Provozní změny infrastruktur MetaCentra a CERIT-SC: VNC prostředí pro GUI aplikace + nový SW

Provozní změny infrastruktur MetaCentra a CERIT-SC: VNC prostředí pro GUI aplikace + nový SW

As we've announced last month, we're sending another regular information about operational news of the MetaCentrum & CERIT-SC infrastructures:

1. Environment supporting work with GUI applications (VNC servers)

• we've prepared an environment based on VNC servers to make a work with applications requiring graphical interface more comfortable
• the environment does not aim to replace common desktops; the goal is to provide an environment for applications, which require (or which may benefit from) a graphical environment available
• the environment may be used on all the nodes (including frontends as well as computing nodes) -- available within both MetaCentrum and CERIT-SC infrastructures
• see more at https://wiki.metacentrum.cz/wiki/Remote_desktop

2. Newly installed/purchased SW:

Note: More information about the installed applications are available on the applications' web page: https://wiki.metacentrum.cz/wiki/Kategorie:Applications

COMMERCIAL APPLICATIONS (available for all the registered users):

• Molpro
  • a complete system of ab initio programs for molecular electronic structure calculations
  • version 2012.1, license purchased by CERIT-SC
• Turbomole
  • a powerful general purpose Quantum Chemistry program package for ab initio Electronic Structure Calculations
  • version 6.5, license purchased by CERIT-SC
• CLCbio Genomics Workbench
  • a tool for analyzing and visualizing next generation sequencing data, which incorporates cutting-edge technology and algorithms
  • version 6.5, 2 licenses purchased by CERIT-SC
• Geneious
  • an integrated, cross-platform bioinformatics software suite for manipulating, finding, sharing, and exploring biological data such as DNA sequences or proteins, phylogenies, 3D structure information and others
  • release R7, 2 licenses purchased by CERIT-SC

OPEN-SOURCE/FREE APPLICATIONS:
* atsas (ver. 2.5.1)  - A program suite for small-angle scattering data analysis from biological macromolecules.
* boost (ver. 1.55)  - a boost library
* cdbfasta   - Fast indexing and retrieval of fasta records from flat file databases
* cmake (ver. 2.8.11)  - a cross-platform, open-source build system
* elk (ver. 2.2.9)  - all-electron full-potential linearised augmented-plane wave (compiled against Intel MKL, MPI + OpenMP support)
* fastQC (ver. 0.10.1)  - a quality control tool for high throughput sequence data
* freebayes (ver. 9.9.2)  - a Bayesian genetic variant detector designed to find small polymorphisms (SNPs & MNPs), and complex events smaller than the length of a short-read sequencing alignment
* garli (ver. 2.01)  - GARLI is a program that performs phylogenetic inference using the maximum-likelihood criterion
* gsl (ver. 1.16, gcc+intel)  - GNU Scientific Library tools collection
* last (ver. 356)  - LAST finds similar regions between sequences.
* mafft (ver. 7.029)  - a multiple sequence alignment program which offers a range of alignment methods
* mrbayes (ver. 3.2.2)  - MrBayes is a program for the Bayesian estimation of phylogeny.
* mrNA (ver. 1.0, gcc+intel)  - rNA is an aligner for short reads produced by Next Generation Sequencers
* rsem (ver. 1.2.8)  - package for estimating gene and isoform expression levels from RNA-Seq data
* rsh-to-ssh (ver. 1.0)  - forces using SSH instead of RSH (useful for some applications, may be further used system-widely)
* sassy (ver. 0.1.1.3)  - SaSSY is a short, paired-read assembler designed primarily to assemble data generated using Illumina platforms.
* seqtk (ver. 1.0)  - fast and lightweight tool for processing sequences in the FASTA or FASTQ format
* spades (ver. 2.5.1)  - St. Petersburg genome assembler. It is intended for both standard (multicell) and single-cell MDA bacteria assemblies.
* sparx   - environment for Cryo-EM image processing
* tablet (ver. 1.13)  - a lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments
* trinity (ver. 201311)  - novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data
* vasp (ver. 4.6, 5.2 and 5.3)  - Vienna Ab initio Simulation Package (VASP) for atomic scale materials modelling (newly compiled with Intel MKL and MPI support, available just for users owning a VASP license)
* visit (ver. 2.6.3)  - a free interactive parallel visualization and graphical analysis tool for viewing scientific data


With best regards,
Tomáš Rebok, MetaCentrum + CERIT-SC.