[Genabel-commits] r696 - pkg/webpages
noreply at r-forge.r-project.org
noreply at r-forge.r-project.org
Wed Mar 9 22:01:14 CET 2011
Author: yurii
Date: 2011-03-09 22:01:14 +0100 (Wed, 09 Mar 2011)
New Revision: 696
Modified:
pkg/webpages/acknowledgements.html
pkg/webpages/contribute.html
pkg/webpages/home.html
pkg/webpages/packages.html
pkg/webpages/people.html
pkg/webpages/pkgMixABEL.html
pkg/webpages/pkgProbABEL.html
pkg/webpages/showcase.html
pkg/webpages/support.html
pkg/webpages/tutorials.html
Log:
webpages: fixing links, patching the content
Modified: pkg/webpages/acknowledgements.html
===================================================================
--- pkg/webpages/acknowledgements.html 2011-03-09 20:09:52 UTC (rev 695)
+++ pkg/webpages/acknowledgements.html 2011-03-09 21:01:14 UTC (rev 696)
@@ -1,6 +1,6 @@
<p>
Above all, we appreciate contribution from GenABEL users, developers and
-the R team [ <a href="http://test.genabel.org/drupal6/?q=node/83">People</a> ].
+the R team [ <a href="?q=people">People</a> ].
</p>
<p>
@@ -9,7 +9,7 @@
<a href="http://www.epib.nl/organization/faculty/vanduijn.html">Genetic Epidemiology Unit</a>
(Prof. Cornelia M. van Duijn),
<a href="http://www.epib.nl/organization/faculty/hofman.html">Department of Epidemiology</a>
-(Prof. Albert Hofman) ,
+(Prof. Albert Hofman),
Erasmus MC Rotterdam, The Netherlands;
the
<a href="http://mga.bionet.nsc.ru/">Laboratory of methods for recombination and segregation analyses</a>
Modified: pkg/webpages/contribute.html
===================================================================
--- pkg/webpages/contribute.html 2011-03-09 20:09:52 UTC (rev 695)
+++ pkg/webpages/contribute.html 2011-03-09 21:01:14 UTC (rev 696)
@@ -8,51 +8,51 @@
<p>
While you are browsing through this web-site, you may find broken links or
some inconsistencies. We will appreciate if you report these to the web-site
-admin ( ADDRESS ).
+admin ( see "People" pages) [ <a href="?q=people">People</a> ]
</p>
-<h3>Help users</h3>
+<h3>Help others</h3>
<p>
-If you are experienced GenABEL user, subscribe to the GenABEL forum
-[ <a href="http://forum.genabel.org">GenABEL forum</a> ],
-and help answering questions from other users.
+If you are experienced GenABEL user, please subscribe to the GenABEL forum,
+and help answering questions from other users
+[ <a href="http://forum.genabel.org">GenABEL forum</a> ]
</p>
<h3>Bug reporting</h3>
<p>
If you think you have identified a bug, please discuss that at the
-forum [ FORUM ], and submit it to the developers
-[ How to report a bug ].
+forum, and submit it to the genabel-devel mailing list
+[ <a href="http://forum.genabel.org">GenABEL forum</a> |
+<a href="?q=developers">For developers</a> ]
</p>
<h3>Cleaning up the documentation</h3>
<p>
You can help cleaning up the documentation: there are some grammatical errors,
awkward phrasing, and unclear parts. If you are willing to do that,
-please contact one of the coordinators
-(see [ <a href="/drupal6/?q=people">People</a> ]).
+please contact one of the coordinators (see "people" pages)
+[ <a href="/drupal6/?q=people">People</a> ]
</p>
<h3>Contribute a tutorial</h3>
<p>
While we try to have complete tutorial, we hope for your
help with new ones. If you think you can contribute a
-tutorial, please contact us at the genabel-dev list
-(genabel-devel [at] lists [dot] r-forge [dot] r-project [dot] org) with your
+tutorial, please contact us at the genabel-devel list with your
suggestion. We then will discuss how how to do that in the best way
-(e.g. we mostly use Sweave for developing the tutorials).
+(e.g. we mostly use Sweave for developing the tutorials)
+[ <a href="?q=developers">For developers</a> ]
</p>
<h3>Fixing the bugs and adding new features</h3>
<p>
There are few bugs, and also missing features in GenABEL suite
-[ <a href="https://r-forge.r-project.org/tracker/?group_id=505">GenABEL tracker</a> ].
We will greatly appreciate your help in fixing the bugs and adding new features.
-If you'd like to do that, please send an e-mail to the genabel-dev list
-(genabel-devel [at] lists [dot] r-forge [dot] r-project [dot] org) with your
-suggestion to co-ordinate your efforts.
+If you'd like to do that, please send an e-mail to the genabel-dev list with your
+suggestion to co-ordinate the efforts
<em>Further information:</em> please read "How to contribute a patch"
-[ How to contribute a patch ]
+[ <a href="https://r-forge.r-project.org/tracker/?group_id=505">GenABEL tracker</a> |
+<a href="?q=developers">For developers</a> ]
</p>
<h3>New functionality</h3>
@@ -61,11 +61,9 @@
into GenABEL suite framework (as a function or as a package),
to start with,
please contact us through
-the genabel-devel list
-(genabel-devel [at] lists [dot] r-forge [dot] r-project [dot] org) with your
-suggestion to co-ordinate your efforts in a case somebody is already working
-on similar or related project.
+the genabel-devel list with your
+suggestion to co-ordinate our efforts
<em>Further information:</em> please read "How to contribute a package"
-[ How to contribute a package ]
+[ <a href="?q=developers">For developers</a> ]
</p>
Modified: pkg/webpages/home.html
===================================================================
--- pkg/webpages/home.html 2011-03-09 20:09:52 UTC (rev 695)
+++ pkg/webpages/home.html 2011-03-09 21:01:14 UTC (rev 696)
@@ -13,17 +13,18 @@
</p>
<ul>
<li>Reach in functionality. Many packages with 100+ functions related to genomic analysis
-[ Packages ]</li>
+[ <a href="?q=packages">Packages</a> ]</li>
<li>Efficient. Meaning you can run a
-genome-wide association scan on a netBook [ Tutorials-Running1000gGWASonNetBook ] </li>
-<li>Flexible. Programming your custom analysis is easy [ Tutorials-RunningCustomAnalysis ] </li>
-<li>Open, transparent, free. Most of the code released under GNU GPL [ License ]</li>
+genome-wide association scan on a netBook</li>
+<li>Flexible. Programming your custom analysis is easy</li>
+<li>Open, transparent, free. Most of the code released under GNU GPL
+[ <a href="http://www.gnu.org/licenses/gpl.html">GNU GPL</a> ]</li>
<li>Well documented. More then 200 pages of reference manuals and about 300 pages of tutorials
-[ Tutorials | Manuals ]</li>
-<li>Supported. By community [ Forum ] </li>
-<li>Collaborative. Community is open for your contribution [ Contribute ] </li>
+[ <a href="?q=tutorials">Tutorials</a> |
+<a href="?q=manuals">Manuals</a> ]</li>
+<li>Supported. By community [ <a href="http://forum.genabel.org">Forum</a> ] </li>
+<li>Collaborative. Community is open for your contribution
+[ <a href="?q=contribute">Contribute</a> ] </li>
</ul>
-Here we need News and news feed
-
-Google Analytics script
+Here we need News and news feed
\ No newline at end of file
Modified: pkg/webpages/packages.html
===================================================================
--- pkg/webpages/packages.html 2011-03-09 20:09:52 UTC (rev 695)
+++ pkg/webpages/packages.html 2011-03-09 21:01:14 UTC (rev 696)
@@ -10,7 +10,7 @@
<p>
Most likely, you only need one of the packages for your specific task.
Figure out which one you need, install, and use! If you have questions,
-please refer to the "<a href="http://test.genabel.org/drupal6/?q=node/5">Support</a>"
+please refer to the "<a href="?q=support">Support</a>"
section of this web-site.
</p>
<p>
@@ -22,39 +22,39 @@
</p>
<a name="GenABEL"></a>
-<h3><a href="/drupal6/?q=packages/GenABEL">GenABEL</a></h3>
+<h3><a href="?q=packages/GenABEL">GenABEL</a></h3>
Genome-wide association analysis for quantitative, binary and time-till-event traits
<p></p>
<a name="MetABEL"></a>
-<h3><a href="/drupal6/?q=packages/MetABEL">MetABEL</a></h3>
+<h3><a href="?q=packages/MetABEL">MetABEL</a></h3>
Meta-analysis of genome-wide SNP association results
Genome-wide association analysis for quantitative, binary and time-till-event traits
<p></p>
<a name="ProbABEL"></a>
-<h3><a href="/drupal6/?q=packages/ProbABEL">ProbABEL</a></h3>
+<h3><a href="?q=packages/ProbABEL">ProbABEL</a></h3>
Genome-wide association analysis of imputed data
<p></p>
<a name="PredictABEL"></a>
-<h3><a href="/drupal6/?q=packages/PredictABEL">PredictABEL</a></h3>
+<h3><a href="?q=packages/PredictABEL">PredictABEL</a></h3>
Assess the performance of risk models for binary outcomes
<p></p>
<a name="DatABEL"></a>
-<h3><a href="/drupal6/?q=packages/DatABEL">DatABEL</a></h3>
+<h3><a href="?q=packages/DatABEL">DatABEL</a></h3>
File-based access to large matrices stored on HDD in binary format
<p></p>
<a name="ParallABEL"></a>
-<h3><a href="/drupal6/?q=packages/ParallABEL">ParallABEL</a></h3>
+<h3><a href="?q=packages/ParallABEL">ParallABEL</a></h3>
Generalized parallelization of Genome-Wide Association Studies
<p></p>
<a name="MixABEL"></a>
-<h3><a href="/drupal6/?q=packages/MixABEL">MixABEL</a></h3>
+<h3><a href="?q=packages/MixABEL">MixABEL</a></h3>
More mixed models for genome-wide association analysis; experimenting with GSL, multiple input formats, iterator, parallelization through threads.
<p></p>
Modified: pkg/webpages/people.html
===================================================================
--- pkg/webpages/people.html 2011-03-09 20:09:52 UTC (rev 695)
+++ pkg/webpages/people.html 2011-03-09 21:01:14 UTC (rev 696)
@@ -63,5 +63,8 @@
<p>
<h3>Note</h3>
-Large part of GenABEL packages are R-package, and we greatly appreciate work done by <a href="http://www.r-project.org">R</a> team, <a href="http://cran.r-project.org/">CRAN</a>, and <a href="http://r-forge.r-project.org/">R-forge</a>
+Large part of GenABEL packages are R-package, and we greatly appreciate work done by
+<a href="http://www.r-project.org">R</a> team,
+<a href="http://cran.r-project.org/">CRAN</a>, and
+<a href="http://r-forge.r-project.org/">R-forge</a>
</p>
Modified: pkg/webpages/pkgMixABEL.html
===================================================================
--- pkg/webpages/pkgMixABEL.html 2011-03-09 20:09:52 UTC (rev 695)
+++ pkg/webpages/pkgMixABEL.html 2011-03-09 21:01:14 UTC (rev 696)
@@ -2,7 +2,8 @@
More mixed models for genome-wide association analysis; experimenting with GSL, multiple input formats, iterator, parallelization through threads.
<ul>
<li><em>Status:</em> beta, experimental</li>
-<li><em>Install:</em> Install <a href="http://www.gnu.org/software/gsl/">GNU GSL</a>, download proper distribution and install [ <a href="http://test.genabel.org/old/software/MixABEL_0.0-9.tar.gz">source code</a> | Windows package | Mac OS package] </li>
+<li><em>Install:</em> Install <a href="http://www.gnu.org/software/gsl/">GNU GSL</a>, download proper distribution and install
+[ <a href="/old/software/MixABEL_0.0-9.tar.gz">source code</a> | Windows package | Mac OS package] </li>
<li><em>Quick start:</em> start R, then library(MixABEL); example(GWFGLS)</li>
<li><em>Tutorial:</em> Will be embed as extension to see "ABEL tutorial", section "GWA analysis in presence of stratiÞcation"</li>
<li><em>Manual:</em> [ <a href="/old/pdfs/MixABEL.pdf">PDF</a> |
Modified: pkg/webpages/pkgProbABEL.html
===================================================================
--- pkg/webpages/pkgProbABEL.html 2011-03-09 20:09:52 UTC (rev 695)
+++ pkg/webpages/pkgProbABEL.html 2011-03-09 21:01:14 UTC (rev 696)
@@ -2,9 +2,10 @@
Genome-wide association analysis of imputed data
<ul>
<li><em>Status:</em> Stable</li>
-<li><em>Install:</em> Download source code, unpack, read ProbABEL/doc/INSTALL [ <a href="http://test.genabel.org/old/software/ProbABEL_0.1-9d.tar.gz">stable source code</a> | Mas OS binary | Win 64 binary | Win 32 binary ]</li>
+<li><em>Install:</em> Download source code, unpack, read ProbABEL/doc/INSTALL
+[ <a href="/old/software/ProbABEL_0.1-9d.tar.gz">stable source code</a> | Mas OS binary | Win 64 binary | Win 32 binary ]</li>
<li><em>Quick start:</em> after install, cd examples; sh example_all.sh</li>
-<li><em>Tutorial:</em> would someone like to <a href="http://test.genabel.org/drupal6/?q=node/9">contribute</a> one?</li>
+<li><em>Tutorial:</em> would someone like to <a href="?q=contribute">contribute</a> one?</li>
<li><em>Manual:</em> [ <a href="/old/pdfs/ProbABEL_manual.pdf">PDF</a> |
<a href="/drupal6/?q=manuals/ProbABEL">HTML</a> ]</li>
<li><em>Reference:</em> <a href="http://www.ncbi.nlm.nih.gov/pubmed/20233392" target="_blank">ProbABEL package for genome-wide association analysis of imputed data</a></li>
Modified: pkg/webpages/showcase.html
===================================================================
--- pkg/webpages/showcase.html 2011-03-09 20:09:52 UTC (rev 695)
+++ pkg/webpages/showcase.html 2011-03-09 21:01:14 UTC (rev 696)
@@ -8,7 +8,8 @@
<li><a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0011117">Genetic Loci Involved in Antibody Response to <i>Mycobacterium avium ssp. paratuberculosis</i> in Cattle</a>, identified with the help of GenABEL (PLoS ONE)
<li> <a href="http://www.ncbi.nlm.nih.gov/pubmed/18252221?ordinalpos=17&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum">Eye colour loci</a> discovered using GenABEL (American Journal of Human Genetics)
<li> ...
-<li> In total: 92 papers citing GenABEL and ProbABEL packages, and GRAMMAR and GRAMMAR-GC methods (ISI Web of Knowledge, 2010.06.18)
+<li> In total: 200+ papers citing packages from the GenABEL suite,
+or methodology developed and implemented as part of GenABEL suite (Google Scholar, 2011.03.09)
</ul>
-<h3>Screenshots</h3>
\ No newline at end of file
+<h3>Here some screenshots</h3>
\ No newline at end of file
Modified: pkg/webpages/support.html
===================================================================
--- pkg/webpages/support.html 2011-03-09 20:09:52 UTC (rev 695)
+++ pkg/webpages/support.html 2011-03-09 21:01:14 UTC (rev 696)
@@ -4,28 +4,43 @@
<em>How do I run specific analysis?</em>
<ul>
-<li>Look through general GenABEL tutorial [ <a href="http://test.genabel.org/drupal6/?q=htmlTut">Tutorials</a> ] and decide on what package to use [ <a href="http://test.genabel.org/drupal6/?q=node/6">Packages</a> ]</li>
-<li>Carefully read tutorial (if available) section specific to your analyses, figure out what functions you need to use, run the examples</li>
-<li>Read help pages for relevant functions (in R, use 'help(functionname)'; or see Manuals section [ <a href="http://test.genabel.org/drupal6/?q=node/84">Manuals</a> ])</li>
-<li>If it is still not clear how to run analysis, search GenABEL forum [ <a href="http://forum.genabel.org">GenABEL forum</a> ] </li>
-<li>If no answer, ask your question at the GenABEL forum [ <a href="http://forum.genabel.org">GenABEL forum</a> ]</li>
+<li>Look through general GenABEL tutorial [ <a href="?q=tutorials">Tutorials</a> ]
+and decide on what package to use [ <a href="?q=packages">Packages</a> ]</li>
+<li>Carefully read tutorial (if available) section specific to your analyses, figure
+out what functions you need to use, run the examples</li>
+<li>Read help pages for relevant functions (in R, use 'help(functionname)'; or see
+Manuals section [ <a href="?q=manuals">Manuals</a> ])</li>
+<li>If it is still not clear how to run analysis, search GenABEL forum
+[ <a href="http://forum.genabel.org">GenABEL forum</a> ] </li>
+<li>If no answer, ask your question at the GenABEL forum
+[ <a href="http://forum.genabel.org">GenABEL forum</a> ]</li>
</ul>
-<em>I want to do some special analysis, which does not seem to be supported. How can I figure out if there is a workaround or if this is a planned feature?</em>
+<em>I want to do some special analysis, which does not seem to be supported.
+How can I figure out if there is a workaround or if this is a planned feature?</em>
<ul>
-<li>Look through general GenABEL tutorial [ <a href="http://test.genabel.org/drupal6/?q=htmlTut">Tutorials</a> ]</li>
-<li>Search Tutorials [ <a href="http://test.genabel.org/drupal6/?q=htmlTut">Tutorials</a> ] and Manuals [ <a href="http://test.genabel.org/drupal6/?q=node/84">Manuals</a> ]</li>
+<li>Look through general GenABEL tutorial
+[ <a href="?q=tutorials">Tutorials</a> ]</li>
+<li>Search Tutorials [ <a href="?q=tutorials">Tutorials</a> ]
+and Manuals [ <a href="?q=manuals">Manuals</a> ]</li>
<li>Search GenABEL forum [ <a href="http://forum.genabel.org">GenABEL forum</a> ] </li>
-<li>If you can not find anything, ask your question at GenABEL forum [ <a href="http://forum.genabel.org">GenABEL forum</a> ]. See <a href="http://forum.genabel.org/viewtopic.php?f=6&t=15">example</a></li>
-<li>If no answer, contact developers to file in feature request genabel-devel [at] lists [dot] r-forge [dot] r-project [dot] org</li>
+<li>If you can not find anything, ask your question at GenABEL forum
+[ <a href="http://forum.genabel.org">GenABEL forum</a> ].
+See <a href="http://forum.genabel.org/viewtopic.php?f=6&t=15">example</a></li>
+<li>If no answer, contact developers to file in feature request
+genabel-devel [at] lists [dot] r-forge [dot] r-project [dot] org</li>
</ul>
<a name="bug"></a>
<em>A command behaves not in a way I expect, is that a bug?</em>
<ul>
-<li>Read help pages for the functions (in R, use 'help(functionname)'; or see Manuals section [ <a href="http://test.genabel.org/drupal6/?q=node/84">Manuals</a> ])</li>
+<li>Read help pages for the functions (in R, use 'help(functionname)';
+or see Manuals section [ <a href="?q=manuals">Manuals</a> ])</li>
<li>Search GenABEL forum [ <a href="http://forum.genabel.org">GenABEL forum</a> ] </li>
-<li>If still not solved, post suggested bug at GenABEL forum [ <a href="http://forum.genabel.org">GenABEL forum</a> ]. See an <a href="http://forum.genabel.org/viewtopic.php?f=6&t=4">example here</a>.</li>
-<li>If no answer, contact developers to file in feature request genabel-devel [at] lists [dot] r-forge [dot] r-project [dot] org</li>
+<li>If still not solved, post suggested bug at GenABEL forum
+[ <a href="http://forum.genabel.org">GenABEL forum</a> ]. See an
+<a href="http://forum.genabel.org/viewtopic.php?f=6&t=4">example here</a>.</li>
+<li>If no answer, contact developers to file in feature request
+genabel-devel [at] lists [dot] r-forge [dot] r-project [dot] org</li>
</ul>
Modified: pkg/webpages/tutorials.html
===================================================================
--- pkg/webpages/tutorials.html 2011-03-09 20:09:52 UTC (rev 695)
+++ pkg/webpages/tutorials.html 2011-03-09 21:01:14 UTC (rev 696)
@@ -1,9 +1,9 @@
<h3>Tutorials</h3>
<ul>
<li>General extensive tutorial on GenABEL suite
-[ <a href="http://test.genabel.org/drupal6/?q=htmlTut/ABEL-tutorial">HTML</a> |
-<a href="http://test.genabel.org/old/pdfs/ABEL-tutorial.pdf">PDF</a> ]</li>
+[ <a href="?q=tutorials/ABEL-tutorial">HTML</a> |
+<a href="/old/pdfs/ABEL-tutorial.pdf">PDF</a> ]</li>
<li>Introduction to DatABEL
-[ <a href="http://test.genabel.org/drupal6/?q=htmlTut/intro_DatABEL">HTML</a> |
-<a href="http://test.genabel.org/old/pdfs/intro_DatABEL.pdf">PDF</a> ]</li>
+[ <a href="?q=tutorials/intro_DatABEL">HTML</a> |
+<a href="/old/pdfs/intro_DatABEL.pdf">PDF</a> ]</li>
</ul>
\ No newline at end of file
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