lazar
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

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 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

4 years agoenm import test
Christoph Helma [Fri, 8 Apr 2016 11:04:56 +0000 (13:04 +0200)]
enm import test

4 years agoMerge branch 'development' into nano
Christoph Helma [Fri, 8 Apr 2016 07:18:37 +0000 (09:18 +0200)]
Merge branch 'development' into nano

4 years agocheck if R packages are correctly installed
Christoph Helma [Thu, 7 Apr 2016 15:54:46 +0000 (17:54 +0200)]
check if R packages are correctly installed

4 years agoinitial ambit import
Christoph Helma [Thu, 7 Apr 2016 15:39:14 +0000 (17:39 +0200)]
initial ambit import

4 years agolast commit doesnt work this way
gebele [Mon, 4 Apr 2016 13:42:30 +0000 (15:42 +0200)]
last commit doesnt work this way

4 years agolast commit doesnt work this way
gebele [Mon, 4 Apr 2016 13:42:03 +0000 (15:42 +0200)]
last commit doesnt work this way

4 years agolast commit doesnt work this way
gebele [Mon, 4 Apr 2016 13:41:25 +0000 (15:41 +0200)]
last commit doesnt work this way

4 years agoload local r packages
gebele [Mon, 4 Apr 2016 11:59:33 +0000 (13:59 +0200)]
load local r packages

4 years agoadded rserve here
gebele [Mon, 4 Apr 2016 11:54:07 +0000 (13:54 +0200)]
added rserve here

4 years agoavoid rserve check at this point
gebele [Mon, 4 Apr 2016 11:53:08 +0000 (13:53 +0200)]
avoid rserve check at this point

4 years agoMerge branch 'development' of github.com:opentox/lazar into development
Christoph Helma [Fri, 1 Apr 2016 17:07:56 +0000 (19:07 +0200)]
Merge branch 'development' of github.com:opentox/lazar into development

4 years agoversion bumped to 0.9.1
Christoph Helma [Fri, 1 Apr 2016 14:09:23 +0000 (16:09 +0200)]
version bumped to 0.9.1

4 years agoregression r^2 fixed
Christoph Helma [Fri, 1 Apr 2016 14:07:55 +0000 (16:07 +0200)]
regression r^2 fixed

4 years agore-added rserve
gebele [Fri, 1 Apr 2016 10:44:04 +0000 (12:44 +0200)]
re-added rserve

4 years agolazar gem, version bumped to 0.9
Christoph Helma [Thu, 31 Mar 2016 08:04:42 +0000 (10:04 +0200)]
lazar gem, version bumped to 0.9

4 years agoensure pls package is loaded
gebele [Wed, 30 Mar 2016 11:43:15 +0000 (13:43 +0200)]
ensure pls package is loaded

4 years agolocal R package installation
Christoph Helma [Thu, 24 Mar 2016 12:43:27 +0000 (13:43 +0100)]
local R package installation

4 years agoprediction interval for regression
Christoph Helma [Wed, 23 Mar 2016 10:46:47 +0000 (11:46 +0100)]
prediction interval for regression

4 years agoadded install script for R packages, updated README with install instructions; change...
gebele [Mon, 21 Mar 2016 09:50:12 +0000 (09:50 +0000)]
added install script for R packages, updated README with install instructions; changed plot format from svg to png

4 years agovalidation test cleanup
Christoph Helma [Tue, 15 Mar 2016 17:53:12 +0000 (18:53 +0100)]
validation test cleanup

4 years agosingle tests pass
Christoph Helma [Tue, 15 Mar 2016 17:46:34 +0000 (18:46 +0100)]
single tests pass

4 years agovalidation tests pass
Christoph Helma [Tue, 15 Mar 2016 16:40:40 +0000 (17:40 +0100)]
validation tests pass

4 years agodescriptor tests
Christoph Helma [Mon, 14 Mar 2016 14:25:50 +0000 (15:25 +0100)]
descriptor tests

4 years agogetconf for number of cores
Christoph Helma [Mon, 14 Mar 2016 09:38:37 +0000 (10:38 +0100)]
getconf for number of cores

4 years agofolds split on unique compounds instead of data entries
Christoph Helma [Mon, 14 Mar 2016 09:06:22 +0000 (10:06 +0100)]
folds split on unique compounds instead of data entries

4 years agomodular regression algorithms
Christoph Helma [Mon, 29 Feb 2016 13:11:30 +0000 (14:11 +0100)]
modular regression algorithms

4 years agocrossvalidation folds fixed for duplicates
Christoph Helma [Mon, 29 Feb 2016 12:02:37 +0000 (13:02 +0100)]
crossvalidation folds fixed for duplicates

4 years agoregression crossvalidation fixed
Christoph Helma [Mon, 29 Feb 2016 07:59:43 +0000 (08:59 +0100)]
regression crossvalidation fixed

4 years agophyschem calculation and storage in compouds
Christoph Helma [Sun, 28 Feb 2016 15:00:15 +0000 (16:00 +0100)]
physchem calculation and storage in compouds

4 years agophyschem feature class
Christoph Helma [Sun, 28 Feb 2016 11:43:38 +0000 (12:43 +0100)]
physchem feature class

4 years agolocal pls regression as default regression algorithm fminer
Christoph Helma [Sat, 27 Feb 2016 15:47:48 +0000 (16:47 +0100)]
local pls regression as default regression algorithm

4 years agoimproved handling of duplicates in validations
Christoph Helma [Sat, 13 Feb 2016 12:15:29 +0000 (13:15 +0100)]
improved handling of duplicates in validations

4 years agopls regression
Christoph Helma [Tue, 9 Feb 2016 10:04:00 +0000 (11:04 +0100)]
pls regression

4 years agomg-mmol conversion fixed
Christoph Helma [Fri, 8 Jan 2016 10:00:20 +0000 (11:00 +0100)]
mg-mmol conversion fixed

4 years agoleave one out validation implemented
Christoph Helma [Mon, 9 Nov 2015 13:58:34 +0000 (14:58 +0100)]
leave one out validation implemented

4 years agoaccuracy threshold for prediction model test adjusted
Christoph Helma [Wed, 4 Nov 2015 17:07:15 +0000 (18:07 +0100)]
accuracy threshold for prediction model test adjusted

4 years agoMerge branch 'development' of github.com:opentox/lazar into development
Christoph Helma [Wed, 4 Nov 2015 16:50:32 +0000 (17:50 +0100)]
Merge branch 'development' of github.com:opentox/lazar into development

4 years agoneighbor search delegated to database backend
Christoph Helma [Wed, 4 Nov 2015 16:50:17 +0000 (17:50 +0100)]
neighbor search delegated to database backend

4 years agoerror methods do only accept 1 argument
Micha Rautenberg [Fri, 30 Oct 2015 13:08:56 +0000 (14:08 +0100)]
error methods do only accept 1 argument

4 years agoerror methods do only accept 1 argument
Micha Rautenberg [Fri, 30 Oct 2015 11:58:17 +0000 (12:58 +0100)]
error methods do only accept 1 argument

4 years agoadded csv encode option windows-1251:utf-8 v7-nestec
gebele [Fri, 30 Oct 2015 10:09:49 +0000 (10:09 +0000)]
added csv encode option windows-1251:utf-8

4 years agoRemoved comment.
davor [Thu, 29 Oct 2015 14:42:53 +0000 (15:42 +0100)]
Removed comment.

4 years agoAdded molecular weight to compound and mg conversions
davor [Thu, 29 Oct 2015 13:33:30 +0000 (13:33 +0000)]
Added molecular weight to compound and mg conversions

Added tests

4 years agocheck for whitespaces in smiles
Christoph Helma [Thu, 29 Oct 2015 11:45:49 +0000 (12:45 +0100)]
check for whitespaces in smiles

4 years agoavoid duplicated obconversion in from_smiles
gebele [Thu, 29 Oct 2015 09:56:37 +0000 (09:56 +0000)]
avoid duplicated obconversion in from_smiles

4 years agoalways collect neighbors even if database hit
gebele [Wed, 28 Oct 2015 09:12:20 +0000 (09:12 +0000)]
always collect neighbors even if database hit

4 years agoadded files and test for create dataset from file (smiles/inchi) without features...
gebele [Thu, 22 Oct 2015 11:35:32 +0000 (11:35 +0000)]
added files and test for create dataset from file (smiles/inchi) without features, used for batch prediction

4 years agoGridFS storage for data_entries removed (will break kazius/fminer models), lazy creat...
Christoph Helma [Mon, 19 Oct 2015 09:42:16 +0000 (11:42 +0200)]
GridFS storage for data_entries removed (will break kazius/fminer models), lazy creation of classification confidence plots.

4 years agonew environment variable LAZAR_ENV for databases and log levels
Christoph Helma [Thu, 8 Oct 2015 12:10:00 +0000 (14:10 +0200)]
new environment variable LAZAR_ENV for databases and log levels

4 years agonew master branch
Christoph Helma [Thu, 8 Oct 2015 08:43:43 +0000 (10:43 +0200)]
new master branch