lazar
3 years agoMerge branch 'development' 1.0.0
gebele [Tue, 20 Dec 2016 16:26:09 +0000 (16:26 +0000)]
Merge branch 'development'

3 years agotrue_rate, predictivity stored in crossvalidation nano-lazar-paper.submission
Christoph Helma [Tue, 20 Dec 2016 15:28:36 +0000 (16:28 +0100)]
true_rate, predictivity stored in crossvalidation

3 years agomodena import modifications removed nano-lazar-paper.review
Christoph Helma [Sun, 18 Dec 2016 11:43:41 +0000 (12:43 +0100)]
modena import modifications removed

3 years ago5 repeated cvs for enm
Christoph Helma [Mon, 12 Dec 2016 12:02:29 +0000 (13:02 +0100)]
5 repeated cvs for enm

3 years agomodena import workarounds
Christoph Helma [Mon, 12 Dec 2016 11:46:24 +0000 (12:46 +0100)]
modena import workarounds

3 years agomerged development
gebele [Mon, 12 Dec 2016 09:15:48 +0000 (09:15 +0000)]
merged development

3 years agomerged origin/development
Christoph Helma [Thu, 8 Dec 2016 12:08:55 +0000 (13:08 +0100)]
merged origin/development

3 years agoOpenTox::Validation::RepeatedCrossValidation fixed, stringi R library added
Christoph Helma [Thu, 8 Dec 2016 12:04:38 +0000 (13:04 +0100)]
OpenTox::Validation::RepeatedCrossValidation fixed, stringi R library added

3 years agofull class name required
gebele [Tue, 6 Dec 2016 09:59:24 +0000 (09:59 +0000)]
full class name required

3 years agoremoved dependency gem version numbers
gebele [Mon, 5 Dec 2016 10:44:24 +0000 (10:44 +0000)]
removed dependency gem version numbers

3 years agoMerge branch 'development' of github.com:opentox/lazar into development
Christoph Helma [Fri, 25 Nov 2016 09:37:30 +0000 (10:37 +0100)]
Merge branch 'development' of github.com:opentox/lazar into development

3 years agoalgorithms accessor for Model::Validation
Christoph Helma [Fri, 25 Nov 2016 09:36:02 +0000 (10:36 +0100)]
algorithms accessor for Model::Validation

3 years agoalways convert to SMILES v9-nestec
gebele [Thu, 24 Nov 2016 07:16:54 +0000 (07:16 +0000)]
always convert to SMILES

3 years agoadded delog10;generalized mmol2-log10 eNM
gebele [Wed, 23 Nov 2016 15:10:58 +0000 (15:10 +0000)]
added delog10;generalized mmol2-log10

3 years agop-chem regression and enm import fixed
Christoph Helma [Fri, 11 Nov 2016 16:19:13 +0000 (17:19 +0100)]
p-chem regression and enm import fixed

3 years agoenm import fixed
Christoph Helma [Fri, 11 Nov 2016 12:07:53 +0000 (13:07 +0100)]
enm import fixed

3 years agoModel::NanoPrediction parameters
Christoph Helma [Thu, 10 Nov 2016 14:27:26 +0000 (15:27 +0100)]
Model::NanoPrediction parameters

3 years agoMerge branch 'development' of github.com:opentox/lazar into development
Christoph Helma [Thu, 10 Nov 2016 11:24:08 +0000 (12:24 +0100)]
Merge branch 'development' of github.com:opentox/lazar into development

3 years agointermediate commit, may be defunct
Christoph Helma [Thu, 10 Nov 2016 11:23:46 +0000 (12:23 +0100)]
intermediate commit, may be defunct

3 years agoMerge branch 'development' of https://github.com/opentox/lazar into development
gebele [Thu, 10 Nov 2016 11:07:03 +0000 (11:07 +0000)]
Merge branch 'development' of https://github.com/opentox/lazar into development

3 years agoadded nanomodel create
gebele [Thu, 10 Nov 2016 11:06:27 +0000 (11:06 +0000)]
added nanomodel create

3 years agoCDK 2.0
Christoph Helma [Wed, 9 Nov 2016 09:03:46 +0000 (10:03 +0100)]
CDK 2.0

3 years agoMerge branch 'development' of github.com:opentox/lazar into development
Christoph Helma [Tue, 8 Nov 2016 15:05:07 +0000 (16:05 +0100)]
Merge branch 'development' of github.com:opentox/lazar into development

3 years agoprobability plot for classification
Christoph Helma [Tue, 8 Nov 2016 15:04:49 +0000 (16:04 +0100)]
probability plot for classification

3 years agoreintroduced Gemfile
gebele [Fri, 4 Nov 2016 11:51:17 +0000 (11:51 +0000)]
reintroduced Gemfile

3 years agoadjusted r^2 removed (does not apply well to local models)
Christoph Helma [Fri, 28 Oct 2016 10:31:53 +0000 (12:31 +0200)]
adjusted r^2 removed (does not apply well to local models)

3 years agoGridFS storage for plots.
Christoph Helma [Thu, 27 Oct 2016 10:09:06 +0000 (12:09 +0200)]
GridFS storage for plots.

3 years agoprobability plot for classification validations
Christoph Helma [Thu, 27 Oct 2016 09:58:07 +0000 (11:58 +0200)]
probability plot for classification validations

3 years agoweighted average for failed caret predictions fixed
Christoph Helma [Fri, 14 Oct 2016 09:09:50 +0000 (11:09 +0200)]
weighted average for failed caret predictions fixed

3 years agogit commit added to model metadata
Christoph Helma [Fri, 14 Oct 2016 07:55:51 +0000 (09:55 +0200)]
git commit added to model metadata

3 years agotests pass
Christoph Helma [Thu, 13 Oct 2016 20:59:45 +0000 (22:59 +0200)]
tests pass

3 years agocompound tests fixed
Christoph Helma [Thu, 13 Oct 2016 17:48:21 +0000 (19:48 +0200)]
compound tests fixed

3 years agomodel tests separated and cleaned
Christoph Helma [Thu, 13 Oct 2016 17:17:03 +0000 (19:17 +0200)]
model tests separated and cleaned

3 years agoclassification fixed
Christoph Helma [Thu, 13 Oct 2016 15:34:31 +0000 (17:34 +0200)]
classification fixed

3 years agodescriptor tests fixed
Christoph Helma [Thu, 13 Oct 2016 12:39:04 +0000 (14:39 +0200)]
descriptor tests fixed

3 years agotest_physchem fixed
Christoph Helma [Thu, 13 Oct 2016 08:47:19 +0000 (10:47 +0200)]
test_physchem fixed

3 years agomolecular_weight fixed
Christoph Helma [Thu, 13 Oct 2016 08:11:09 +0000 (10:11 +0200)]
molecular_weight fixed

3 years agoR NAs fixed
Christoph Helma [Wed, 12 Oct 2016 19:44:29 +0000 (21:44 +0200)]
R NAs fixed

3 years agophyschem regression, correlation_filter for fingerprints
Christoph Helma [Wed, 12 Oct 2016 19:32:27 +0000 (21:32 +0200)]
physchem regression, correlation_filter for fingerprints

3 years agoREADME.md updated
Christoph Helma [Fri, 7 Oct 2016 11:53:26 +0000 (13:53 +0200)]
README.md updated

3 years agoremaining tests fixed
Christoph Helma [Fri, 7 Oct 2016 11:34:22 +0000 (13:34 +0200)]
remaining tests fixed

3 years agounified interface for prediction algorithms
Christoph Helma [Fri, 7 Oct 2016 08:25:58 +0000 (10:25 +0200)]
unified interface for prediction algorithms

3 years agonano caret regression fixed
Christoph Helma [Thu, 6 Oct 2016 17:14:10 +0000 (19:14 +0200)]
nano caret regression fixed

3 years agoclassification and regression tests
Christoph Helma [Wed, 5 Oct 2016 12:43:18 +0000 (14:43 +0200)]
classification and regression tests

3 years agocompound and descriptor tests fixed
Christoph Helma [Wed, 5 Oct 2016 12:10:25 +0000 (14:10 +0200)]
compound and descriptor tests fixed

3 years agosubstance and nanoparticle model creation and predictions
Christoph Helma [Wed, 5 Oct 2016 11:22:12 +0000 (13:22 +0200)]
substance and nanoparticle model creation and predictions

3 years agoinitial model creation tests
Christoph Helma [Mon, 3 Oct 2016 17:49:55 +0000 (19:49 +0200)]
initial model creation tests

3 years agonpo uri as source, spectral count unit f proteomics features
Christoph Helma [Fri, 30 Sep 2016 15:11:30 +0000 (17:11 +0200)]
npo uri as source, spectral count unit f proteomics features

3 years agopubchem uri fixed athens-workshop
Christoph Helma [Mon, 26 Sep 2016 14:20:37 +0000 (16:20 +0200)]
pubchem uri fixed

3 years ago resource_not_found_error changed to not_found_error to match new RestClient errors
Christoph Helma [Mon, 26 Sep 2016 13:31:01 +0000 (15:31 +0200)]
   resource_not_found_error changed to not_found_error to match new RestClient errors

3 years agoChembl URI fixed
Christoph Helma [Mon, 26 Sep 2016 13:16:59 +0000 (15:16 +0200)]
Chembl URI fixed

3 years agoCACTUS_URI updated
Christoph Helma [Mon, 26 Sep 2016 13:11:38 +0000 (15:11 +0200)]
CACTUS_URI updated

3 years agoupdated copyright date
Micha Rautenberg [Tue, 13 Sep 2016 11:04:29 +0000 (13:04 +0200)]
updated copyright date

4 years agoNanoPrediction model
Christoph Helma [Tue, 26 Jul 2016 11:21:57 +0000 (13:21 +0200)]
NanoPrediction model

4 years agolocal_weighted_average fallback fixed, cv predictions pulled from validations to...
Christoph Helma [Mon, 25 Jul 2016 13:53:22 +0000 (15:53 +0200)]
local_weighted_average fallback fixed, cv predictions pulled from validations to avoid mongo document size errors

4 years agocorrelation plot fixed
Christoph Helma [Thu, 21 Jul 2016 15:35:20 +0000 (17:35 +0200)]
correlation plot fixed

4 years agocompound tests fixed
Christoph Helma [Wed, 8 Jun 2016 16:26:07 +0000 (18:26 +0200)]
compound tests fixed

4 years ago(repeated)crossvalidation plots
Christoph Helma [Tue, 7 Jun 2016 16:07:28 +0000 (18:07 +0200)]
(repeated)crossvalidation plots

4 years agorandom forest regression
Christoph Helma [Fri, 3 Jun 2016 17:15:36 +0000 (19:15 +0200)]
random forest regression

4 years agoproteomics regression validation
Christoph Helma [Thu, 2 Jun 2016 17:01:18 +0000 (19:01 +0200)]
proteomics regression validation

4 years agolocal pls regression for nanoparticle proteomics
Christoph Helma [Thu, 2 Jun 2016 15:54:48 +0000 (17:54 +0200)]
local pls regression for nanoparticle proteomics

4 years agolocal pls regression for nanoparticles
Christoph Helma [Thu, 2 Jun 2016 10:22:39 +0000 (12:22 +0200)]
local pls regression for nanoparticles

4 years agoall tests fixed
Christoph Helma [Wed, 1 Jun 2016 10:46:03 +0000 (12:46 +0200)]
all tests fixed

4 years agovalidation tests fixed
Christoph Helma [Wed, 1 Jun 2016 08:37:00 +0000 (10:37 +0200)]
validation tests fixed

4 years agocleanup of validation modules/classes
Christoph Helma [Tue, 31 May 2016 16:08:08 +0000 (18:08 +0200)]
cleanup of validation modules/classes

4 years agofirst correlation of nanoparticle predictions
Christoph Helma [Fri, 27 May 2016 17:16:16 +0000 (19:16 +0200)]
first correlation of nanoparticle predictions

4 years agotests fixed. DescriptorTest#test_compound_all may fail within all.rb
Christoph Helma [Tue, 24 May 2016 13:41:24 +0000 (15:41 +0200)]
tests fixed. DescriptorTest#test_compound_all may fail within all.rb

4 years agodataset tests fixed
Christoph Helma [Tue, 24 May 2016 11:05:53 +0000 (13:05 +0200)]
dataset tests fixed

4 years agocompound tests fixed
Christoph Helma [Fri, 13 May 2016 11:38:24 +0000 (13:38 +0200)]
compound tests fixed

4 years agoenm study import fixed
Christoph Helma [Thu, 12 May 2016 13:23:01 +0000 (15:23 +0200)]
enm study import fixed

4 years ago-log10 transformed datasets added
Christoph Helma [Tue, 10 May 2016 07:39:57 +0000 (09:39 +0200)]
-log10 transformed datasets added

4 years agoenm test data added
Christoph Helma [Mon, 9 May 2016 14:20:33 +0000 (16:20 +0200)]
enm test data added

4 years agodevelopment branch merged v0.9.3
Christoph Helma [Mon, 9 May 2016 13:51:50 +0000 (15:51 +0200)]
development branch merged

4 years agophyschem crossvalidation fixed, test_compound_descriptor_parameters assertions fixed
Christoph Helma [Mon, 9 May 2016 13:44:29 +0000 (15:44 +0200)]
physchem crossvalidation fixed, test_compound_descriptor_parameters assertions fixed

4 years agonanoparticle models fixed
Christoph Helma [Mon, 9 May 2016 13:11:46 +0000 (15:11 +0200)]
nanoparticle models fixed

4 years agophyschem crossvalidation fixed
Christoph Helma [Mon, 9 May 2016 12:05:29 +0000 (14:05 +0200)]
physchem crossvalidation fixed

4 years agoregression crossvalidation fixed
Christoph Helma [Sun, 8 May 2016 10:57:10 +0000 (12:57 +0200)]
regression crossvalidation fixed

4 years agodefault validations fixed
Christoph Helma [Sun, 8 May 2016 10:22:58 +0000 (12:22 +0200)]
default validations fixed

4 years agogridfs test added
Christoph Helma [Sun, 8 May 2016 07:29:13 +0000 (09:29 +0200)]
gridfs test added

4 years ago-log10 for regression datasets, test cleanups
Christoph Helma [Sat, 7 May 2016 08:34:03 +0000 (10:34 +0200)]
-log10 for regression datasets, test cleanups

4 years agodataset tests cleanup
Christoph Helma [Fri, 6 May 2016 10:49:28 +0000 (12:49 +0200)]
dataset tests cleanup

4 years agoambit mirror, import from mirrored json, proteomics import
Christoph Helma [Thu, 5 May 2016 14:14:02 +0000 (16:14 +0200)]
ambit mirror, import from mirrored json, proteomics import

4 years agofirst reasonable results for nanoparticle crossvalidation
Christoph Helma [Wed, 4 May 2016 17:24:42 +0000 (19:24 +0200)]
first reasonable results for nanoparticle crossvalidation

4 years agocompound validations fixed
Christoph Helma [Thu, 28 Apr 2016 10:19:48 +0000 (12:19 +0200)]
compound validations fixed

4 years agocompound classification fixed
Christoph Helma [Thu, 28 Apr 2016 09:05:05 +0000 (11:05 +0200)]
compound classification fixed

4 years agonanoparticle crossvalidation technically working
Christoph Helma [Thu, 28 Apr 2016 06:11:12 +0000 (08:11 +0200)]
nanoparticle crossvalidation technically working

4 years agofirst nanomaterial prediction
Christoph Helma [Tue, 26 Apr 2016 15:38:15 +0000 (17:38 +0200)]
first nanomaterial prediction

4 years agoprobabilities branch merged
Christoph Helma [Thu, 21 Apr 2016 13:06:10 +0000 (15:06 +0200)]
probabilities branch merged

4 years agoinitial classification probabilities
Christoph Helma [Thu, 21 Apr 2016 12:29:23 +0000 (14:29 +0200)]
initial classification probabilities

4 years agoAMBIT import expanded
Christoph Helma [Thu, 21 Apr 2016 07:56:12 +0000 (09:56 +0200)]
AMBIT import expanded

4 years agoenm study import
Christoph Helma [Fri, 15 Apr 2016 12:58:17 +0000 (14:58 +0200)]
enm study import

4 years agodata_entries removed from datasets. datasets are now just containers for compounds...
Christoph Helma [Fri, 15 Apr 2016 09:01:16 +0000 (11:01 +0200)]
data_entries removed from datasets. datasets are now just containers for compounds and features, feature values have to be retrieved from substances.

4 years agofeatures/toxicities fixed
Christoph Helma [Thu, 14 Apr 2016 17:43:24 +0000 (19:43 +0200)]
features/toxicities fixed

4 years agoimproved enm import
Christoph Helma [Wed, 13 Apr 2016 16:18:36 +0000 (18:18 +0200)]
improved enm import

4 years agonew files added
Christoph Helma [Wed, 13 Apr 2016 13:35:01 +0000 (15:35 +0200)]
new files added

4 years agovalidation tests pass
Christoph Helma [Wed, 13 Apr 2016 13:15:51 +0000 (15:15 +0200)]
validation tests pass

4 years agoVERSION bumped to 0.9.3
Christoph Helma [Tue, 12 Apr 2016 10:49:32 +0000 (12:49 +0200)]
VERSION bumped to 0.9.3

4 years agonew dataset structure
Christoph Helma [Tue, 12 Apr 2016 10:37:37 +0000 (12:37 +0200)]
new dataset structure

4 years ago fixed check check for R packages
gebele [Mon, 11 Apr 2016 11:33:22 +0000 (13:33 +0200)]
 fixed check check for R packages

4 years agoenm import test
Christoph Helma [Fri, 8 Apr 2016 11:05:52 +0000 (13:05 +0200)]
enm import test