Unix

Linux software for employees and students of the Faculty of Science

Available software on C&CZ managed Linux-computers

Name	Version	Category	Description	Installer available	On CD/DVD	Run from network share	Standard for Windows	Frequently installed	Optionally installed	Windows	Linux	OS X
Aips		Astronomy	The NRAO Astronomical Image Processing System (AIPS) is a software package for interactive (and, optionally, batch) calibration and editing of radio interferometric data and for the calibration, construction, display and analysis of astronomical images made from those data using Fourier synthesis methods.								✓
Anaconda	2.4.4	Scienctific	Anaconda is a freemium open source distribution of the Python and R programming languages for large-scale data processing, predictive analytics, and scientific computing, that aims to simplify package management and deployment. Package versions are managed by the package management system conda.								✓
	3										✓
Atom		Editors	A hackable text editor for the 21st Century								✓
Brig	0.95	Science	BRIG is a cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data.								✓
Cabal			Cabal is a system for building and packaging Haskell libraries and programs.								✓
Caffe		Scientific	Caffe is a deep learning framework made with expression, speed, and modularity in mind.								✓
Dropbox			Dropbox is a file hosting service.								✓
Fail2ban			Fail2ban is an intrusion prevention software framework which protects computer servers from brute-force attacks.								✓
Famias			FAMIAS (Frequency Analysis and Mode Identification for Asteroseismology) is a package of state-of-the art software tools for the analysis of photometric and spectroscopic time-series data.								✓
Freesurfer	5.3		An open source software suite for processing and analyzing (human) brain MRI images.								✓
Geany		Software Development	Geany is a text editor using the GTK2 toolkit with basic features of an integrated development environment.								✓
Gfortran	4.6										✓
	4.8										✓
	4.9										✓
GitLfs	v1.2.1		An open source Git extension for versioning large files								✓
Graphviz			Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks.								✓
Grass	7.2	Science	GRASS GIS, commonly referred to as GRASS (Geographic Resources Analysis Support System), is a free and open source Geographic Information System (GIS) software suite used for geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization.								✓
Haskell	8.0.1		Haskell is a standardized, general-purpose purely functional programming language, with non-strict semantics and strong static typing. It is named after logician Haskell Curry.								✓
Iraf			Image Reduction and Analysis Facility, a general purpose software system for the reduction and analysis of astronomical data.								✓
Jags	4.2.0	Science	JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS.								✓
Magma											✓
Mathematica			Mathematica is a symbolic mathematical computation program								✓
Matlab	R2010b										✓
	R2012b										✓
	R2014b										✓
	R2015a										✓
	R2015b							✓		✓	✓
	R2016a										✓
	R2017a										✓
	R2018a										✓
	R2018b			✓						✓	✓
MatlabR2017b											✓
MongoDB			MongoDB is an open-source, document database designed for ease of development and scaling								✓
Parallel	20150322	Utils	GNU parallel is a shell tool for executing jobs in parallel using one or more computers.								✓
Ponysay	3.0.3		Cowsay reimplemention for ponies (essential banner software for the ponyland cluster)								✓
Povray	3.7	Graphics	Persistence of Vision Raytracer								✓
Pyzo	4.4.1		Pyzo is a free and open-source computing environment based on Python.								✓
R		Statistics	R is a free software environment for statistical computing and graphics.					✓		✓	✓	✓
Root	5.34	Scientific	The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficient way.								✓
	6.08										✓
Rstudio			RStudio IDE is a powerful and productive user interface for R.								✓
SPSS	19										✓
Skype			Skype is a telecommunications application software providing video chat and voice calls via the internet								✓
Spyder		Software development	Python IDE								✓
Sqlite	3	Software development	Command line client for sqlite3 databases.								✓
Taskspooler			Task spooler is a Unix batch system where the tasks spooled run one after the other.								✓
TauDEM	5		TauDEM (Terrain Analysis Using Digital Elevation Models) is a suite of Digital Elevation Model (DEM) tools for the extraction and analysis of hydrologic information from topography as represented by a DEM.								✓
Triqs		Scientific	TRIQS (Toolbox for Research on Interacting Quantum Systems) is a scientific project providing a set of C++ and Python libraries to develop new tools for the study of interacting quantum systems.								✓
Utrecht		Scientific	Eval Program Suite								✓
Vagrant	1.8.5		Vagrant enables users to create and configure lightweight, reproducible, and portable development environments.								✓
Vesta		Scientific	VESTA is a 3D visualization program for structural models, volumetric data such as electron/nuclear densities, and crystal morphologies.								✓
Wireshark			Wireshark is a network packet analyzer.								✓
Wkhtmltopdf	0.12.3		Open source command line tools to render HTML into PDF and various image formats using the Qt WebKit rendering engine.								✓
Workrave			Workrave assists in the recovery and prevention of Repetitive Strain Injury (RSI)						✓	✓	✓
jq			jq is a lightweight and flexible command-line JSON processor								✓
kpcli	3.1		A command line interface (interactive shell) to work with KeePass database files								✓

• All kinds of software in /usr/local, /opt/ and /vol/

• Ubuntu packages
  • A complete list of the thousands of installed Ubuntu packages can be seen with the command:

       aptitude search "[a-z]" | grep ^i 

An even larger list of all Ubuntu packages that can be installed, can be seen with the command:

       aptitude search "[a-z]"

Send an email to postmaster if you want an extra package to be installed.

To install on your own Linux PC

The Install share contains the following Linux software:

• Mathematics software:
  • Maple
  • Matlab
  • Mathematica
  • IBM - SPSS (Statistics)
• Office software:
  • Konica Minolta printerdrivers
  • TeX: TeX Live
• Data acquisition programming environment:
  • National Instruments LabVIEW

To be borrowed from C&CZ

At this moment the following Linux software can be borrowed from C&CZ in room HG03.055 by employees and students of the Faculty of Science:

• Operating system:
  • Ubuntu Linux