diff --git a/docs.it4i/anselm-cluster-documentation/software/bio-gentoo.md b/docs.it4i/anselm-cluster-documentation/software/bio-gentoo.md
deleted file mode 100644
index 649fe3be4ed1ce3b0c8b9c9add3fe3584599bdf4..0000000000000000000000000000000000000000
--- a/docs.it4i/anselm-cluster-documentation/software/bio-gentoo.md
+++ /dev/null
@@ -1,72 +0,0 @@
-Bioinformatics Applications
-==========================
-
-Introduction
-------------
-
-In addition to the many applications available through modules (deployed through EasyBuild packaging system) we provide an alternative source of applications on our clusters inferred from Gentoo Linux ( www.gentoo.org ). The user's environment is setup through a script which returns a bash instance to the user (you can think of it a starting a whole virtual machine but inside your current namespace) . The applications were optimized by gcc compiler for the SandyBridge and IvyBridge platforms. The binaries use paths from /apps/gentoo prefix to find the required runtime dependencies, config files, etc. The Gentoo Linux is a standalone installation not even relying on the glibc provided by host operating system (Redhat). The trick which allowed us to install Gentoo Linux on the host Redhat system is called Gentoo::RAP and uses a modified loader with a hardcoded path ( https://wiki.gentoo.org/wiki/Prefix/libc ).
-
-
-Starting the environment
-------------------------
-
-```bash
-$ /apps/gentoo/startprefix
-```
-
-Starting PBS jobs using the applications
-----------------------------------------
-
-Create a template file which can be used and an argument to qsub command. Notably, the 'PBS -S' line specifies full PATH to the Bourne shell of the Gentoo Linux environment.
-
-```bash
-$ cat myjob.pbs
-#PBS -S /apps/gentoo/bin/sh
-#PBS -l nodes=1:ppn=16,walltime=12:00:00
-#PBS -q qfree
-#PBS -M my_email@foo.bar
-#PBS -m ea
-#PBS -N sample22
-#PBS -A DD-13-5
-#source ~/.bashrc
-
-cd $PBS_O_WORKDIR || exit 255
-
-myscript.sh foo 1>myjob.log 2>&1
-
-$ head -n 1 myscript.sh
-#! /apps/gentoo/bin/sh
-$ qsub myjob.pbs
-$ qstat
-```
-
-Reading manual pages for installed applications
------------------------------------------------
-
-```bash
-$ man -M /apps/gentoo/usr/share/man bwa
-$ man -M /apps/gentoo/usr/share/man samtools
-```
-
-Listing of bioinformatics applications
---------------------------------------
-
-[gentoo_apps_on_anselm.doc](src/gentoo_apps_on_anselm.doc)
-
-
-Classification of applications
-------------------------------
-
-[gentoo_apps_on_anselm.xls](src/gentoo_apps_on_anselm.xls)
-
-
-Other applications available through Gentoo Linux
--------------------------------------------------
-
-Gentoo Linux is a allows compilation of its applications from source code while using compiler and optimize flags set to user's wish. This facilitates creation of optimized binaries for the host platform. Users maybe also use several versions of gcc, python and other tools.
-
-```bash
-$ gcc-config -l
-$ java-config -L
-$ eselect
-```
diff --git a/docs.it4i/img/bio-graphs.png b/docs.it4i/img/bio-graphs.png
new file mode 100644
index 0000000000000000000000000000000000000000..2bd3b67f8e9ecb8818df8fd0b494347bb283d7ea
Binary files /dev/null and b/docs.it4i/img/bio-graphs.png differ
diff --git a/docs.it4i/salomon/software/chemistry/nwchem.md b/docs.it4i/salomon/software/chemistry/nwchem.md
index 7b8723087be11bc4458eb9e5f2084607e6a563d2..3db648754f6ad50e0ae89758ae825c4cb20956d7 100644
--- a/docs.it4i/salomon/software/chemistry/nwchem.md
+++ b/docs.it4i/salomon/software/chemistry/nwchem.md
@@ -44,4 +44,4 @@ Options
Please refer to [the documentation](http://www.nwchem-sw.org/index.php/Release62:Top-level) and in the input file set the following directives :
- MEMORY : controls the amount of memory NWChem will use
-- SCRATCH_DIR : set this to a directory in [SCRATCH filesystem](../../storage/storage/) (or run the calculation completely in a scratch directory). For certain calculations, it might be advisable to reduce I/O by forcing "direct" mode, eg. "scf direct"
+- SCRATCH_DIR : set this to a directory in [SCRATCH filesystem](../../storage/storage/) (or run the calculation completely in a scratch directory). For certain calculations, it might be advisable to reduce I/O by forcing "direct" mode, eg. "scf direct"
diff --git a/docs.it4i/salomon/software/numerical-languages/r.md b/docs.it4i/salomon/software/numerical-languages/r.md
index 721c67cbef7a875695a724f13e4b52760092d904..2c1f610d2c35ded501c8fe862d5ebd8052b97080 100644
--- a/docs.it4i/salomon/software/numerical-languages/r.md
+++ b/docs.it4i/salomon/software/numerical-languages/r.md
@@ -20,7 +20,7 @@ Modules
|Application|Version|module|
|---|---|
|**R**|R 3.1.1|R/3.1.1-intel-2015b|
-|**Rstudio**|Rstudio 0.97|Rstudio|
+|**Rstudio**|Rstudio 0.98.1103|Rstudio|
```bash
$ module load R
@@ -97,7 +97,7 @@ Download the package [parallell](package-parallel-vignette.pdf) vignette.
The forking is the most simple to use. Forking family of functions provide parallelized, drop in replacement for the serial apply() family of functions.
-!!! Note "Note"
+!!! warning
Forking via package parallel provides functionality similar to OpenMP construct omp parallel for
Only cores of single node can be utilized this way!
diff --git a/docs.it4i/software/bio-gentoo.md b/docs.it4i/software/bio-gentoo.md
new file mode 100644
index 0000000000000000000000000000000000000000..c96a6bf0646740a11d8508bd11bc61b86fe65d0d
--- /dev/null
+++ b/docs.it4i/software/bio-gentoo.md
@@ -0,0 +1,260 @@
+Bioinformatics Applications
+==========================
+
+Introduction
+------------
+
+In addition to the many applications available through modules (deployed through EasyBuild packaging system) we provide an alternative source of applications on our clusters inferred from Gentoo Linux ( www.gentoo.org ). The user's environment is setup through a script which returns a bash instance to the user (you can think of it a starting a whole virtual machine but inside your current namespace) . The applications were optimized by gcc compiler for the SandyBridge and IvyBridge platforms. The binaries use paths from /apps/gentoo prefix to find the required runtime dependencies, config files, etc. The Gentoo Linux is a standalone installation not even relying on the glibc provided by host operating system (Redhat). The trick which allowed us to install Gentoo Linux on the host Redhat system is called Gentoo::RAP and uses a modified loader with a hardcoded path ( https://wiki.gentoo.org/wiki/Prefix/libc ).
+
+
+Starting the environment
+------------------------
+
+```bash
+$ /apps/gentoo/startprefix
+```
+
+Starting PBS jobs using the applications
+----------------------------------------
+
+Create a template file which can be used and an argument to qsub command. Notably, the 'PBS -S' line specifies full PATH to the Bourne shell of the Gentoo Linux environment.
+
+```bash
+$ cat myjob.pbs
+#PBS -S /apps/gentoo/bin/sh
+#PBS -l nodes=1:ppn=16,walltime=12:00:00
+#PBS -q qfree
+#PBS -M my_email@foo.bar
+#PBS -m ea
+#PBS -N sample22
+#PBS -A DD-13-5
+#source ~/.bashrc
+
+cd $PBS_O_WORKDIR || exit 255
+
+myscript.sh foo 1>myjob.log 2>&1
+
+$ head -n 1 myscript.sh
+#! /apps/gentoo/bin/sh
+$ qsub myjob.pbs
+$ qstat
+```
+
+Reading manual pages for installed applications
+-----------------------------------------------
+
+```bash
+$ man -M /apps/gentoo/usr/share/man bwa
+$ man -M /apps/gentoo/usr/share/man samtools
+```
+
+Listing of bioinformatics applications
+--------------------------------------
+
+```bash
+mmokrejs@login2 ~ $ grep biology /scratch/mmokrejs/gentoo_rap/installed.txt
+sci-biology/ANGLE-bin-20080813-r1
+sci-biology/AlignGraph-9999
+sci-biology/Atlas-Link-0.01-r1
+sci-biology/BRANCH-9999
+sci-biology/EBARDenovo-1.2.2
+sci-biology/FLASH-1.2.9
+sci-biology/GAL-0.2.2
+sci-biology/Gambit-0.4.145
+sci-biology/HTSeq-0.6.1
+sci-biology/InterMine-0.98
+sci-biology/MochiView-1.45
+sci-biology/MuSeqBox-5.4
+sci-biology/ONTO-PERL-1.41
+sci-biology/ORFcor-20130507
+sci-biology/Rcorrector-9999
+sci-biology/SSAKE-3.8.2
+sci-biology/STAR-9999
+sci-biology/YASRA-2.33
+sci-biology/abacas-1.3.1
+sci-biology/align_to_scf-1.06
+sci-biology/assembly-stats-9999
+sci-biology/bambus-2.33
+sci-biology/bamtools-9999
+sci-biology/bcftools-1.2
+sci-biology/bedtools-2.22.1
+sci-biology/bfast-0.7.0a
+sci-biology/biobambam2-9999
+sci-biology/bismark-0.13.0
+sci-biology/blat-34-r1
+sci-biology/blue-1.1.3
+sci-biology/bowtie-2.2.9
+sci-biology/brat-1.2.4
+sci-biology/bwa-0.7.13
+sci-biology/bx-python-9999
+sci-biology/cast-bin-20080813
+sci-biology/cd-hit-4.6.5
+sci-biology/cdbfasta-0.1
+sci-biology/clover-2011.10.24
+sci-biology/clustalw-2.1
+sci-biology/cnrun-2.0.3
+sci-biology/codonw-1.4.4-r2
+sci-biology/conform-gt-1174
+sci-biology/conifer-0.2.2
+sci-biology/coral-1.4
+sci-biology/cross_genome-20140822
+sci-biology/cutadapt-9999
+sci-biology/dawg-1.1.2
+sci-biology/dna2pep-1.1
+sci-biology/edena-3.131028
+sci-biology/epga-9999
+sci-biology/erpin-5.5b
+sci-biology/estscan-3.0.3
+sci-biology/eugene-4.1d
+sci-biology/exonerate-gff3-9999
+sci-biology/fastx_toolkit-0.0.14
+sci-biology/gemini-9999
+sci-biology/geneid-1.4.4
+sci-biology/genepop-4.2.1
+sci-biology/glimmerhmm-3.0.1-r1
+sci-biology/gmap-2015.12.31.5
+sci-biology/hexamer-19990330
+sci-biology/hts-python-9999
+sci-biology/jellyfish-2.1.4
+sci-biology/jigsaw-3.2.10
+sci-biology/kallisto-9999
+sci-biology/karect-1.0.0
+sci-biology/lastz-1.03.66
+sci-biology/libgtextutils-0.6.1
+sci-biology/lucy-1.20
+sci-biology/megahit-9999
+sci-biology/merlin-1.1.2
+sci-biology/miranda-3.3a
+sci-biology/mreps-2.5
+sci-biology/mrfast-2.6.0.1
+sci-biology/mummer-3.22-r1
+sci-biology/muscle-3.8.31
+sci-biology/nrcl-110625
+sci-biology/nwalign-0.3.1
+sci-biology/oases-9999
+sci-biology/parafly-20130121
+sci-biology/phrap-1.080812-r1
+sci-biology/phred-071220
+sci-biology/phylip-3.696-r1
+sci-biology/plinkseq-0.10
+sci-biology/primer3-2.3.7
+sci-biology/prinseq-lite-0.20.4
+sci-biology/proda-1.0
+sci-biology/pybedtools-0.6.9
+sci-biology/pysam-0.9.0
+sci-biology/pysamstats-0.24.2
+sci-biology/quast-2.3
+sci-biology/quorum-1.0.0
+sci-biology/reaper-15348
+sci-biology/repeatmasker-libraries-20150807
+sci-biology/reptile-1.1
+sci-biology/samstat-20130708
+sci-biology/samtools-0.1.20-r2
+sci-biology/samtools-1.3-r1
+sci-biology/scaffold_builder-20131122-r1
+sci-biology/scan_for_matches-20121220
+sci-biology/screed-0.7.1
+sci-biology/scythe-0.992
+sci-biology/seqan-2.1.1
+sci-biology/seqtools-4.34.5
+sci-biology/sff_dump-1.04
+sci-biology/sgp2-1.1
+sci-biology/shrimp-2.2.3
+sci-biology/sickle-9999
+sci-biology/smalt-0.7.6
+sci-biology/snpomatic-9999
+sci-biology/ssaha2-bin-2.5.5
+sci-biology/stampy-1.0.28
+sci-biology/stringtie-1.2.2
+sci-biology/subread-1.4.6
+sci-biology/swissknife-1.72
+sci-biology/tagdust-20101028
+sci-biology/tclust-110625
+sci-biology/tigr-foundation-libs-2.0-r1
+sci-biology/trans-abyss-1.4.8
+sci-biology/trf-4.07b
+sci-biology/uchime-4.2.40
+sci-biology/velvet-1.2.10
+sci-biology/velvetk-20120606
+sci-biology/zmsort-110625
+```
+
+```bash
+mmokrejs@login2 ~ $ grep sci-libs /scratch/mmokrejs/gentoo_rap/installed.txt
+sci-libs/amd-2.3.1
+sci-libs/blas-reference-20151113-r1
+sci-libs/camd-2.3.1
+sci-libs/cbflib-0.9.3.3
+sci-libs/ccolamd-2.8.0
+sci-libs/cholmod-2.1.2
+sci-libs/coinor-cbc-2.8.9
+sci-libs/coinor-cgl-0.58.6
+sci-libs/coinor-clp-1.15.6-r1
+sci-libs/coinor-dylp-1.9.4
+sci-libs/coinor-osi-0.106.6
+sci-libs/coinor-utils-2.9.11
+sci-libs/coinor-vol-1.4.4
+sci-libs/colamd-2.8.0
+sci-libs/cxsparse-3.1.2
+sci-libs/dcmtk-3.6.0
+sci-libs/gsl-2.1
+sci-libs/hdf5-1.8.15_p1
+sci-libs/htslib-1.3
+sci-libs/io_lib-1.14.7
+sci-libs/lapack-reference-3.6.0-r1
+sci-libs/lemon-1.3-r2
+sci-libs/libmaus2-9999
+sci-libs/qrupdate-1.1.2-r1
+sci-libs/scikits-0.1-r1
+sci-libs/suitesparseconfig-4.2.1
+sci-libs/umfpack-5.6.2
+mmokrejs@login2 ~ $
+
+ error-correctors
+ aligners
+ clusterers
+ assemblers
+ scaffolders
+ motif searching
+ ORF/gene prediction/genome annotation
+ genotype/haplotype/popullation genetics
+ phylogenetics
+ transcriptome analysis
+ utilities
+ GUI
+ libraries
+```
+
+Classification of applications
+------------------------------
+
+|Applications for bioinformatics at IT4I |
+|---|---|
+|error-correctors|6|
+|aligners|20|
+|clusterers|5|
+|assemblers|9|
+|scaffolders|6|
+|motif searching|6|
+|ORF/gene prediction/genome annotation|13|
+|genotype/haplotype/popullation genetics|3|
+|phylogenetics|1|
+|transcriptome analysis|2|
+|utilities|15|
+|GUI|3|
+|libraries|4|
+|**Total**|**93**|
+
+
+
+
+Other applications available through Gentoo Linux
+-------------------------------------------------
+
+Gentoo Linux is a allows compilation of its applications from source code while using compiler and optimize flags set to user's wish. This facilitates creation of optimized binaries for the host platform. Users maybe also use several versions of gcc, python and other tools.
+
+```bash
+$ gcc-config -l
+$ java-config -L
+$ eselect
+```
diff --git a/docs.it4i/software/orca.md b/docs.it4i/software/orca.md
new file mode 100644
index 0000000000000000000000000000000000000000..93e6473431ea7172c6cde0a1f16d383023c82b00
--- /dev/null
+++ b/docs.it4i/software/orca.md
@@ -0,0 +1,104 @@
+ORCA
+====
+
+ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects.
+
+Making orca available
+---------------------
+
+The following module command makes the latest version of orca available to your session
+
+```bash
+$ module load ORCA/3_0_3-linux_x86-64
+```
+
+**Dependency**
+
+```bash
+$ module list
+Currently Loaded Modulefiles:
+ 1) /opt/modules/modulefiles/oscar-modules/1.0.3(default)
+ 2) GCC/4.9.3-binutils-2.25
+ 3) binutils/2.25-GCC-4.9.3-binutils-2.25
+ 4) GNU/4.9.3-2.25
+ 5) icc/2015.3.187-GNU-4.9.3-2.25
+ 6) ifort/2015.3.187-GNU-4.9.3-2.25
+ 7) iccifort/2015.3.187-GNU-4.9.3-2.25
+ 8) numactl/2.0.10-iccifort-2015.3.187-GNU-4.9.3-2.25
+ 9) hwloc/1.11.1-iccifort-2015.3.187-GNU-4.9.3-2.25
+ 10) OpenMPI/1.8.8-iccifort-2015.3.187-GNU-4.9.3-2.25
+ 11) ORCA/3_0_3-linux_x86-64
+```
+
+Example single core job
+-----------------------
+
+Create a file called orca_serial.inp that contains the following orca commands
+
+```
+# My first ORCA calculation :-)
+#
+# Taken from the Orca manual
+# https://orcaforum.cec.mpg.de/OrcaManual.pdf
+! HF SVP
+* xyz 0 1
+ C 0 0 0
+ O 0 0 1.13
+*
+```
+
+Create a Sun Grid Engine submission file called submit_serial.sh that looks like this
+
+```bash
+!/bin/bash
+
+module load ORCA/3_0_3-linux_x86-64
+orca orca_serial.inp
+```
+
+Submit the job to the queue with the command
+
+```bash
+$ qsub -q qexp -I -l select=1
+qsub: waiting for job 196821.isrv5 to start
+qsub: job 196821.isrv5 ready
+[username@r37u04n944 ~]$ ./submit_serial.sh
+
+
+ *****************
+ * O R C A *
+ *****************
+
+ --- An Ab Initio, DFT and Semiempirical electronic structure package ---
+
+ #######################################################
+ # -***- #
+ # Department of molecular theory and spectroscopy #
+ # Directorship: Frank Neese #
+ # Max Planck Institute for Chemical Energy Conversion #
+ # D-45470 Muelheim/Ruhr #
+ # Germany #
+ # #
+ # All rights reserved #
+ # -***- #
+ #######################################################
+
+...
+
+ ****ORCA TERMINATED NORMALLY****
+TOTAL RUN TIME: 0 days 0 hours 0 minutes 2 seconds 796 msec
+[username@r37u04n944 orca]$ logout
+
+qsub: job 196821.isrv5 completed
+```
+
+Register as a user
+------------------
+
+You are encouraged to register as a user of Orca at [Here](https://orcaforum.cec.mpg.de/) in order to take advantage of updates, announcements and also of the users forum.
+
+Documentation
+-------------
+
+A comprehensive [.pdf](https://orcaforum.cec.mpg.de/OrcaManual.pdf) manual is available online.
+
diff --git a/docs.it4i/src/.~lock.gentoo_apps_on_anselm.xls# b/docs.it4i/src/.~lock.gentoo_apps_on_anselm.xls#
new file mode 100644
index 0000000000000000000000000000000000000000..49f490840e73df8765eb9e296eaf161220b52cc5
--- /dev/null
+++ b/docs.it4i/src/.~lock.gentoo_apps_on_anselm.xls#
@@ -0,0 +1 @@
+,kru0052,kru0052,24.01.2017 06:58,file:///home/kru0052/.config/libreoffice/4;
\ No newline at end of file
diff --git a/docs.it4i/src/gentoo_apps_on_anselm.doc b/docs.it4i/src/gentoo_apps_on_anselm.doc
new file mode 100644
index 0000000000000000000000000000000000000000..71272d3aae07cd65930ce580a5c5c6ef68cedbd7
Binary files /dev/null and b/docs.it4i/src/gentoo_apps_on_anselm.doc differ
diff --git a/docs.it4i/src/gentoo_apps_on_anselm.xls b/docs.it4i/src/gentoo_apps_on_anselm.xls
new file mode 100644
index 0000000000000000000000000000000000000000..4524fdcc4bc1218c25cad3ff70f98913269da6bd
Binary files /dev/null and b/docs.it4i/src/gentoo_apps_on_anselm.xls differ
diff --git a/mkdocs.yml b/mkdocs.yml
index 9279364c5176bd4fd7419cf0c21edc266d964f2d..7e21b8a0015a94225128237938c457b386d983a6 100644
--- a/mkdocs.yml
+++ b/mkdocs.yml
@@ -53,7 +53,7 @@ pages:
- ANSYS MAPDL: anselm-cluster-documentation/software/ansys/ansys-mechanical-apdl.md
- LS-DYNA: anselm-cluster-documentation/software/ansys/ls-dyna.md
- 'Bioinformatics':
- - Bioinformatics Applications: anselm-cluster-documentation/software/bio-gentoo.md
+ - Bioinformatics Applications: software/bio-gentoo.md
- 'Debuggers':
- Allinea Forge (DDT,MAP): anselm-cluster-documentation/software/debuggers/allinea-ddt.md
- Allinea Performance Reports: anselm-cluster-documentation/software/debuggers/allinea-performance-reports.md
@@ -70,6 +70,7 @@ pages:
- 'Chemistry':
- Molpro: anselm-cluster-documentation/software/chemistry/molpro.md
- NWChem: anselm-cluster-documentation/software/chemistry/nwchem.md
+ - ORCA: software/orca.md
- COMSOL: anselm-cluster-documentation/software/comsol-multiphysics.md
- Compilers: anselm-cluster-documentation/software/compilers.md
- GPI-2: anselm-cluster-documentation/software/gpi2.md
@@ -138,10 +139,13 @@ pages:
- Workbench: salomon/software/ansys/workbench.md
- Setting License Preferences: salomon/software/ansys/licensing.md
- Licensing and Available Versions: salomon/software/ansys/setting-license-preferences.md
+ - 'Bioinformatics':
+ - Bioinformatics Applications: software/bio-gentoo.md
- 'Chemistry':
- Molpro: salomon/software/chemistry/molpro.md
- NWChem: salomon/software/chemistry/nwchem.md
- Phono3py: salomon/software/chemistry/phono3py.md
+ - ORCA: software/orca.md
- Compilers: salomon/software/compilers.md
- 'COMSOL':
- COMSOL: salomon/software/comsol/comsol-multiphysics.md