->

docs.it4i/anselm-cluster-documentation/software/debuggers/papi.md

@@ -20,7 +20,7 @@ This will load the default version. Execute module avail papi for a list of inst
 
 ## Utilities
 
-The  bin directory of PAPI (which is automatically added to  $PATH upon loading the module) contains various utilites.
+The bin directory of PAPI (which is automatically added to  $PATH upon loading the module) contains various utilites.
 
 ### Papi_avail
 

docs.it4i/anselm-cluster-documentation/software/debuggers/score-p.md

@@ -34,14 +34,14 @@ $ mpif90 -o myapp foo.o bar.o
 with:
 
 ```bash
-$ scorep  mpif90 -c foo.f90
-$ scorep  mpif90 -c bar.f90
-$ scorep  mpif90 -o myapp foo.o bar.o
+$ scorep mpif90 -c foo.f90
+$ scorep mpif90 -c bar.f90
+$ scorep mpif90 -o myapp foo.o bar.o
 ```
 
-Usually your program is compiled using a Makefile or similar script, so it advisable to add the  scorep command to your definition of variables  CC, CXX, FCC etc.
+Usually your program is compiled using a Makefile or similar script, so it advisable to add the scorep command to your definition of variables CC, CXX, FCC etc.
 
-It is important that  scorep is prepended also to the linking command, in order to link with Score-P instrumentation libraries.
+It is important that scorep is prepended also to the linking command, in order to link with Score-P instrumentation libraries.
 
 ### Manual Instrumentation Using API Calls
 
@@ -78,7 +78,7 @@ Please refer to the [documentation for description of the API](https://silc.zih.
 
 ### Manual Instrumentation Using Directives
 
-This method uses POMP2 directives to mark regions to be instrumented. To use this method, use command  scorep --pomp.
+This method uses POMP2 directives to mark regions to be instrumented. To use this method, use command scorep --pomp.
 
 Example directives in C/C++ :
 

docs.it4i/anselm-cluster-documentation/software/debuggers/total-view.md

@@ -20,7 +20,7 @@ You can check the status of the licenses here:
 
     # totalview
     # -------------------------------------------------
-    # FEATURE                       TOTAL   USED  AVAIL
+    # FEATURE                       TOTAL   USED AVAIL
     # -------------------------------------------------
     TotalView_Team                     64      0     64
     Replay                             64      0     64

docs.it4i/anselm-cluster-documentation/software/debuggers/valgrind.md

@@ -156,7 +156,7 @@ The default version without MPI support will however report a large number of fa
     ==30166== by 0x4008BD: main (valgrind-example-mpi.c:18)
 ```
 
-so it is better to use the MPI-enabled valgrind from module. The MPI version requires library /apps/tools/valgrind/3.9.0/impi/lib/valgrind/libmpiwrap-amd64-linux.so, which must be included in the  LD_PRELOAD environment variable.
+so it is better to use the MPI-enabled valgrind from module. The MPI version requires library /apps/tools/valgrind/3.9.0/impi/lib/valgrind/libmpiwrap-amd64-linux.so, which must be included in the LD_PRELOAD environment variable.
 
 Lets look at this MPI example :
 

docs.it4i/anselm-cluster-documentation/software/intel-suite/intel-mkl.md

@@ -11,7 +11,7 @@ Intel Math Kernel Library (Intel MKL) is a library of math kernel subroutines, e
 *   Vector Math Library (VML) routines for optimized mathematical operations on vectors.
 *   Vector Statistical Library (VSL) routines, which offer high-performance vectorized random number generators (RNG) for    several probability distributions, convolution and correlation routines, and summary statistics functions.
 *   Data Fitting Library, which provides capabilities for spline-based approximation of functions, derivatives and integrals of functions, and search.
-*   Extended Eigensolver, a shared memory  version of an eigensolver based on the Feast Eigenvalue Solver.
+*   Extended Eigensolver, a shared memory version of an eigensolver based on the Feast Eigenvalue Solver.
 
 For details see the [Intel MKL Reference Manual](http://software.intel.com/sites/products/documentation/doclib/mkl_sa/11/mklman/index.htm).
 
@@ -39,7 +39,7 @@ The MKL library provides number of interfaces. The fundamental once are the LP64
 
 Linking MKL libraries may be complex. Intel [mkl link line advisor](http://software.intel.com/en-us/articles/intel-mkl-link-line-advisor) helps. See also [examples](intel-mkl/#examples) below.
 
-You will need the mkl module loaded to run the mkl enabled executable. This may be avoided, by compiling library search paths into the executable. Include  rpath on the compile line:
+You will need the mkl module loaded to run the mkl enabled executable. This may be avoided, by compiling library search paths into the executable. Include rpath on the compile line:
 
 ```bash
     $ icc .... -Wl,-rpath=$LIBRARY_PATH ...
@@ -74,7 +74,7 @@ Number of examples, demonstrating use of the MKL library and its linking is avai
     $ make sointel64 function=cblas_dgemm
 ```
 
-In this example, we compile, link and run the cblas_dgemm  example, demonstrating use of MKL example suite installed on Anselm.
+In this example, we compile, link and run the cblas_dgemm example, demonstrating use of MKL example suite installed on Anselm.
 
 ### Example: MKL and Intel Compiler
 
@@ -88,14 +88,14 @@ In this example, we compile, link and run the cblas_dgemm  example, demonstratin
     $ ./cblas_dgemmx.x data/cblas_dgemmx.d
 ```
 
-In this example, we compile, link and run the cblas_dgemm  example, demonstrating use of MKL with icc -mkl option. Using the -mkl option is equivalent to:
+In this example, we compile, link and run the cblas_dgemm example, demonstrating use of MKL with icc -mkl option. Using the -mkl option is equivalent to:
 
 ```bash
     $ icc -w source/cblas_dgemmx.c source/common_func.c -o cblas_dgemmx.x
     -I$MKL_INC_DIR -L$MKL_LIB_DIR -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -liomp5
 ```
 
-In this example, we compile and link the cblas_dgemm  example, using LP64 interface to threaded MKL and Intel OMP threads implementation.
+In this example, we compile and link the cblas_dgemm example, using LP64 interface to threaded MKL and Intel OMP threads implementation.
 
 ### Example: MKL and GNU Compiler
 
@@ -111,7 +111,7 @@ In this example, we compile and link the cblas_dgemm  example, using LP64 interf
     $ ./cblas_dgemmx.x data/cblas_dgemmx.d
 ```
 
-In this example, we compile, link and run the cblas_dgemm  example, using LP64 interface to threaded MKL and gnu OMP threads implementation.
+In this example, we compile, link and run the cblas_dgemm example, using LP64 interface to threaded MKL and gnu OMP threads implementation.
 
 ## MKL and MIC Accelerators
 

docs.it4i/anselm-cluster-documentation/software/isv_licenses.md

@@ -38,7 +38,7 @@ Example of the Commercial Matlab license state:
     $ cat /apps/user/licenses/matlab_features_state.txt
     # matlab
     # -------------------------------------------------
-    # FEATURE                       TOTAL   USED  AVAIL
+    # FEATURE                       TOTAL   USED AVAIL
     # -------------------------------------------------
     MATLAB                              1      1      0
     SIMULINK                            1      0      1

docs.it4i/anselm-cluster-documentation/software/kvirtualization.md

@@ -198,7 +198,7 @@ Example run script (run.bat) for Windows virtual machine:
     call application.bat z:data z:output
 ```
 
-Run script runs application from shared job directory (mapped as drive z:), process input data (z:data) from job directory  and store output to job directory (z:output).
+Run script runs application from shared job directory (mapped as drive z:), process input data (z:data) from job directory and store output to job directory (z:output).
 
 ### Run Jobs
 

docs.it4i/anselm-cluster-documentation/software/mpi/mpi.md

@@ -19,7 +19,7 @@ Look up section modulefiles/mpi in module avail
 ```bash
     $ module avail
     ------------------------- /opt/modules/modulefiles/mpi -------------------------
-    bullxmpi/bullxmpi-1.2.4.1  mvapich2/1.9-icc
+    bullxmpi/bullxmpi-1.2.4.1 mvapich2/1.9-icc
     impi/4.0.3.008             openmpi/1.6.5-gcc(default)
     impi/4.1.0.024             openmpi/1.6.5-gcc46
     impi/4.1.0.030             openmpi/1.6.5-icc

docs.it4i/anselm-cluster-documentation/software/mpi/running-mpich2.md

@@ -41,7 +41,7 @@ You need to preload the executable, if running on the local scratch /lscratch fi
     Hello world! from rank 3 of 4 on host cn110
 ```
 
-In this example, we assume the executable helloworld_mpi.x is present on shared home directory. We run the cp command via mpirun, copying the executable from shared home to local scratch . Second  mpirun will execute the binary in the /lscratch/15210.srv11 directory on nodes cn17, cn108, cn109 and cn110, one process per node.
+In this example, we assume the executable helloworld_mpi.x is present on shared home directory. We run the cp command via mpirun, copying the executable from shared home to local scratch . Second mpirun will execute the binary in the /lscratch/15210.srv11 directory on nodes cn17, cn108, cn109 and cn110, one process per node.
 
 !!! note
     MPI process mapping may be controlled by PBS parameters.

docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab.md

@@ -274,7 +274,7 @@ You can use MATLAB on UV2000 in two parallel modes:
 
 ### Threaded Mode
 
-Since this is a SMP machine, you can completely avoid using Parallel Toolbox and use only MATLAB's threading. MATLAB will automatically detect the number of cores you have allocated and will set maxNumCompThreads accordingly and certain operations, such as  fft, , eig, svd, etc. will be automatically run in threads. The advantage of this mode is that you don't need to modify your existing sequential codes.
+Since this is a SMP machine, you can completely avoid using Parallel Toolbox and use only MATLAB's threading. MATLAB will automatically detect the number of cores you have allocated and will set maxNumCompThreads accordingly and certain operations, such as fft, , eig, svd, etc. will be automatically run in threads. The advantage of this mode is that you don't need to modify your existing sequential codes.
 
 ### Local Cluster Mode
 

docs.it4i/anselm-cluster-documentation/software/numerical-languages/matlab_1314.md

@@ -72,7 +72,7 @@ extras = {};
 System MPI library allows Matlab to communicate through 40 Gbit/s InfiniBand QDR interconnect instead of slower 1 Gbit Ethernet network.
 
 !!! note
-    The path to MPI library in "mpiLibConf.m" has to match with version of loaded Intel MPI module. In this example the version 4.1.1.036 of Intel MPI is used by Matlab and therefore module impi/4.1.1.036  has to be loaded prior to starting Matlab.
+    The path to MPI library in "mpiLibConf.m" has to match with version of loaded Intel MPI module. In this example the version 4.1.1.036 of Intel MPI is used by Matlab and therefore module impi/4.1.1.036 has to be loaded prior to starting Matlab.
 
 ### Parallel Matlab Interactive Session
 

docs.it4i/anselm-cluster-documentation/software/numerical-languages/r.md

@@ -70,7 +70,7 @@ This script may be submitted directly to the PBS workload manager via the qsub c
 
 ## Parallel R
 
-Parallel execution of R may be achieved in many ways. One approach is the implied parallelization due to linked libraries or specially enabled functions, as [described above](r/#interactive-execution). In the following sections, we focus on explicit parallelization, where  parallel constructs are directly stated within the R script.
+Parallel execution of R may be achieved in many ways. One approach is the implied parallelization due to linked libraries or specially enabled functions, as [described above](r/#interactive-execution). In the following sections, we focus on explicit parallelization, where parallel constructs are directly stated within the R script.
 
 ## Package Parallel
 
@@ -375,7 +375,7 @@ Example jobscript for [static Rmpi](r/#static-rmpi) parallel R execution, runnin
     #PBS -N Rjob
     #PBS -l select=100:ncpus=16:mpiprocs=16:ompthreads=1
 
-    # change to  scratch directory
+    # change to scratch directory
     SCRDIR=/scratch/$USER/myjob
     cd $SCRDIR || exit
 

docs.it4i/anselm-cluster-documentation/software/numerical-libraries/fftw.md

@@ -2,7 +2,7 @@
 
 The discrete Fourier transform in one or more dimensions, MPI parallel
 
-FFTW is a C subroutine library for computing the discrete Fourier transform  in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, e.g. the discrete cosine/sine transforms or DCT/DST). The FFTW library allows for MPI parallel, in-place discrete Fourier transform, with data distributed over number of nodes.
+FFTW is a C subroutine library for computing the discrete Fourier transform in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, e.g. the discrete cosine/sine transforms or DCT/DST). The FFTW library allows for MPI parallel, in-place discrete Fourier transform, with data distributed over number of nodes.
 
 Two versions, **3.3.3** and **2.1.5** of FFTW are available on Anselm, each compiled for **Intel MPI** and **OpenMPI** using **intel** and **gnu** compilers. These are available via modules:
 

docs.it4i/anselm-cluster-documentation/software/numerical-libraries/magma-for-intel-xeon-phi.md

@@ -23,7 +23,7 @@ Compilation example:
 ```bash
     $ icc -mkl -O3 -DHAVE_MIC -DADD_ -Wall $MAGMA_INC -c testing_dgetrf_mic.cpp -o testing_dgetrf_mic.o
 
-    $ icc -mkl -O3 -DHAVE_MIC -DADD_ -Wall -fPIC -Xlinker -zmuldefs -Wall -DNOCHANGE -DHOST  testing_dgetrf_mic.o  -o testing_dgetrf_mic $MAGMA_LIBS
+    $ icc -mkl -O3 -DHAVE_MIC -DADD_ -Wall -fPIC -Xlinker -zmuldefs -Wall -DNOCHANGE -DHOST testing_dgetrf_mic.o  -o testing_dgetrf_mic $MAGMA_LIBS
 ```
 
 ### Running MAGMA Code
@@ -54,15 +54,15 @@ To test if the MAGMA server runs properly we can run one of examples that are pa
 
       M     N     CPU GFlop/s (sec)   MAGMA GFlop/s (sec)   ||PA-LU||/(||A||*N)
     =========================================================================
-     1088  1088     ---   (  ---  )     13.93 (   0.06)     ---
-     2112  2112     ---   (  ---  )     77.85 (   0.08)     ---
-     3136  3136     ---   (  ---  )    183.21 (   0.11)     ---
-     4160  4160     ---   (  ---  )    227.52 (   0.21)     ---
-     5184  5184     ---   (  ---  )    258.61 (   0.36)     ---
-     6208  6208     ---   (  ---  )    333.12 (   0.48)     ---
-     7232  7232     ---   (  ---  )    416.52 (   0.61)     ---
-     8256  8256     ---   (  ---  )    446.97 (   0.84)     ---
-     9280  9280     ---   (  ---  )    461.15 (   1.16)     ---
+     1088 1088     ---   (  ---  )     13.93 (   0.06)     ---
+     2112 2112     ---   (  ---  )     77.85 (   0.08)     ---
+     3136 3136     ---   (  ---  )    183.21 (   0.11)     ---
+     4160 4160     ---   (  ---  )    227.52 (   0.21)     ---
+     5184 5184     ---   (  ---  )    258.61 (   0.36)     ---
+     6208 6208     ---   (  ---  )    333.12 (   0.48)     ---
+     7232 7232     ---   (  ---  )    416.52 (   0.61)     ---
+     8256 8256     ---   (  ---  )    446.97 (   0.84)     ---
+     9280 9280     ---   (  ---  )    461.15 (   1.16)     ---
     10304 10304     ---   (  ---  )    500.70 (   1.46)     ---
 ```
 

docs.it4i/anselm-cluster-documentation/software/numerical-libraries/petsc.md

@@ -10,7 +10,7 @@ PETSc (Portable, Extensible Toolkit for Scientific Computation) is a suite of bu
 
 *   [project webpage](http://www.mcs.anl.gov/petsc/)
 *   [documentation](http://www.mcs.anl.gov/petsc/documentation/)
-   * [PETSc Users  Manual (PDF)](http://www.mcs.anl.gov/petsc/petsc-current/docs/manual.pdf)
+   * [PETSc Users Manual (PDF)](http://www.mcs.anl.gov/petsc/petsc-current/docs/manual.pdf)
    * [index of all manual pages](http://www.mcs.anl.gov/petsc/petsc-current/docs/manualpages/singleindex.html)
 *   PRACE Video Tutorial [part1](http://www.youtube.com/watch?v=asVaFg1NDqY), [part2](http://www.youtube.com/watch?v=ubp_cSibb9I), [part3](http://www.youtube.com/watch?v=vJAAAQv-aaw), [part4](http://www.youtube.com/watch?v=BKVlqWNh8jY), [part5](http://www.youtube.com/watch?v=iXkbLEBFjlM)
 

docs.it4i/anselm-cluster-documentation/software/omics-master/overview.md

@@ -68,7 +68,7 @@ corresponding information is unavailable.
 | 1         | QNAME      | Query NAME of the read or the read pai                |
 | 2         | FLAG       | Bitwise FLAG (pairing,strand,mate strand,etc.)        |
 | 3         | RNAME      | <p>Reference sequence NAME                            |
-| 4         | POS        | <p>1-Based  leftmost POSition of clipped alignment    |
+| 4         | POS        | <p>1-Based leftmost POSition of clipped alignment    |
 | 5         | MAPQ       | <p>MAPping Quality (Phred-scaled)                     |
 | 6         | CIGAR      | <p>Extended CIGAR string (operations:MIDNSHP)         |
 | 7         | MRNM       | <p>Mate REference NaMe ('=' if same RNAME)            |
@@ -121,7 +121,7 @@ Identification of single nucleotide variants and indels on the alignments is per
 
 VCF (3) is a standardized format for storing the most prevalent types of sequence variation, including SNPs, indels and larger structural variants, together with rich annotations. The format was developed with the primary intention to represent human genetic variation, but its use is not restricted >to diploid genomes and can be used in different contexts as well. Its flexibility and user extensibility allows representation of a wide variety of genomic variation with respect to a single reference sequence.
 
-A VCF file consists of a header section and a data section. The header contains an arbitrary number of metainformation lines, each starting with characters ‘##’, and a TAB delimited field definition line, starting with a single ‘#’ character. The meta-information header lines provide a standardized description of tags and annotations used in the data section. The use of meta-information allows the information stored within a VCF file to be tailored to the dataset in question. It can be also used to provide information about the means of file creation, date of creation, version of the reference sequence, software used and any other information relevant to the history of the file. The field definition line names eight mandatory columns, corresponding to data columns representing the chromosome (CHROM), a 1-based position of the start of the variant (POS), unique identifiers of the variant (ID), the reference allele (REF), a comma separated list of  alternate non-reference alleles (ALT), a phred-scaled quality score (QUAL), site filtering information (FILTER) and a semicolon separated list of additional, user extensible annotation (INFO). In addition, if samples are present in the file, the mandatory header columns are followed by a FORMAT column and an arbitrary number of sample IDs that define the samples included in the VCF file. The FORMAT column is used to define  the information contained within each subsequent genotype column, which consists of a colon separated list of fields. For example, the FORMAT field GT:GQ:DP in the fourth data entry of Figure 1a indicates that the subsequent entries contain information regarding the genotype, genotype quality and  read depth for each sample. All data lines are TAB delimited and the number of fields in each data line must match the number of fields in the header line. It is strongly recommended that all annotation tags used are declared in the VCF header section.
+A VCF file consists of a header section and a data section. The header contains an arbitrary number of metainformation lines, each starting with characters ‘##’, and a TAB delimited field definition line, starting with a single ‘#’ character. The meta-information header lines provide a standardized description of tags and annotations used in the data section. The use of meta-information allows the information stored within a VCF file to be tailored to the dataset in question. It can be also used to provide information about the means of file creation, date of creation, version of the reference sequence, software used and any other information relevant to the history of the file. The field definition line names eight mandatory columns, corresponding to data columns representing the chromosome (CHROM), a 1-based position of the start of the variant (POS), unique identifiers of the variant (ID), the reference allele (REF), a comma separated list of alternate non-reference alleles (ALT), a phred-scaled quality score (QUAL), site filtering information (FILTER) and a semicolon separated list of additional, user extensible annotation (INFO). In addition, if samples are present in the file, the mandatory header columns are followed by a FORMAT column and an arbitrary number of sample IDs that define the samples included in the VCF file. The FORMAT column is used to define the information contained within each subsequent genotype column, which consists of a colon separated list of fields. For example, the FORMAT field GT:GQ:DP in the fourth data entry of Figure 1a indicates that the subsequent entries contain information regarding the genotype, genotype quality and read depth for each sample. All data lines are TAB delimited and the number of fields in each data line must match the number of fields in the header line. It is strongly recommended that all annotation tags used are declared in the VCF header section.
 
 ![a) Example of valid VCF. The header lines ##fileformat and #CHROM are mandatory, the rest is optional but strongly recommended. Each line of the body describes variants present in the sampled population at one genomic position or region. All alternate alleles are listed in the ALT column and referenced from the genotype fields as 1-based indexes to
 this list; the reference haplotype is designated as 0. For multiploid data, the separator indicates whether the data are phased (|) or unphased (/). Thus, the two alleles C and G at the positions 2 and 5 in this figure occur on the same chromosome in SAMPLE1. The first data line shows an example of a deletion (present in SAMPLE1) and a replacement of
@@ -173,13 +173,13 @@ resources. We successfully solved the problem of storing data released in BioPAX
 
 ## Usage
 
-First of all, we should load  ngsPipeline module:
+First of all, we should load ngsPipeline module:
 
 ```bash
     $ module load ngsPipeline
 ```
 
-This command will load  python/2.7.5 module and all the required modules (hpg-aligner, gatk, etc)
+This command will load python/2.7.5 module and all the required modules (hpg-aligner, gatk, etc)
 
 If we launch ngsPipeline with ‘-h’, we will get the usage help:
 
@@ -192,7 +192,7 @@ If we launch ngsPipeline with ‘-h’, we will get the usage help:
     Python pipeline
 
     optional arguments:
-      -h, --help  show this help message and exit
+      -h, --help show this help message and exit
       -i INPUT, --input INPUT
       -o OUTPUT, --output OUTPUT
         Output Data directory
@@ -364,7 +364,7 @@ Each prioritization (‘job’) has three associated screens that facilitate the
 2.  McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA: The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. _Genome Res_ >2010, 20:1297-1303.
 3.  Petr Danecek, Adam Auton, Goncalo Abecasis, Cornelis A. Albers, Eric Banks, Mark A. DePristo, Robert E. Handsaker, Gerton Lunter, Gabor T. Marth, Stephen T. Sherry, Gilean McVean, Richard Durbin, and 1000 Genomes Project Analysis Group. The variant call format and VCFtools. Bioinformatics 2011, 27: 2156-2158.
 4.  Medina I, De Maria A, Bleda M, Salavert F, Alonso R, Gonzalez CY, Dopazo J: VARIANT: Command Line, Web service and Web interface for fast and accurate functional characterization of variants found by Next-Generation Sequencing. Nucleic Acids Res 2012, 40:W54-58.
-5.  Bleda M, Tarraga J, de Maria A, Salavert F, Garcia-Alonso L, Celma M, Martin A, Dopazo J, Medina I: CellBase, a  comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources. Nucleic Acids Res 2012, 40:W609-614.
+5.  Bleda M, Tarraga J, de Maria A, Salavert F, Garcia-Alonso L, Celma M, Martin A, Dopazo J, Medina I: CellBase, a comprehensive collection of RESTful web services for retrieving relevant biological information from heterogeneous sources. Nucleic Acids Res 2012, 40:W609-614.
 6.  Flicek,P., Amode,M.R., Barrell,D., Beal,K., Brent,S., Carvalho-Silva,D., Clapham,P., Coates,G., Fairley,S., Fitzgerald,S. et al. (2012) Ensembl 2012. Nucleic Acids Res., 40, D84–D90.
 7.  UniProt Consortium. (2012) Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic   Acids Res., 40, D71–D75.
 8.  Kozomara,A. and Griffiths-Jones,S. (2011) miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res., 39, D152–D157.
@@ -373,7 +373,7 @@ Each prioritization (‘job’) has three associated screens that facilitate the
 11. Friedman,R.C., Farh,K.K., Burge,C.B. and Bartel,D.P. (2009) Most mammalian mRNAs are conserved targets of microRNAs. Genome Res., 19, 92–105. 12. Betel,D., Wilson,M., Gabow,A., Marks,D.S. and Sander,C. (2008) The microRNA.org resource: targets and expression. Nucleic Acids Res., 36, D149–D153.
 12. Dreszer,T.R., Karolchik,D., Zweig,A.S., Hinrichs,A.S., Raney,B.J., Kuhn,R.M., Meyer,L.R., Wong,M., Sloan,C.A., Rosenbloom,K.R. et al. (2012) The UCSC genome browser database: extensions and updates 2011. Nucleic Acids Res.,40, D918–D923.
 13. Smith,B., Ashburner,M., Rosse,C., Bard,J., Bug,W., Ceusters,W., Goldberg,L.J., Eilbeck,K., Ireland,A., Mungall,C.J. et al. (2007) The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol., 25, 1251–1255.
-14. Hunter,S., Jones,P., Mitchell,A., Apweiler,R., Attwood,T.K.,Bateman,A., Bernard,T., Binns,D., Bork,P., Burge,S. et al. (2012) InterPro in 2011: new developments in the family and domain prediction  database. Nucleic Acids Res.,40, D306–D312.
+14. Hunter,S., Jones,P., Mitchell,A., Apweiler,R., Attwood,T.K.,Bateman,A., Bernard,T., Binns,D., Bork,P., Burge,S. et al. (2012) InterPro in 2011: new developments in the family and domain prediction database. Nucleic Acids Res.,40, D306–D312.
 15. Sherry,S.T., Ward,M.H., Kholodov,M., Baker,J., Phan,L., Smigielski,E.M. and Sirotkin,K. (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res., 29, 308–311.
 16. Altshuler,D.M., Gibbs,R.A., Peltonen,L., Dermitzakis,E., Schaffner,S.F., Yu,F., Bonnen,P.E., de Bakker,P.I.,  Deloukas,P., Gabriel,S.B. et al. (2010) Integrating common and rare genetic variation in diverse human populations. Nature, 467, 52–58.
 17. 1000 Genomes Project Consortium. (2010) A map of human genome variation from population-scale sequencing. Nature, 467, 1061–1073.

docs.it4i/anselm-cluster-documentation/software/paraview.md

@@ -53,7 +53,7 @@ Because a direct connection is not allowed to compute nodes on Anselm, you must
     ssh -TN -L 12345:cn77:11111 username@anselm.it4i.cz
 ```
 
-replace  username with your login and cn77 with the name of compute node your ParaView server is running on (see previous step). If you use PuTTY on Windows, load Anselm connection configuration, t>hen go to Connection-> SSH>->Tunnels to set up the port forwarding. Click Remote radio button. Insert 12345 to Source port textbox. Insert cn77:11111. Click Add button, then Open.
+replace username with your login and cn77 with the name of compute node your ParaView server is running on (see previous step). If you use PuTTY on Windows, load Anselm connection configuration, t>hen go to Connection-> SSH>->Tunnels to set up the port forwarding. Click Remote radio button. Insert 12345 to Source port textbox. Insert cn77:11111. Click Add button, then Open.
 
 Now launch ParaView client installed on your desktop PC. Select File->Connect..., click Add Server. Fill in the following :
 

docs.it4i/anselm-cluster-documentation/storage.md

@@ -23,7 +23,7 @@ If multiple clients try to read and write the same part of a file at the same ti
 There is default stripe configuration for Anselm Lustre filesystems. However, users can set the following stripe parameters for their own directories or files to get optimum I/O performance:
 
 1.  stripe_size: the size of the chunk in bytes; specify with k, m, or g to use units of KB, MB, or GB, respectively; the size must be an even multiple of 65,536 bytes; default is 1MB for all Anselm Lustre filesystems
-2.  stripe_count the number of OSTs to stripe across; default is 1 for Anselm Lustre filesystems  one can specify -1 to use all OSTs in the filesystem.
+2.  stripe_count the number of OSTs to stripe across; default is 1 for Anselm Lustre filesystems one can specify -1 to use all OSTs in the filesystem.
 3.  stripe_offset The index of the OST where the first stripe is to be placed; default is -1 which results in random selection; using a non-default value is NOT recommended.
 
 !!! note
@@ -76,7 +76,7 @@ Read more on <http://doc.lustre.org/lustre_manual.xhtml#managingstripingfreespac
 
 ### Lustre on Anselm
 
-The  architecture of Lustre on Anselm is composed of two metadata servers (MDS) and four data/object storage servers (OSS). Two object storage servers are used for file system HOME and another two object storage servers are used for file system SCRATCH.
+The architecture of Lustre on Anselm is composed of two metadata servers (MDS) and four data/object storage servers (OSS). Two object storage servers are used for file system HOME and another two object storage servers are used for file system SCRATCH.
 
  Configuration of the storages
 
@@ -132,7 +132,7 @@ Default stripe size is 1MB, stripe count is 1. There are 22 OSTs dedicated for t
 The SCRATCH filesystem is mounted in directory /scratch. Users may freely create subdirectories and files on the filesystem. Accessible capacity is 146TB, shared among all users. Individual users are restricted by filesystem usage quotas, set to 100TB per user. The purpose of this quota is to prevent runaway programs from filling the entire filesystem and deny service to other users. If 100TB should prove as insufficient for particular user, please contact [support](https://support.it4i.cz/rt), the quota may be lifted upon request.
 
 !!! note
-    The Scratch filesystem is intended  for temporary scratch data generated during the calculation as well as for high performance access to input and output files. All I/O intensive jobs must use the SCRATCH filesystem as their working directory.
+    The Scratch filesystem is intended for temporary scratch data generated during the calculation as well as for high performance access to input and output files. All I/O intensive jobs must use the SCRATCH filesystem as their working directory.
 
     >Users are advised to save the necessary data from the SCRATCH filesystem to HOME filesystem after the calculations and clean up the scratch files.
 
@@ -166,11 +166,11 @@ Example for Lustre HOME directory:
 ```bash
 $ lfs quota /home
 Disk quotas for user user001 (uid 1234):
-    Filesystem  kbytes   quota   limit   grace   files   quota   limit   grace
-         /home  300096       0 250000000       -    2102       0  500000    -
+    Filesystem kbytes   quota   limit   grace   files   quota   limit   grace
+         /home 300096       0 250000000       -    2102       0 500000    -
 Disk quotas for group user001 (gid 1234):
-    Filesystem  kbytes   quota   limit   grace   files   quota   limit   grace
-        /home  300096       0       0       -    2102       0       0       -
+    Filesystem kbytes   quota   limit   grace   files   quota   limit   grace
+        /home 300096       0       0       -    2102       0       0       -
 ```
 
 In this example, we view current quota size limit of 250GB and 300MB currently used by user001.
@@ -180,7 +180,7 @@ Example for Lustre SCRATCH directory:
 ```bash
 $ lfs quota /scratch
 Disk quotas for user user001 (uid 1234):
-     Filesystem  kbytes   quota   limit   grace   files   quota   limit   grace
+     Filesystem kbytes   quota   limit   grace   files   quota   limit   grace
           /scratch       8       0 100000000000       -       3       0       0       -
 Disk quotas for group user001 (gid 1234):
  Filesystem kbytes quota limit grace files quota limit grace
@@ -229,7 +229,7 @@ ACLs on a Lustre file system work exactly like ACLs on any Linux file system. Th
 [vop999@login1.anselm ~]$ umask 027
 [vop999@login1.anselm ~]$ mkdir test
 [vop999@login1.anselm ~]$ ls -ld test
-drwxr-x--- 2 vop999 vop999 4096 Nov  5 14:17 test
+drwxr-x--- 2 vop999 vop999 4096 Nov 5 14:17 test
 [vop999@login1.anselm ~]$ getfacl test
 # file: test
 # owner: vop999
@@ -240,7 +240,7 @@ other::---
 
 [vop999@login1.anselm ~]$ setfacl -m user:johnsm:rwx test
 [vop999@login1.anselm ~]$ ls -ld test
-drwxrwx---+ 2 vop999 vop999 4096 Nov  5 14:17 test
+drwxrwx---+ 2 vop999 vop999 4096 Nov 5 14:17 test
 [vop999@login1.anselm ~]$ getfacl test
 # file: test
 # owner: vop999
@@ -267,7 +267,7 @@ Use local scratch in case you need to access large amount of small files during
 
 The local scratch disk is mounted as /lscratch and is accessible to user at /lscratch/$PBS_JOBID directory.
 
-The local scratch filesystem is intended  for temporary scratch data generated during the calculation as well as for high performance access to input and output files. All I/O intensive jobs that access large number of small files within the calculation must use the local scratch filesystem as their working directory. This is required for performance reasons, as frequent access to number of small files may overload the metadata servers (MDS) of the Lustre filesystem.
+The local scratch filesystem is intended for temporary scratch data generated during the calculation as well as for high performance access to input and output files. All I/O intensive jobs that access large number of small files within the calculation must use the local scratch filesystem as their working directory. This is required for performance reasons, as frequent access to number of small files may overload the metadata servers (MDS) of the Lustre filesystem.
 
 !!! note
     The local scratch directory /lscratch/$PBS_JOBID will be deleted immediately after the calculation end. Users should take care to save the output data from within the jobscript.
@@ -349,7 +349,7 @@ Once registered for CESNET Storage, you may [access the storage](https://du.cesn
 !!! note
     SSHFS: The storage will be mounted like a local hard drive
 
-The SSHFS  provides a very convenient way to access the CESNET Storage. The storage will be mounted onto a local directory, exposing the vast CESNET Storage as if it was a local removable hard drive. Files can be than copied in and out in a usual fashion.
+The SSHFS provides a very convenient way to access the CESNET Storage. The storage will be mounted onto a local directory, exposing the vast CESNET Storage as if it was a local removable hard drive. Files can be than copied in and out in a usual fashion.
 
 First, create the mount point
 

docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/vnc.md

@@ -18,7 +18,7 @@ Verify:
 ## Start Vncserver
 
 !!! note
-    To access VNC a local vncserver must be  started first and also a tunnel using SSH port forwarding must be established.
+    To access VNC a local vncserver must be started first and also a tunnel using SSH port forwarding must be established.
 
 [See below](vnc.md#linux-example-of-creating-a-tunnel) for the details on SSH tunnels. In this example we use port 61.
 
@@ -26,8 +26,8 @@ You can find ports which are already occupied. Here you can see that ports " /us
 
 ```bash
 [username@login2 ~]$ ps aux | grep Xvnc
-username    5971  0.0  0.0 201072 92564 ?        SN   Sep22   4:19 /usr/bin/Xvnc :79 -desktop login2:79 (username) -auth /home/gre196/.Xauthority -geometry 1024x768 -rfbwait 30000 -rfbauth /home/username/.vnc/passwd -rfbport 5979 -fp catalogue:/etc/X11/fontpath.d -pn
-username    10296  0.0  0.0 131772 21076 pts/29   SN   13:01   0:01 /usr/bin/Xvnc :60 -desktop login2:61 (username) -auth /home/username/.Xauthority -geometry 1600x900 -depth 16 -rfbwait 30000 -rfbauth /home/jir13/.vnc/passwd -rfbport 5960 -fp catalogue:/etc/X11/fontpath.d -pn
+username    5971 0.0 0.0 201072 92564 ?        SN   Sep22   4:19 /usr/bin/Xvnc :79 -desktop login2:79 (username) -auth /home/gre196/.Xauthority -geometry 1024x768 -rfbwait 30000 -rfbauth /home/username/.vnc/passwd -rfbport 5979 -fp catalogue:/etc/X11/fontpath.d -pn
+username    10296 0.0 0.0 131772 21076 pts/29   SN   13:01   0:01 /usr/bin/Xvnc :60 -desktop login2:61 (username) -auth /home/username/.Xauthority -geometry 1600x900 -depth 16 -rfbwait 30000 -rfbauth /home/jir13/.vnc/passwd -rfbport 5960 -fp catalogue:/etc/X11/fontpath.d -pn
 .....
 ```
 
@@ -58,7 +58,7 @@ Another command:
 ```bash
 [username@login2 .vnc]$  ps aux | grep Xvnc
 
-username    10296  0.0  0.0 131772 21076 pts/29   SN   13:01   0:01 /usr/bin/Xvnc :61 -desktop login2:61 (username) -auth /home/jir13/.Xauthority -geometry 1600x900 -depth 16 -rfbwait 30000 -rfbauth /home/username/.vnc/passwd -rfbport 5961 -fp catalogue:/etc/X11/fontpath.d -pn
+username    10296 0.0 0.0 131772 21076 pts/29   SN   13:01   0:01 /usr/bin/Xvnc :61 -desktop login2:61 (username) -auth /home/jir13/.Xauthority -geometry 1600x900 -depth 16 -rfbwait 30000 -rfbauth /home/username/.vnc/passwd -rfbport 5961 -fp catalogue:/etc/X11/fontpath.d -pn
 ```
 
 To access the VNC server you have to create a tunnel between the login node using TCP **port 5961** and your machine using a free TCP port (for simplicity the very same, in this case).
@@ -162,8 +162,8 @@ If the screen gets locked you have to kill the screensaver. Do not to forget to
 
 ```bash
 [username@login2 .vnc]$ ps aux | grep screen
-username     1503  0.0  0.0 103244   892 pts/4    S+   14:37   0:00 grep screen
-username     24316  0.0  0.0 270564  3528 ?        Ss   14:12   0:00 gnome-screensaver
+username     1503 0.0 0.0 103244   892 pts/4    S+   14:37   0:00 grep screen
+username     24316 0.0 0.0 270564 3528 ?        Ss   14:12   0:00 gnome-screensaver
 
 [username@login2 .vnc]$ kill 24316
 ```

docs.it4i/get-started-with-it4innovations/accessing-the-clusters/graphical-user-interface/x-window-system.md

@@ -99,7 +99,7 @@ xserver-xephyr, on OS X it is part of [XQuartz](http://xquartz.macosforge.org/la
 local $ Xephyr -ac -screen 1024x768 -br -reset -terminate :1 &
 ```
 
-This will open a new X window with size 1024 x 768 at DISPLAY :1. Next, ssh to the cluster with DISPLAY environment variable set and launch  gnome-session
+This will open a new X window with size 1024 x 768 at DISPLAY :1. Next, ssh to the cluster with DISPLAY environment variable set and launch gnome-session
 
 ```bash
 local $ DISPLAY=:1.0 ssh -XC yourname@cluster-name.it4i.cz -i ~/.ssh/path_to_your_key