Christoph Helma [Mon, 16 Jul 2012 15:33:54 +0000 (17:33 +0200)]
Regenerate gemspec for version 4.0.0

8 years agoMerge branch 'release/v3.2.0' v4.0.0
rautenberg [Fri, 13 Jul 2012 07:45:46 +0000 (09:45 +0200)]
Merge branch 'release/v3.2.0'

8 years agoreadme date release/v3.2.0
rautenberg [Fri, 13 Jul 2012 07:45:28 +0000 (09:45 +0200)]
readme date

8 years agoadd yardopts
rautenberg [Fri, 13 Jul 2012 07:40:38 +0000 (09:40 +0200)]
add yardopts

8 years agoMerge branch 'release/v3.2.0' of github.com:opentox/opentox-ruby into release/v3.2.0
rautenberg [Fri, 13 Jul 2012 07:29:53 +0000 (09:29 +0200)]
Merge branch 'release/v3.2.0' of github.com:opentox/opentox-ruby into release/v3.2.0

8 years agoedit changelog
rautenberg [Fri, 13 Jul 2012 07:29:12 +0000 (09:29 +0200)]
edit changelog

8 years agoMerge branch 'development' into release/v3.2.0
Andreas Maunz [Thu, 12 Jul 2012 14:17:55 +0000 (16:17 +0200)]
Merge branch 'development' into release/v3.2.0

8 years agoWeight evaluation prepared
Andreas Maunz [Thu, 12 Jul 2012 14:17:10 +0000 (16:17 +0200)]
Weight evaluation prepared

8 years agoset version to 4.0.0, add entries to ChangeLog
rautenberg [Thu, 12 Jul 2012 11:41:02 +0000 (13:41 +0200)]
set version to 4.0.0, add entries to ChangeLog

8 years agoFixed container format for CSV
David Vorgrimmler [Fri, 29 Jun 2012 12:26:17 +0000 (14:26 +0200)]
Fixed container format for CSV

8 years agoPerformance for CSV download
David Vorgrimmler [Fri, 29 Jun 2012 09:50:26 +0000 (11:50 +0200)]
Performance for CSV download

8 years agoAdded subjectid.
David Vorgrimmler [Wed, 20 Jun 2012 15:39:39 +0000 (17:39 +0200)]
Added subjectid.

8 years agoAdded subjectids.
David Vorgrimmler [Wed, 20 Jun 2012 12:36:44 +0000 (14:36 +0200)]
Added subjectids.

8 years agoForce redis version 2.2.2
David Vorgrimmler [Tue, 19 Jun 2012 09:51:29 +0000 (11:51 +0200)]
Force redis version 2.2.2

8 years agoReplaced nominal check with numeric check
David Vorgrimmler [Tue, 19 Jun 2012 09:14:28 +0000 (11:14 +0200)]
Replaced nominal check with numeric check

8 years agoFixed minor bugs.
David Vorgrimmler [Fri, 8 Jun 2012 13:13:10 +0000 (15:13 +0200)]
Fixed minor bugs.

Set min_frequency if not given and ignore features with nil values.

8 years agoMerge branch 'bbrc-sample' into development
David Vorgrimmler [Tue, 5 Jun 2012 14:03:30 +0000 (16:03 +0200)]
Merge branch 'bbrc-sample' into development

8 years agoAdded fminer support for percentage and per-mil min frequencies bbrc-sample
Andreas Maunz [Wed, 23 May 2012 06:54:45 +0000 (08:54 +0200)]
Added fminer support for percentage and per-mil min frequencies

8 years agoFixed read-in of smiles for fminer
Andreas Maunz [Mon, 21 May 2012 14:28:16 +0000 (16:28 +0200)]
Fixed read-in of smiles for fminer

8 years agoMerge branch 'bbrc-sample' of github.com:opentox/opentox-ruby into bbrc-sample
Andreas Maunz [Tue, 15 May 2012 13:20:45 +0000 (15:20 +0200)]
Merge branch 'bbrc-sample' of github.com:opentox/opentox-ruby into bbrc-sample

8 years agoFixed empty entries
Andreas Maunz [Tue, 15 May 2012 13:20:25 +0000 (15:20 +0200)]
Fixed empty entries

8 years agoMerge branch 'development' into bbrc-sample
David Vorgrimmler [Tue, 15 May 2012 10:00:10 +0000 (12:00 +0200)]
Merge branch 'development' into bbrc-sample

8 years agoMerge branch 'master' into development
davor [Tue, 15 May 2012 09:37:47 +0000 (11:37 +0200)]
Merge branch 'master' into development

Conflicts:
ChangeLog

8 years agoChecks if given URI is valid.
davor [Tue, 15 May 2012 09:25:49 +0000 (11:25 +0200)]
Checks if given URI is valid.

At the beginning of the compound initialization.

8 years agochecking instance if data should be added to fminer
Andreas Maunz [Mon, 7 May 2012 12:11:23 +0000 (14:11 +0200)]
checking instance if data should be added to fminer

8 years agoOrdered addition of entries to fminer
Andreas Maunz [Thu, 3 May 2012 14:35:18 +0000 (16:35 +0200)]
Ordered addition of entries to fminer

8 years agoMerge branch 'development' of github.com:opentox/opentox-ruby into development
davor [Fri, 27 Apr 2012 06:48:20 +0000 (08:48 +0200)]
Merge branch 'development' of github.com:opentox/opentox-ruby into development

8 years agoReplace some special character in feature name.
davor [Fri, 27 Apr 2012 06:42:32 +0000 (08:42 +0200)]
Replace some special character in feature name.

Depending on commit c8ee811414d06c27c13c622295e056ec169c3e5a

8 years agoCreating R image commented out.
davor [Tue, 24 Apr 2012 14:18:24 +0000 (16:18 +0200)]
Creating R image commented out.

8 years agoReplace ".", "\" and brackets with "_".
David Vorgrimmler [Mon, 23 Apr 2012 13:56:53 +0000 (15:56 +0200)]
Replace ".", "\" and brackets with "_".

8 years agoMerge branch 'development' of github.com:opentox/opentox-ruby into development
David Vorgrimmler [Mon, 23 Apr 2012 13:27:53 +0000 (15:27 +0200)]
Merge branch 'development' of github.com:opentox/opentox-ruby into development

8 years agoReplace "/" in feature name with "_"
David Vorgrimmler [Mon, 23 Apr 2012 13:27:06 +0000 (15:27 +0200)]
Replace "/" in feature name with "_"

8 years agoMerge branch 'development' of github.com:opentox/opentox-ruby into development
mguetlein [Mon, 23 Apr 2012 09:17:58 +0000 (11:17 +0200)]
Merge branch 'development' of github.com:opentox/opentox-ruby into development

8 years agoenable validation list filtering for multiple arguments
mguetlein [Mon, 23 Apr 2012 09:17:49 +0000 (11:17 +0200)]
enable validation list filtering for multiple arguments

8 years agoUndo changes (wrong branch).
davor [Fri, 20 Apr 2012 10:17:34 +0000 (13:17 +0300)]
Undo changes (wrong branch).

8 years agoAdded pc/ jl changes.
davor [Fri, 20 Apr 2012 10:16:57 +0000 (13:16 +0300)]
Added pc/ jl changes.

8 years agoAdded pc/jl log.
davor [Fri, 20 Apr 2012 10:06:18 +0000 (13:06 +0300)]
Added pc/jl log.

8 years agoManual merge with development.
David Vorgrimmler [Thu, 19 Apr 2012 14:06:33 +0000 (16:06 +0200)]
Manual merge with development.

8 years agoImproved compounds comparison in lookup pc_unified_from_jl
David Vorgrimmler [Wed, 18 Apr 2012 12:27:41 +0000 (14:27 +0200)]
Improved compounds comparison in lookup

8 years agoMajor fix: CSV download
Andreas Maunz [Wed, 18 Apr 2012 08:56:15 +0000 (10:56 +0200)]
Major fix: CSV download

8 years agoCorrected: CSV download, fminer prediction f detect
Andreas Maunz [Tue, 17 Apr 2012 13:14:02 +0000 (15:14 +0200)]
Corrected: CSV download, fminer prediction f detect

CSV: order of rows in order of compounds
fminer check_params: auto-detecting prediction feature in case of a
single feature in the dataset

8 years agoMerge branch 'jl' into pc_unified_from_jl
Andreas Maunz [Fri, 13 Apr 2012 13:07:21 +0000 (15:07 +0200)]
Merge branch 'jl' into pc_unified_from_jl

8 years agoFix: verbose prediction ds for Substructure.lookup jl
ot5 [Fri, 13 Apr 2012 12:56:37 +0000 (14:56 +0200)]
Fix: verbose prediction ds for Substructure.lookup

8 years agoMajor bug fixed: order of compounds was unsure in transform.rb
Andreas Maunz [Thu, 12 Apr 2012 09:52:16 +0000 (11:52 +0200)]
Major bug fixed: order of compounds was unsure in transform.rb

8 years agoRem debug
Andreas Maunz [Thu, 12 Apr 2012 06:49:06 +0000 (08:49 +0200)]
Rem debug

8 years agopc_type and lib autodetection from feature dataset
Andreas Maunz [Wed, 11 Apr 2012 11:27:53 +0000 (13:27 +0200)]
pc_type and lib autodetection from feature dataset

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

8 years agoRemoved value_map from params
Andreas Maunz [Tue, 10 Apr 2012 11:32:51 +0000 (13:32 +0200)]
Removed value_map from params

8 years agoFixed value map creation for multi type encoding
Andreas Maunz [Tue, 10 Apr 2012 09:05:19 +0000 (11:05 +0200)]
Fixed value map creation for multi type encoding

8 years agonominal fixed as 1st feature in metadata
Andreas Maunz [Tue, 10 Apr 2012 07:32:16 +0000 (09:32 +0200)]
nominal fixed as 1st feature in metadata

8 years agoMerge branch 'jl' into pc_unified_from_jl
Andreas Maunz [Thu, 5 Apr 2012 13:55:01 +0000 (15:55 +0200)]
Merge branch 'jl' into pc_unified_from_jl

Conflicts:
lib/compound.rb

8 years agoUploading master via RestClient
Andreas Maunz [Thu, 5 Apr 2012 13:11:55 +0000 (15:11 +0200)]
Uploading master via RestClient

8 years agoparser.rb modified to allow for several feature types
Andreas Maunz [Thu, 5 Apr 2012 12:01:55 +0000 (14:01 +0200)]
parser.rb modified to allow for several feature types

8 years agoMerge commit '1111dbc2f0751802c63dd42f120d4cc64e4cc4d6' into jl
davor [Thu, 5 Apr 2012 09:29:51 +0000 (11:29 +0200)]
Merge commit '1111dbc2f0751802c63dd42f120d4cc64e4cc4d6' into jl

Only merged lib/compound.rb

8 years agoMerge commit 'd82a5daa6c9218ee7b52eb5f933fd75b85e84d55' into development
davor [Thu, 5 Apr 2012 09:09:13 +0000 (11:09 +0200)]
Merge commit 'd82a5daa6c9218ee7b52eb5f933fd75b85e84d55' into development

Upstream fix from master branch: Bugfix. Lookup problem for external
compound uri fixed.
Now external hostname/port in compound uri doesn't influence lookup in
external feature datasets.

8 years agoPOST target for all descriptors changed to /pc/AllDescriptors
Andreas Maunz [Thu, 5 Apr 2012 08:40:35 +0000 (10:40 +0200)]
POST target for all descriptors changed to /pc/AllDescriptors

8 years agoBugfix. Lookup problem for external compound uri fixed.
davor [Thu, 5 Apr 2012 08:36:05 +0000 (11:36 +0300)]
Bugfix. Lookup problem for external compound uri fixed.

Now external hostname/port in compound uri doesn't influence lookup in external feature datasets.

8 years agotask progress and feature metadata fixed
Andreas Maunz [Thu, 5 Apr 2012 07:18:30 +0000 (09:18 +0200)]
task progress and feature metadata fixed

8 years agoRemoved necessity to track names
Andreas Maunz [Wed, 4 Apr 2012 14:33:12 +0000 (16:33 +0200)]
Removed necessity to track names

8 years agoSupporting task progress
Andreas Maunz [Wed, 4 Apr 2012 14:00:19 +0000 (16:00 +0200)]
Supporting task progress

8 years agoSupporint lookup
Andreas Maunz [Wed, 4 Apr 2012 12:53:52 +0000 (14:53 +0200)]
Supporint lookup

8 years agoFixed feature meta data
Andreas Maunz [Wed, 4 Apr 2012 11:39:48 +0000 (13:39 +0200)]
Fixed feature meta data

8 years agoAdded openbabel
Andreas Maunz [Tue, 3 Apr 2012 14:27:12 +0000 (16:27 +0200)]
Added openbabel

8 years agoset new Version No
mr [Tue, 3 Apr 2012 10:29:31 +0000 (12:29 +0200)]
set new Version No

8 years agoSingle descriptor selection, using new YAML file
Andreas Maunz [Mon, 2 Apr 2012 14:47:32 +0000 (16:47 +0200)]
Single descriptor selection, using new YAML file

8 years agoadd metadta when splitting, add non-split-features to split-result-dataset, add k...
mguetlein [Mon, 2 Apr 2012 14:13:29 +0000 (16:13 +0200)]
add metadta when splitting, add non-split-features to split-result-dataset, add k-fold-split method for crossvalidation, add sammon plotting

8 years agoRegenerate gemspec for version 3.1.0
rautenberg [Mon, 26 Mar 2012 15:27:21 +0000 (17:27 +0200)]
Regenerate gemspec for version 3.1.0

8 years agoRegenerate gemspec for version 3.1.0
Christoph Helma [Mon, 26 Mar 2012 15:18:14 +0000 (17:18 +0200)]
Regenerate gemspec for version 3.1.0

8 years agouse sammon plotting for feature value plots, fix to-dataframe for duplicate row names
mguetlein [Mon, 26 Mar 2012 09:26:42 +0000 (11:26 +0200)]
use sammon plotting for feature value plots, fix to-dataframe for duplicate row names

8 years agoRegenerate gemspec for version 3.1.0
rautenberg [Fri, 23 Mar 2012 11:36:23 +0000 (12:36 +0100)]
Regenerate gemspec for version 3.1.0

8 years agoMerged back to d7c0289 but includes fixes.
davor [Tue, 20 Mar 2012 12:22:38 +0000 (13:22 +0100)]
Merged back to d7c0289 but includes fixes.

Moved back to setting with best performance (see table 18,
http://goo.gl/uGMJN).

8 years agoMerge branch 'jl_dv' into jl
davor [Tue, 20 Mar 2012 12:13:42 +0000 (13:13 +0100)]
Merge branch 'jl_dv' into jl

8 years agoBackup including important chances from dev jl_dv
davor [Tue, 20 Mar 2012 12:04:53 +0000 (13:04 +0100)]
Backup including important chances from dev

train_succeess and dataset cleanup + own chances (get compound name
function, small dataset fix)

8 years agoRegenerate gemspec for version 3.1.0
mr [Wed, 14 Mar 2012 15:34:44 +0000 (16:34 +0100)]
Regenerate gemspec for version 3.1.0

8 years agoTwo fixes related to transformation and model building
Andreas Maunz [Wed, 14 Mar 2012 15:08:02 +0000 (16:08 +0100)]
Two fixes related to transformation and model building

train() failure for censoring predictions (algorithm.rb),
transformation log for creating n_prop and q_prop fixed (transform.rb)

8 years agoRegenerate gemspec for version 3.1.0
rautenberg [Wed, 14 Mar 2012 14:46:32 +0000 (15:46 +0100)]
Regenerate gemspec for version 3.1.0

8 years agoFixed https://github.com/opentox/model/issues/8
Andreas Maunz [Wed, 14 Mar 2012 11:30:59 +0000 (12:30 +0100)]
Fixed https://github.com/opentox/model/issues/8

8 years agoreset s.rubygems_version to 1.5.3 v3.1.0
rautenberg [Tue, 13 Mar 2012 18:29:30 +0000 (19:29 +0100)]
reset s.rubygems_version to 1.5.3

8 years agoRegenerate gemspec for version 3.1.0
mr [Tue, 13 Mar 2012 18:20:12 +0000 (19:20 +0100)]
Regenerate gemspec for version 3.1.0

8 years agoRegenerate gemspec for version 3.1.0
rautenberg [Tue, 13 Mar 2012 18:12:09 +0000 (19:12 +0100)]
Regenerate gemspec for version 3.1.0

8 years agoVersion bump to 3.1.0
rautenberg [Tue, 13 Mar 2012 18:11:12 +0000 (19:11 +0100)]
Version bump to 3.1.0

8 years agoMerge branch 'release/v3.1.0' into development
rautenberg [Tue, 13 Mar 2012 14:33:22 +0000 (15:33 +0100)]
Merge branch 'release/v3.1.0' into development

8 years agopre v3.1.0
rautenberg [Tue, 13 Mar 2012 14:32:57 +0000 (15:32 +0100)]
pre v3.1.0

8 years agoadd logger warn if opensso connect fails
rautenberg [Tue, 13 Mar 2012 10:47:53 +0000 (11:47 +0100)]
add logger warn if opensso connect fails

8 years agoWorkaround for small datasets.
David Vorgrimmler [Fri, 9 Mar 2012 14:24:59 +0000 (15:24 +0100)]
Workaround for small datasets.

8 years agorepeat send policy to opensso if connection fails
rautenberg [Thu, 8 Mar 2012 08:54:40 +0000 (09:54 +0100)]
repeat send policy to opensso if connection fails

8 years agoAdded del_nominal switch to load_csv which removes all nominal features
davor [Wed, 7 Mar 2012 16:07:44 +0000 (17:07 +0100)]
Added del_nominal switch to load_csv which removes all nominal features
(del_nomnial is false by default).

8 years agoAdjusted rfe settings and fixed minor bug.
davor [Tue, 6 Mar 2012 14:41:00 +0000 (15:41 +0100)]
Adjusted rfe settings and fixed minor bug.

8 years agoMerge branch 'jl' of git://github.com/opentox/opentox-ruby into jl
Andreas Maunz [Mon, 5 Mar 2012 12:32:58 +0000 (13:32 +0100)]
Merge branch 'jl' of git://github.com/opentox/opentox-ruby into jl

Conflicts:
lib/algorithm.rb

8 years agoRFE selects proper subset of features
Andreas Maunz [Mon, 5 Mar 2012 12:21:57 +0000 (13:21 +0100)]
RFE selects proper subset of features