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authorChristoph Helma <helma@in-silico.ch>2012-07-20 11:18:34 +0200
committerChristoph Helma <helma@in-silico.ch>2012-07-20 11:18:34 +0200
commit81cbb13b930f671b82dabdbac8cb0461bdc49151 (patch)
tree4910a4237c8e7de32d76e42f65ac694aea9d479f
parentaedcab76a0a0ad31eb9cc3f94f0c2811f6640da8 (diff)
pages restructured, new publication list from google scholardevelopment
-rw-r--r--application.rb21
-rw-r--r--config.ru2
-rw-r--r--views/index.haml12
-rw-r--r--views/layout.haml27
-rw-r--r--views/projects.haml30
-rw-r--r--views/publications.haml770
-rw-r--r--views/software.haml90
-rw-r--r--views/style.sass22
8 files changed, 133 insertions, 841 deletions
diff --git a/application.rb b/application.rb
index db9d365..ddc8495 100644
--- a/application.rb
+++ b/application.rb
@@ -1,17 +1,19 @@
[ 'rubygems', 'sinatra', 'haml','sass' ].each do |lib|
require lib
end
+require 'restclient'
+require 'json'
get '/?' do
- haml :index
+ haml :software
end
get '/software/?' do
haml :software
end
-get '/services/?' do
- haml :services
+get '/commercial/?' do
+ haml :commercial
end
get '/projects/?' do
@@ -19,9 +21,18 @@ get '/projects/?' do
end
get '/publications/?' do
+ #@publications = JSON.parse(RestClient.get("http://entrezajax.appspot.com/esearch+esummary?db=pubmed&term=Helma+C[Auth]&apikey=cfcd208495d565ef66e7dff9f98764da"))
+ #@publications = JSON.parse(RestClient.get("http://entrezajax.appspot.com/esearch+esummary?db=pubmed&retmax=100&term=Helma+C[Auth]&apikey=cfcd208495d565ef66e7dff9f98764da"))
+ #@publications = JSON.parse(RestClient.get("http://entrezajax.appspot.com/esearch+esummary?db=pubmed&retmax=100&max=100&term=Helma+C[Auth]&apikey=cfcd208495d565ef66e7dff9f98764da"))
+ #http://scholar.google.com/scholar?as_q=&num=10&btnG=Search+Scholar&as_epq=&as_oq=&as_eq=&as_occt=any&as_sauthors=Helma&as_publication=&as_ylo=&as_yhi=&as_allsubj=all&hl=en&lr=
haml :publications
end
+get '/blog/?' do
+ #redirect "http://opentox.github.com"
+ haml :blog
+end
+
get '/contact/?' do
haml :contact
end
@@ -34,6 +45,10 @@ get '/awards/?' do
haml :awards
end
+get '/about/?' do
+ haml :about
+end
+
get '/style.css' do
#headers 'Content-Type' => 'text/css; charset=utf-8'
sass :style
diff --git a/config.ru b/config.ru
index 95e58ae..b0aca0b 100644
--- a/config.ru
+++ b/config.ru
@@ -1,6 +1,6 @@
require 'rubygems'
require 'sinatra'
-require 'application.rb'
+require './application.rb'
if ENV["RACK_ENV"] == 'production'
FileUtils.mkdir_p 'log' unless File.exists?('log')
diff --git a/views/index.haml b/views/index.haml
deleted file mode 100644
index 10c76fe..0000000
--- a/views/index.haml
+++ /dev/null
@@ -1,12 +0,0 @@
-%p
- %em in silico
- toxicology gmbh provides customised solutions
- for the computer based prediction of toxic activities.
-
- %em in silico
- toxicology gmbh is a spin-off company of the
- %a{ :href => "http://ml.informatik.uni-freiburg.de/", :target => "_top" } Machine Learning Lab
- (
- %a{ :href => "http://www.uni-freiburg.de", :target => "_top" } University Freiburg
- ). It was founded in 2004 as a single person enterprise by Christoph Helma and transformed into a gmbh (ltd) in 2010.
-
diff --git a/views/layout.haml b/views/layout.haml
index 9c29579..e45fddb 100644
--- a/views/layout.haml
+++ b/views/layout.haml
@@ -14,18 +14,27 @@
.index
%ul
%li{:class => ("selected" if /^\/$/ =~ request.path )}
- %a{ :href => "/" } Home
- %li{:class => ("selected" if /software/ =~ request.path )}
- %a{ :href => "/software" } Software
- %li{:class => ("selected" if /services/ =~ request.path )}
- %a{ :href => "/services" } Services
- %li{:class => ("selected" if /projects/ =~ request.path )}
- %a{ :href => "/projects" } Projects
+ %a{ :href => "/" } Software and services
+ %li{:class => ("selected" if /commercial/ =~ request.path )}
+ %a{ :href => "/commercial" } Commercial
%li{:class => ("selected" if /publications/ =~ request.path )}
%a{ :href => "/publications" } Publications
+ %li{:class => ("selected" if /blog/ =~ request.path )}
+ %a{ :href => "/blog" } Blog
+ %li{:class => ("selected" if /projects/ =~ request.path )}
+ %a{ :href => "/projects" } Projects
%li{:class => ("selected" if /awards/ =~ request.path )}
%a{ :href => "/awards" } Awards
- %li{:class => ("selected" if /contact/ =~ request.path )}
+ %li{:class => ("selected" if /about/ =~ request.path )}
+ %a{ :href => "/about" } About
+ /
+ %li{:class => ("selected" if /^\/$/ =~ request.path )}
+ %a{ :href => "/" } Home
+ %li{:class => ("selected" if /software/ =~ request.path )}
+ %a{ :href => "/software" }
+ %li{:class => ("selected" if /services/ =~ request.path )}
+ %a{ :href => "/services" } Products and Services
+ %li{:class => ("selected" if /contact/ =~ request.path )}
%a{ :href => "/contact" } Contact
.content
@@ -34,4 +43,4 @@
.footer
&copy;
%a{ :href => "http://www.in-silico.ch/" } in silico toxicology gmbh
- 2004-2011
+ 2004-#{Time.now.year}
diff --git a/views/projects.haml b/views/projects.haml
index d28b9a2..352176c 100644
--- a/views/projects.haml
+++ b/views/projects.haml
@@ -1,25 +1,27 @@
-Apart from industry collaborations
%em in silico
-toxicology gmbh participates in several EU projects
-
-%p Current projects:
-%ul
- %li
+toxicology gmbh has customers from pharmaceutical, chemical and food industries, collaborates with registration authorities in the establishment of common standards for QSAR predictions and is actively involved in academic research. We participate also in several EU funded projects:
+%dl
+ %dt
%a{ :href => "http://www.toxbank.net"} ToxBank
+ %dd
Supporting integrated data analysis and servicing of alternative testing methods in toxicology (WP leader)
- %li
- ModNanoTox
+ %dt
+ %a{:href => "http://www.birmingham.ac.uk/generic/modnanotox/index.aspx"} ModNanoTox
+ %dd
Modelling toxicity behaviour of engineered nanoparticles (WP leader)
-Finished projects:
-%ul
- %li
+%h1 Completed:
+%dl
+ %dt
%a{ :href => "http://www.opentox.org"} OpenTox
- An open source predictive toxicology framework (scientific leader, WP1 leader)
- %li
+ %dd
+ An open source predictive toxicology framework (scientific leader, WP leader)
+ %dt
%a{ :href => "www.sens-it-iv.eu/"} Sens-it-iv
+ %dd
Novel testing strategies for in vitro assessment of allergens (bioinformatics WP leader, through University Freiburg)
- %li
+ %dt
%a{ :href => "www.scarlet-project.eu/"} Scarlet
+ %dd
Workshop on in silico methods for carcinogenicity and mutagenicity
diff --git a/views/publications.haml b/views/publications.haml
index a04aec1..adf8a70 100644
--- a/views/publications.haml
+++ b/views/publications.haml
@@ -1,768 +1,2 @@
-!!!
-%html
- %head
- %title helma
- %body
- /
- This document was automatically generated with bibtex2html 1.96
- (see http://www.lri.fr/~filliatr/bibtex2html/),
- with the following command:
- bibtex2html -r -d -dl -nobibsource -nofooter helma.bib
- %dl
- %dt
- [
- %a{:name => "suenderhof10"}> 1
- ]
- %dd
- Claudia Suenderhauf, Felix Hammann, Andreas Maunz, Christoph Helma, and Jorg
- Huwyler.
- Combinatorial qsar modeling of human intestinal absorption.
- = succeed "," do
- %em Molecular Pharmaceutics
- 8(1):213-224, 2011.
- [&nbsp;
- %a{:href => "http://dx.doi.org/10.1021/mp100279d"}> DOI
- &nbsp;|
- = succeed "&nbsp;|" do
- %a{:href => "http://arxiv.org/abs/http://pubs.acs.org/doi/pdf/10.1021/mp100279d"} arXiv
- = succeed "&nbsp;]" do
- %a{:href => "http://pubs.acs.org/doi/abs/10.1021/mp100279d"} http
- %dt
- [
- %a{:name => "maunz10a"}> 2
- ]
- %dd
- Andreas Maunz, Christoph Helma, and Stefan Kramer.
- Efficient mining for structurally diverse subgraph patterns in large
- molecular databases.
- = succeed "," do
- %em Machine Learning
- pages 1-26, 2010.
- [&nbsp;
- %a{:href => "http://dx.doi.org/10.1007/s10994-010-5187-6"}> http
- \&nbsp;]
- %dt
- [
- %a{:name => "hardy10"}> 3
- ]
- %dd
- Barry Hardy, Nicki Douglas, Christoph Helma, Micha Rautenberg, Nina Jeliazkova,
- Vedrin Jeliazkov, Ivelina Nikolova, Romualdo Benigni, Olga Tcheremenskaia,
- Stefan Kramer, Tobias Girschick, Fabian Buchwald, Joerg Wicker, Andreas
- Karwath, Martin Gutlein, Andreas Maunz, Haralambos Sarimveis, Georgia
- Melagraki, Antreas Afantitis, Pantelis Sopasakis, David Gallagher, Vladimir
- Poroikov, Dmitry Filimonov, Alexey Zakharov, Alexey Lagunin, Tatyana
- Gloriozova, Sergey Novikov, Natalia Skvortsova, Dmitry Druzhilovsky, Sunil
- Chawla, Indira Ghosh, Surajit Ray, Hitesh Patel, and Sylvia Escher.
- Collaborative development of predictive toxicology applications.
- = succeed "," do
- %em Journal of Cheminformatics
- 2:7, 2010.
- [&nbsp;
- %a{:href => "http://www.jcheminf.com/content/2/1/7"}> http
- \&nbsp;]
- %dt
- [
- %a{:name => "maunz08b"}> 4
- ]
- %dd
- A.&nbsp;Maunz and C.&nbsp;Helma.
- Prediction of toxic effects of pharmaceutical agents.
- In K.&nbsp;V. Balakin, editor,
- = succeed "," do
- %em
- Pharmaceutical Data Mining: Approaches
- and Applications for Drug Discovery
- New York, 2009. J. Wiley &amp; Sons, Inc.
- [&nbsp;
- %a{:href => "http://www.in-silico.de/articles/chapter_mh.pdf"}> .pdf
- \&nbsp;]
- %dt
- [
- %a{:name => "maunz09a"}> 5
- ]
- %dd
- A.&nbsp;Maunz, C.&nbsp;Helma, and S.&nbsp;Kramer.
- Large-scale graph mining using backbone refinement classes.
- In
- = succeed "," do
- %em
- Proceedings of the 15th ACM SIGKDD International Conference
- on Knowledge Discovery and Data Mining (KDD-09)
- page in press, 2009.
- [&nbsp;
- %a{:href => "http://www.maunz.de/ls_graph_mining_using_bbrcs.pdf"}> .pdf
- \&nbsp;]
- %dt
- [
- %a{:name => "hammann09a"}> 6
- ]
- %dd
- F.&nbsp;Hammann, H.&nbsp;Gutmann, U.&nbsp;Jecklin, A.&nbsp;Maunz, C.&nbsp;Helma, and J.&nbsp;Drewe.
- Development of decision tree models for substrates, inhibitors and
- inducers of P-glycoprotein.
- = succeed "," do
- %em Current Drug Metabolism
- 10:339-46, 2009.
- %dt
- [
- %a{:name => "hammann09b"}> 7
- ]
- %dd
- Felix Hammann, Heike Gutmann, Ulli Baumann, Christoph Helma, and Juergen Drewe.
- Classification of cytochrome p(450) activities using machine learning
- methods.
- = succeed "," do
- %em Molecular pharmaceutics
- 6:1920-6, 2009.
- %dt
- [
- %a{:name => "maunz08a"}> 8
- ]
- %dd
- A.&nbsp;Maunz and C.&nbsp;Helma.
- Prediction of chemical toxicity with local support vector regression
- and activity-specific kernels.
- = succeed "," do
- %em SAR QSAR Environ. Res.
- 19:413-431, 2008.
- [&nbsp;
- %a{:href => "http://www.in-silico.de/articles/mh_tf.pdf"}> .pdf
- \&nbsp;]
- %dt
- [
- %a{:name => "benigni07"}> 9
- ]
- %dd
- R.&nbsp;Benigni, T.&nbsp;I. Netzeva, E.&nbsp;Benfenati, C.&nbsp;Bossa, R.&nbsp;Franke, C.&nbsp;Helma,
- E.&nbsp;Hulzebos, C.&nbsp;Marchant, A.&nbsp;Richard, Y.-T. Woo, and C.&nbsp;Yang.
- The expanding role of predictive toxicology: an update on the (Q)SAR
- models for mutagens and carcinogens.
- = succeed "," do
- %em J Environ Sci Health C Environ Carcinog Ecotoxicol Rev.
- 25:53-97, 2007.
- %dt
- [
- %a{:name => "helma06a"}> 10
- ]
- %dd
- C.&nbsp;Helma.
- Lazy structure-activity relationships (
- %tt> lazar
- ) for the
- prediction of rodent carcinogenicity and
- %em Salmonella
- mutagenicity.
- = succeed "," do
- %em Molecular Diversity
- 10:147-158, 2006.
- [&nbsp;
- %a{:href => "http://www.in-silico.de/articles/modi020905.pdf"}> .pdf
- \&nbsp;]
- %dt
- [
- %a{:name => "helma06b"}> 11
- ]
- %dd
- C.&nbsp;Helma and J.&nbsp;Kazius.
- Artificial intelligence and data mining for toxicity prediction.
- = succeed "," do
- %em Current Computer-Aided Drug Design
- 2:1-19, 2006.
- [&nbsp;
- %a{:href => "http://www.in-silico.de/articles/helma_kazius_ccadd.pdf"}> .pdf
- \&nbsp;]
- %dt
- [
- %a{:name => "vracko06"}> 12
- ]
- %dd
- M.&nbsp;Vracko, V.&nbsp;Bandelj, P.&nbsp;Barbieri, E.&nbsp;Benfenati, Q.&nbsp;Chaudhry, M.&nbsp;Cronin,
- J.&nbsp;Devillers, A.&nbsp;Gallegos, G.&nbsp;Gini, P.&nbsp;Gramatica, C.&nbsp;Helma, D.&nbsp;Neagu,
- T.&nbsp;Netzeva, M.&nbsp;Pavan, G.&nbsp;Patlevicz, M.&nbsp;Randic, I.&nbsp;Tsakovska, and A.&nbsp;Worth.
- Validation of counter propagation neural network models for
- predictive toxicology according to the OECD principles. A case study.
- = succeed "," do
- %em SAR QSAR Environ. Res.
- 17:265-84, 2006.
- %dt
- [
- %a{:name => "helma05a"}> 13
- ]
- %dd
- C.&nbsp;Helma.
- = succeed "." do
- %em Predictive Toxicology
- CRC Press, Boca Raton, 2005.
- %dt
- [
- %a{:name => "helma05b"}> 14
- ]
- %dd
- C.&nbsp;Helma.
- %tt lazar:
- Lazy Structure - Activity Relationships for toxicity
- prediction.
- In C.&nbsp;Helma, editor,
- = succeed "," do
- %em Predictive Toxicology
- pages 479-499. CRC
- Press, Boca Raton, 2005.
- %dt
- [
- %a{:name => "helma05c"}> 15
- ]
- %dd
- C.&nbsp;Helma.
- %em In Silico
- predictive toxicology: The state-of-the-art and
- strategies to predict human health effects.
- = succeed "," do
- %em Current Opinions in Drug Discovery &amp; Development
- 8:27-31,
- 2005.
- [&nbsp;
- %a{:href => "http://www.in-silico.de/articles/helma_coddd.pdf"}> .pdf
- \&nbsp;]
- %dt
- [
- %a{:name => "helma05d"}> 16
- ]
- %dd
- C.&nbsp;Helma.
- A brief introduction to predictive toxicology.
- In C.&nbsp;Helma, editor,
- = succeed "." do
- %em Predictive Toxicology
- CRC Press, Boca
- Raton, 2005.
- %dt
- [
- %a{:name => "kramer05"}> 17
- ]
- %dd
- S.&nbsp;Kramer and C.&nbsp;Helma.
- Machine learning and data mining.
- In C.&nbsp;Helma, editor,
- = succeed "," do
- %em Predictive Toxicology
- pages 223-254. CRC
- Press, Boca Raton, 2005.
- %dt
- [
- %a{:name => "helma04a"}> 18
- ]
- %dd
- C.&nbsp;Helma, T.&nbsp;Kramer, S.&nbsp;Kramer, and L.&nbsp;DeRaedt.
- Data Mining and Machine Learning techniques for the
- identification of mutagenicity inducing substructures and
- Structure-Activity Relationships of noncongeneric compounds.
- = succeed "," do
- %em J. Chem. Inf. Comput. Sci.
- 44:1402-1411, 2004.
- [&nbsp;
- %a{:href => "http://pubs3.acs.org/acs/journals/doilookup?in_doi=10.1021/ci034254q"}> http
- \&nbsp;]
- %dt
- [
- %a{:name => "helma04b"}> 19
- ]
- %dd
- C.&nbsp;Helma.
- Data mining and knowledge discovery in predictive toxicology.
- = succeed "," do
- %em SAR QSAR Environ. Res.
- 15:367-383, 2004.
- %dt
- [
- %a{:name => "helma03a"}> 20
- ]
- %dd
- C.&nbsp;Helma and S.&nbsp;Kramer.
- A survey of the Predictive Toxicology Challenge.
- = succeed "," do
- %em Bioinformatics
- 19:1179-1182, 2003.
- [&nbsp;
- %a{:href => "http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/10/1179"}> http
- \&nbsp;]
- %dt
- [
- %a{:name => "helma03b"}> 21
- ]
- %dd
- C.&nbsp;Helma, S.&nbsp;Kramer, and L.&nbsp;DeRaedt.
- The molecular feature miner MolFea.
- In M.&nbsp;Hicks and C.&nbsp;Kettner, editors,
- = succeed "," do
- %em
- Proceedings of the
- Beilstein Workshop 2002: Molecular Informatics: Confronting Complexity
- pages 79-93. Beilstein Institut, Frankfurt, 2003.
- %dt
- [
- %a{:name => "toivonen03"}> 22
- ]
- %dd
- H.&nbsp;Toivonen, A.&nbsp;Srinivasan, R.&nbsp;D. King, S.&nbsp;Kramer, and C.&nbsp;Helma.
- Statistical evaluation of the Predictive Toxicology Challenge
- 2000-2001.
- = succeed "," do
- %em Bioinformatics
- 19:1183-1193, 2003.
- [&nbsp;
- %a{:href => "http://bioinformatics.oxfordjournals.org/cgi/content/abstract/19/10/1183"}> http
- \&nbsp;]
- %dt
- [
- %a{:name => "helma02a"}> 23
- ]
- %dd
- C.&nbsp;Helma.
- Data mining in toxicology.
- In J.P.V. Heuvel, W.F. Greenlee, G.H. Perdew, and W.B. Mattes,
- editors,
- = succeed "," do
- %em
- Comprehensive Toxicology Vol XX. Cellular and Molecular
- Toxicology
- pages 611-624. Elsevier, 2002.
- %dt
- [
- %a{:name => "kassie02"}> 24
- ]
- %dd
- F.&nbsp;Kassie, S.&nbsp;Rabot, M.&nbsp;Uhl, W.&nbsp;Huber, H.M. Qin, C.&nbsp;Helma, R.&nbsp;Schulte-Hermann,
- and S.&nbsp;Knasm&uuml;ller.
- Chemoprotective effects of garden cress (lepidium sativum) and its
- constituents towards 2-amino-3-methyl-imidazo[4,5-f]quinoline (IQ)-induced
- genotoxic effects and colonicneoplastic lesions.
- = succeed "," do
- %em Carcinogenesis
- 23:1155-1161, 2002.
- %dt
- [
- %a{:name => "kramer02"}> 25
- ]
- %dd
- S.&nbsp;Kramer, E.&nbsp;Frank, and C.&nbsp;Helma.
- Fragment generation and Support Vector Machines for inducing
- SARs.
- = succeed "," do
- %em SAR and QSAR in Environmental Research
- 13:509-523, 2002.
- %dt
- [
- %a{:name => "gottmann01"}> 26
- ]
- %dd
- E.&nbsp;Gottmann, S.&nbsp;Kramer, B.&nbsp;Pfahringer, and C.&nbsp;Helma.
- Data quality in predictive toxicology: Reproducibility of rodent
- carcinogenicity experiments.
- = succeed "," do
- %em Environ. Health Perspect.
- 109:509-514, 2001.
- [&nbsp;
- %a{:href => "http://www.ehponline.org/members/2001/109p509-514gottmann/gottmann-full.html"}> .html
- \&nbsp;]
- %dt
- [
- %a{:name => "helma01b"}> 27
- ]
- %dd
- C.&nbsp;Helma, R.D. King, S.&nbsp;Kramer, and A.&nbsp;Srinivasan.
- The Predictive Toxicology Challenge 2000-2001.
- = succeed "," do
- %em Bioinformatics
- 17:107-108, 2001.
- [&nbsp;
- %a{:href => "http://bioinformatics.oupjournals.org/cgi/reprint/17/1/107.pdf"}> .pdf
- \&nbsp;]
- %dt
- [
- %a{:name => "kramer01e"}> 28
- ]
- %dd
- S.&nbsp;Kramer, L.&nbsp;De&nbsp;Raedt, and C.&nbsp;Helma.
- Molecular feature mining in HIV data.
- In
- = succeed "," do
- %em
- Proceedings of the Seventh ACM SIGKDD International
- Conference on Knowledge Discovery and Data Mining (KDD-01)
- pages 136-143,
- 2001.
- %dt
- [
- %a{:name => "helma00a"}> 29
- ]
- %dd
- C.&nbsp;Helma, S.&nbsp;Kramer, B.&nbsp;Pfahringer, and E.&nbsp;Gottmann.
- Data quality in predictive toxicology: Identification of chemical
- structures and calculation of chemical properties.
- = succeed "," do
- %em Environ. Health Perspect.
- 108:1029-1033, 2000.
- [&nbsp;
- %a{:href => "http://ehpnet1.niehs.nih.gov/docs/2000/108p1029-1033helma/abstract.html"}> .html
- \&nbsp;]
- %dt
- [
- %a{:name => "helma00b"}> 30
- ]
- %dd
- C.&nbsp;Helma, E.&nbsp;Gottmann, and S.&nbsp;Kramer.
- Knowledge discovery and data mining in toxicology.
- = succeed "," do
- %em Stat Methods Med Res.
- 9:329-358, 2000.
- [&nbsp;
- %a{:href => "http://www.in-silico.de/articles/smmr.pdf"}> .pdf
- \&nbsp;]
- %dt
- [
- %a{:name => "helma00c"}> 31
- ]
- %dd
- C.&nbsp;Helma, S.&nbsp;Kramer, and B.&nbsp;Pfahringer.
- Carcinogenicity prediction for noncongeneric compounds: Experiments
- with the Machine Learning Program SRT and various sets of chemical
- descriptors.
- In
- = succeed "," do
- %em Molecular Modelling and Prediction of Bioactivity
- page 464,
- 2000.
- %dt
- [
- %a{:name => "helma00d"}> 32
- ]
- %dd
- C.&nbsp;Helma and M.&nbsp;Uhl.
- A public domain image analysis program for the single cell gel
- electrophoresis (comet) assay.
- = succeed "," do
- %em Mutation Res.
- 466:9-15, 2000.
- [&nbsp;
- %a{:href => "http://www.in-silico.de/articles/comet.pdf"}> .pdf
- \&nbsp;]
- %dt
- [
- %a{:name => "helma00e"}> 33
- ]
- %dd
- C.&nbsp;Helma, E.&nbsp;Gottmann, S.&nbsp;Kramer, and B.&nbsp;Pfahringer.
- The application of machine learning algorithms to detect chemical
- properties responsible for carcinogenicity.
- In K.&nbsp;Gundertofte and F.S. Jorgensen, editors,
- = succeed "," do
- %em
- Molecular
- Modeling and Prediction of Bioactivity
- pages 464-466, New York, 2000.
- Kluwer Academic/Plenum Publishers.
- %dt
- [
- %a{:name => "helma00f"}> 34
- ]
- %dd
- C.&nbsp;Helma, E.&nbsp;Gottmann, S.&nbsp;Kramer, and B.&nbsp;Pfahringer.
- Artificial Intelligence Methoden zur Vorhersage der
- Kanzerogenit&auml;t organischer Verbindungen.
- In H.&nbsp;Sch&ouml;ffl, H.&nbsp;Spielmann, and H.A. Tritthart, editors,
- = succeed "," do
- %em
- Ersatz- und Erg&auml;nzungsmethoden zu Tierversuchen: Forschung ohne
- Tierversuche
- pages 128-134, Wien-New York, 2000. Springer Verlag.
- %dt
- [
- %a{:name => "uhl00"}> 35
- ]
- %dd
- M.&nbsp;Uhl, C.&nbsp;Helma, and S.&nbsp;Knasm&uuml;ller.
- Evaluation of the single cell gel electrophoretic assay with human
- hepatoma (HepG2) cells.
- = succeed "," do
- %em Mutation Res.
- 468:213-225, 2000.
- %dt
- [
- %a{:name => "helma99a"}> 36
- ]
- %dd
- C.&nbsp;Helma, E.&nbsp;Gottmann, S.&nbsp;Kramer, and B.&nbsp;Pfahringer.
- Data quality issues in toxicological knowledge discovery.
- In
- = succeed "," do
- %em
- Predictive Toxicology of Chemicals: Experiences and Impact of
- AI Tools
- pages 8-11, Menlo Park, California, 1999. AAAI Press.
- %dt
- [
- %a{:name => "pfahringer99"}> 37
- ]
- %dd
- B.&nbsp;Pfahringer, E.&nbsp;Gottmann, C.&nbsp;Helma, and S.&nbsp;Kramer.
- Efficiency/representational issues in toxicological knowledge
- discovery.
- In
- = succeed "," do
- %em
- Predictive Toxicology of Chemicals: Experiences and Impact of
- AI Tools
- pages 86-89, Menlo Park, California, 1999. AAAI Press.
- %dt
- [
- %a{:name => "uhl99"}> 38
- ]
- %dd
- M.&nbsp;Uhl, C.&nbsp;Helma, and S.&nbsp;Knasm&uuml;ller.
- Single-cell gel electrophoresis assays with human-derived hepatoma
- (HepG2) cells.
- = succeed "," do
- %em Mutation Res.
- 441:215-224, 1999.
- %dt
- [
- %a{:name => "helma98a"}> 39
- ]
- %dd
- C.&nbsp;Helma, E.&nbsp;Gottmann, S.&nbsp;Kramer, and B.&nbsp;Pfahringer.
- The application of machine learning algorithms to detect chemical
- properties responsible for carcinogenicity.
- In
- = succeed "," do
- %em
- Molecular Modelling and Prediction of Bioactivity.
- Proceedings of the 12th European Symposium on Quantitative Structure-Activity
- Relationships
- 1998.
- %dt
- [
- %a{:name => "helma98b"}> 40
- ]
- %dd
- C.&nbsp;Helma, P.&nbsp;Eckl, E.&nbsp;Gottmann, F.&nbsp;Kassie, W.&nbsp;Rodinger, H.&nbsp;Steinkellner,
- C.&nbsp;Windpassinger, R.&nbsp;Schulte-Hermann, and S.&nbsp;Knasm&uuml;ller.
- Genotoxic and ecotoxic effects of groundwaters and their relation to
- routinely measured chemical parameters.
- = succeed "," do
- %em Environ. Sci. Technol.
- 32:1799-1805, 1998.
- %dt
- [
- %a{:name => "knasmueller98"}> 41
- ]
- %dd
- S.&nbsp;Knasm&uuml;ller, C.&nbsp;Helma, P.&nbsp;Eckl, E.&nbsp;Gottmann, H.&nbsp;Steinkellner, F.&nbsp;Kassie,
- T.&nbsp;Haider, W.&nbsp;Parzefall, and R.&nbsp;Schulte-Hermann.
- Investigations on genotoxic effects of groundwater from the
- Mitterndorfer Senke from the vicinity of Wiener Neustadt.
- = succeed "," do
- %em Wiener Klinische Wochenschrift
- 110:824-833, 1998.
- %dt
- [
- %a{:name => "kramer98"}> 42
- ]
- %dd
- S.&nbsp;Kramer, B.&nbsp;Pfahringer, and C.&nbsp;Helma.
- Stochastic propositionalization of non-determinate background
- knowledge.
- In
- = succeed "," do
- %em
- Proceedings of the 8th International Workshop on Inductive
- Logic Programming (ILP-98)
- pages 80-94, Berlin Heidelberg New York, 1998.
- Springer.
- %dt
- [
- %a{:name => "steinkellner98"}> 43
- ]
- %dd
- H.&nbsp;Steinkellner, M.S. Kong, C.&nbsp;Helma, S.&nbsp;Ecker, T.H. Ma, O.&nbsp;Horak, M.&nbsp;Kundi,
- and S.&nbsp;Knasm&uuml;ller.
- Genotoxic effects of heavy metals: Comparative investigation with
- plant bioassays.
- = succeed "," do
- %em Environ. Mol. Mutagen.
- 31:183-191, 1998.
- %dt
- [
- %a{:name => "helma97a"}> 44
- ]
- %dd
- C.&nbsp;Helma and S.&nbsp;Knasm&uuml;ller.
- Die Belastung von Gew&auml;ssern mit gentoxischen Substanzen
- IIa: Die Quellen gentoxischer Kontaminationen (Industrielle
- Emissionen).
- = succeed "," do
- %em UWSF-Z.Umweltchem.&Ouml;kotox.
- 9:41-48, 1997.
- %dt
- [
- %a{:name => "helma97b"}> 45
- ]
- %dd
- C.&nbsp;Helma and S.&nbsp;Knasm&uuml;ller.
- Die Belastung von Gew&auml;ssern mit gentoxischen Substanzen
- IIb: Die Quellen gentoxischer Kontaminationen (Nichtindustrielle
- Emissionen).
- = succeed "," do
- %em UWSF-Z.Umweltchem.&Ouml;kotox.
- 9:163-168, 1997.
- %dt
- [
- %a{:name => "helma97c"}> 46
- ]
- %dd
- C.&nbsp;Helma.
- Die Situation der Chlorchemie in &Ouml;stereich: Chlorh&auml;ltige
- Pflanzenschutz- Holzschutz und Wasserdesinfektionsmittel - Entwicklungen im
- Zeitraum 1993 bis 1997.
- Technical report, Gesellschaft &Ouml;sterreichischer Chemiker, 1997.
- %dt
- [
- %a{:name => "knasmueller97"}> 47
- ]
- %dd
- S.&nbsp;Knasm&uuml;ller, W.&nbsp;Parzefall, C.&nbsp;Helma, F.&nbsp;Kassie, S.&nbsp;Ecker, and
- R.&nbsp;Schulte-Hermann.
- Toxic effects of griseofulvin: Disease models, mechanisms, and risk
- assessment.
- = succeed "," do
- %em Critical Reviews in Toxicology
- 27:495-537, 1997.
- %dt
- [
- %a{:name => "kramer97a"}> 48
- ]
- %dd
- S.&nbsp;Kramer, B.&nbsp;Pfahringer, and C.&nbsp;Helma.
- Mining for causes of cancer: Machine learning experiments at various
- levels of detail.
- In
- = succeed "," do
- %em
- Proceedings of the Third International Conference on
- Knowledge Discovery and Data Mining (KDD-97)
- Menlo Park, CA, 1997. AAAI
- Press.
- %dt
- [
- %a{:name => "helma96a"}> 49
- ]
- %dd
- C.&nbsp;Helma, V.&nbsp;Mersch-Sundermann, V.S. Houk, U.&nbsp;Glasbrenner, C.&nbsp;Klein,
- L.&nbsp;Wenquing, K.&nbsp;Fekadu, R.&nbsp;Schulte-Hermann, and S.&nbsp;Knasm&uuml;ller.
- Comparative evaluation of four bacterial assays for the detection of
- genotoxic effects in water samples.
- = succeed "," do
- %em Environ. Sci. Technol.
- 30:897-907, 1996.
- %dt
- [
- %a{:name => "helma95"}> 50
- ]
- %dd
- C.&nbsp;Helma, L.&nbsp;Kronberg, T.H. Ma, and S.&nbsp;Knasm&uuml;ller.
- Genotoxic effects of the chlorinated hydroxyfuranones
- 3-chloro-4-(dichloromethyl)-5-hydroxy-2[5H]-furanone and
- 3,4-dichloro-5-hydroxy-2[5H]-furanone in
- %i Tradescantia
- micronucleus assays.
- = succeed "," do
- %em Mutation Res.
- 346:181-186, 1995.
- %dt
- [
- %a{:name => "helma95b"}> 51
- ]
- %dd
- C.&nbsp;Helma.
- Erfahrungen mit dem Einsatz biologischer Mutationstests zur
- Verfahrensoptimierung und Umweltkontrolle.
- In
- = succeed "," do
- %em Handbuch der Umwelttechnik 1995
- pages 266-267. Wien, 1995.
- %dt
- [
- %a{:name => "helma95c"}> 52
- ]
- %dd
- C.&nbsp;Helma.
- Detection of genotoxic contaminations in water.
- In M.&nbsp;Guminska and J.&nbsp;Miedzobrodzki, editors,
- = succeed "," do
- %em
- Molecular Biology
- for Environment and Man
- pages 99-111. 1995.
- %dt
- [
- %a{:name => "helma94a"}> 53
- ]
- %dd
- C.&nbsp;Helma, R.&nbsp;Sommer, R.&nbsp;Schulte-Hermann, and S.&nbsp;Knasm&uuml;ller.
- Enhanced clastogenicity of contaminated ground water following UV
- irradiation detected by the
- %em Tradescantia
- micronucleus assay.
- = succeed "," do
- %em Mutation Res.
- 323:93-98, 1994.
- %dt
- [
- %a{:name => "helma94b"}> 54
- ]
- %dd
- C.&nbsp;Helma, S.&nbsp;Knasm&uuml;ller, and R.&nbsp;Schulte-Hermann.
- Die Belastung von W&auml;ssern mit gentoxischen Substanzen I. Methoden
- zur Pr&uuml;fung der Gentoxizit&auml;t.
- = succeed "," do
- %em UWSF-Z.Umweltchem.&Ouml;kotox.
- 6:277-288, 1994.
- %dt
- [
- %a{:name => "helma94c"}> 55
- ]
- %dd
- C.&nbsp;Helma, S.&nbsp;Knasm&uuml;ller, and R.&nbsp;Schulte-Hermann.
- Biologische Tests zur Pr&uuml;fung der Gentoxizit&auml;t:
- Einsatzm&ouml;glichkeiten zur Verfahrensoptimierung und Emissionskontrolle.
- In Brandl et&nbsp;al., editor,
- = succeed "," do
- %em
- Ecoinforma 94. Bd 9, Kanzerogenese
- durch Umweltchemikalien
- pages 497-512. Wien, 1994.
- %dt
- [
- %a{:name => "fassold93"}> 56
- ]
- %dd
- E.&nbsp;Fassold, C.&nbsp;Helma, S.&nbsp;Knasm&uuml;ller, and R.&nbsp;Sattelberger.
- Die Situation der Chlorchemie in &Ouml;stereich, 8. Teil:
- Chlorh&auml;ltige Pflanzenschutz- Holzschutz und Wasserdesinfektionsmittel.
- Technical report, Gesellschaft &Ouml;sterreichischer Chemiker, 1993.
- %dt
- [
- %a{:name => "helma92"}> 57
- ]
- %dd
- C.&nbsp;Helma et.al.
- Abfallarme Gro&szlig;k&uuml;che.
- Technical report, &Ouml;sterreichisches &Ouml;kologie Institut, 1992.
- %dt
- [
- %a{:name => "helma91"}> 58
- ]
- %dd
- C.&nbsp;Helma et.al.
- Ausstieg aus der M&uuml;llverbrennung.
- Technical report, &Ouml;sterreichisches &Ouml;kologie Institut, 1991.
+View publications and citations at
+%a{:href => "http://scholar.google.com/citations?user=D7z0GgoAAAAJ"} Google scholar.
diff --git a/views/software.haml b/views/software.haml
index a231252..01ac88b 100644
--- a/views/software.haml
+++ b/views/software.haml
@@ -1,34 +1,66 @@
-%em in silico
-toxicology develops
-%a{:href => "http://en.wikipedia.org/wiki/Open_source_software"} open source
-software:
+%dl
+ %dt
+ %a{ :href => "http://lazar.in-silico.ch/" } lazar
-%ul
- %li
- Webservices and applications for the
- %a{:href => "http://www.opentox.org"} OpenTox
- framework
- %li
- The
- %code
- %a{ :href => "http://lazar.in-silico.de/" } lazar
+ %dd
+ %code lazar
(
%em Lazy Structure- Activity Relationships
- ) program for the prediction of toxic activities and webservices.
+ )
+ takes a chemical structure as input and provides predictions for a variety of toxic properties.
%code lazar
- can be used from a free
- %a{ :href => "http://lazar.in-silico.de/" } webinterface
- or by compiling the
- %a{ :href => "http://github.com/helma/lazar-core/" } source code
- (
- %a{ :href => "http://www.gnu.org/copyleft/gpl.html" } GNU License
- ) for a local installation.
-%p
-Please visit our
-%a{ :href => "http://github.com/helma"} GitHub repository
-to view and download the source code of our projects.
-%p
-We offer also
-%a{ :href => '/services' } commercial services
-for in-house installations, custom developments, consulting and support.
+ uses a automated and reproducible
+ %em read across
+ procedure to calculate predictions.
+ Rationales for predictions, applicability domain estimations and validation results are presented in a clear graphical interface for the critical examination by toxicological experts.
+ %code lazar
+ is built on top of the
+ %a{:href => "http://www.opentox.org"} OpenTox
+ framework.
+
+ %br
+ %code lazar
+ can be used
+ %ul
+ %li
+ from a free
+ %a{ :href => "http://lazar.in-silico.ch/" } webinterface,
+ %li
+ by installing public
+ %a{ :href => "http://github.com/opentox/lazar"} source code
+ (
+ %a{ :href => "http://www.gnu.org/copyleft/gpl.html" } GNU License
+ )
+ from GitHub
+ %li
+ or by purchasing a
+ %a{ :href => '/commercial' } virtual appliance with commercial support
+ for desktop or intranet installations
+ %dt
+ %a{:href => "http://www.opentox.org"} OpenTox
+ %dd
+ OpenTox webservices are the building blocks for a predictive toxicology framework. We maintain webservices for
+ %ul
+ %li compounds
+ %li features
+ %li datasets
+ %li algorithms
+ %li models
+ %li validation
+ %li authentication and authorisation
+ %li tasks
+
+ and have access to a variety of other OpenTox webservices (e.g. AMBIT database, QMRF/QPRF reporting services).
+
+ %dt
+ %a{:href => "http://www.toxbank.org"} ToxBank
+ %dd
+ provides the computational infrastructure for the SEURAT cluster of EU projects. We develop and maintain OpenTox compatible webservices for storing, searching and analysing experimental data.
+
+All projects are
+hosted under the
+%a{ :href => "http://www.gnu.org/copyleft/gpl.html" } GNU License
+at
+%a{ :href => "http://github.com/opentox"} GitHub.
+/ %a{:href => "http://en.wikipedia.org/wiki/Open_source_software"} open source
diff --git a/views/style.sass b/views/style.sass
index 2f0bf8a..4a9ffad 100644
--- a/views/style.sass
+++ b/views/style.sass
@@ -4,9 +4,26 @@ $hl: yellow
body
margin: 3em
+ height: 100%
font-family: Verdana
background-color: white
color: $fg
+
+ h1
+ font-size: medium
+
+ dt
+ font-weight: bold
+
+ iframe
+ display: block
+ overflow-y: hidden
+
+ width: 100%
+ height: 100%
+ margin: 0
+ padding: 0
+ border: 0
.logo
margin: 0.5em
@@ -60,11 +77,6 @@ body
padding: 1.5em
padding-top: 2.5em
border: 1px solid white
-
- dt
- padding-right: 0.5em
- float: left
- clear: left
.footer
background-color: white