Applications

COPASI is a software application for simulation and analysis of biochemical networks and their dynamics.

COPASI is a stand-alone program that supports models in the SBML standard and can simulate their behavior using ODEs or Gillespie's stochastic simulation algorithm; arbitrary discrete events can be included in such simulations.

COPASI carries out several analyses of the network and its dynamics and has extensive support for parameter estimation and optimization. COPASI provides means to visualize data in customizable plots, histograms and animations of network diagrams.

The Charles River RC Flight Simulator (CRRCSim) is a flight simulator to test fly model aircraft. CRRCSim comes with over 15 different types of model gliders and planes, and lets you fly in 3 different locations.

"Cube" (CUBE Uniform Behavioral Encoding) is a presentation component suitable for displaying a wide variety of performance data for parallel programs including MPI and OpenMP applications.

Program performance is represented in a multi-dimensional space including various program and system resources. The tool allows the interactive exploration of this space in a scalable fashion and browsing the different kinds of performance behavior with ease. All metrics are uniformly accommodated in the same display and thus provide the ability to easily compare the effects of different kinds of program behavior.

"Cube" also includes a library to read and write performance data as well as operators to compare, integrate, and summarize data from different experiments.

The Cube 4.x release series uses an incompatible API and file format compared to previous versions, however, existing files in CUBE3 format can still be processed for backwards-compatibility.

TOPPAS is the OpenMS TOPP Pipeline Assistant. It can create processing pipelines using OpenMS TOPP tools as building blocks.

OpenMS is a powerful set of tools as well as a C++ library to process low and high-resolution LC-MS(-MS) mass spectrometry data.

OpenMS is modular, consisting of more than 80 chainable TOPP tools (executables). It features a graphical data viewer (TOPPView), a pipeline editor (TOPPAS) and wrappers for most tandem-MS search engines (like Mascot, MSGF+ and X!Tandem). The OpenMS library itself comes with Python bindings for rapid prototyping.

TOPPView is a viewer for MS and HPLC-MS data supporting many common formats, e.g. mzML, mzData, mzXML and several others. The viewer supports 1D, 2D, 3D views, zooming, distance measurements and data annotations. It also allows to run many OpenMS TOPP tools and immediately inspect the data.

OpenMS is a powerful set of tools as well as a C++ library to process low and high-resolution LC-MS(-MS) mass spectrometry data.

OpenMS is modular, consisting of more than 80 chainable tools (executables). It features a graphical data viewer (TOPPView), a pipeline editor (TOPPAS) and wrappers for most tandem-MS search engines (like Mascot, MSGF+ and X!Tandem). The OpenMS library itself comes with Python bindings for rapid prototyping.

A program that will semi-automatically download album cover images for your music collection. All you have to do is point it at the root of your music directory and for each directory, the program will download a set of corresponding (well, best guess) album covers from the Internet, from which you can choose one that suits your fancy.

Currently supported image providers:

• Yahoo! Images
• Wal-Mart
• Buy.com

At least the following programs make use of the cover images:

• KDE, GNOME and others that follow the FreeDesktop.org .desktop-entry spec
• Windows XP Explorer
• Windows Media Player 9+
• CDcover, an XMMS plugin
• CoverViewer, another XMMS plugin
• wmalbum, a WindowMaker dock applet
• Various WinAMP plugins, for example Cover TAG

In addition, some portable music players can show the cover image if it is embedded in the MP3 file.

Ardour is a digital audio workstation that permits you to record and create music. Ardour supports multi-track recording, and allows you to use plug-ins to create music in a virtual studio.

Ardour is intended to be a one-stop complete solution for your digital audio needs.

Ardour is a multi-channel digital audio workstation, allowing you to record, edit, mix and master audio and MIDI projects.

It is targeted at audio engineers, musicians, soundtrack editors and composers.

Ardour is a multi-channel digital audio workstation, allowing you to record, edit, mix and master audio and MIDI projects.

It is targeted at audio engineers, musicians, soundtrack editors and composers.

Asylum is a Linux port of the game "Asylum" written originally for the Acorn Archimedes.

Enter the surreal world inside a young boy's brain and help destroy malfunctioning brain cells.

TILP2 is a communication program between Texas Instruments handhelds and computers. It is able to use any supported type of link cable (Gray/Black/Silver/Direct Link) with any TI graphing calculator.

With TiLP, you can transfer files from your PC to your Texas Instruments graphing calculator, and vice-versa. You can also make a screen dump, send/receive data, backup/restore contents, install FLASH applications, or upgrade the OS.

Dungeon Crawl Stone Soup is a free roguelike game of exploration and treasure-hunting in dungeons filled with dangerous and unfriendly monsters in a quest for the mystifyingly fabulous Orb of Zot.

Dungeon Crawl Stone Soup has diverse species and many different character backgrounds to choose from, deep tactical game-play, sophisticated magic, religion and skill systems, and a grand variety of monsters to fight and run from, making each game unique and challenging.

dsi or dspaceinvadors is a simple 2D scrolling game where you prevent aliens landing on top of you.

It has simple controls, 5 levels, a smooth scrolling experience, sound effects and customizable graphics.

Escape is a puzzle game that relies less on reflexes and more on solving the puzzle. The player has to move blocks and detonate bombs and other devices in a certain sequence to be able to solve the puzzle, and escape the maze. It features many levels of varying difficulty.

Ettercap supports active and passive dissection of many protocols (even encrypted ones) and includes many feature for network and host analysis. Data injection in an established connection and filtering (substitute or drop a packet) on the fly is also possible, keeping the connection synchronized.

Many sniffing modes are implemented, for a powerful and complete sniffing suite. It is possible to sniff in four modes: IP Based, MAC Based, ARP Based (full-duplex) and PublicARP Based (half-duplex). Ettercap also has the ability to detect a switched LAN, and to use OS fingerprints (active or passive) to find the geometry of the LAN.

Font Manager is intended to provide a way for average users to easily manage desktop fonts, without having to resort to command line tools or editing configuration files by hand.

While designed primarily with the Gnome Desktop Environment in mind, it should work well with other Gtk+ desktop environments.

Font Manager is NOT a professional-grade font management solution.

Dink Smallwood is an adventure/role-playing game, similar to Zelda, made by RTsoft. Besides twisted humour, it includes the actual game editor, allowing players to create hundreds of new adventures called Dink Modules or D-Mods for short.

GNU FreeDink is a new and portable version of the game engine, which runs the original game as well as its D-Mods, with close compatibility, under multiple platforms.

GAP is a system for computational discrete algebra, with particular emphasis on Computational Group Theory.

GAP provides a programming language, a library of thousands of functions implementing algebraic algorithms written in the GAP language as well as large data libraries of algebraic objects. GAP is used in research and teaching for studying groups and their representations, rings, vector spaces, algebras, combinatorial structures, and more.

Gnofract 4D is a free, open source program which allows anyone to create beautiful images called fractals.

The fractals are automatically created by the computer based on mathematical principles. These include the Mandelbrot and Julia sets and many more. You don't need to do any math: you can explore a universe of images just using a mouse.

Guido van Robot is an educational game where players use a basic programming language to control a robotic triangle through streets and press buttons. The simplistic language that is used helps students understand the basics of programming including command sequences, conditional statements, loops, and abstracting procedures.

In HexGlass the object is to rotate shaped pieces as the fall to the bottom so that they don't leave gaps. The pieces are made of small numbers of hexagons stuck together, and it is hard to work out the right way to rotate each piece as there are 6 possible orientations.

When a row is completed without any gaps, it is removed and all the hexagonal blocks above it move down one row. As the pieces fall faster, make sure not to let the screen fill up!

HgView is a tool to visually navigate the tree and history of a Mecurial repository. HgView has a wide range of features for browsing and interacting with a Mecurial repository graphically, including:

IrScrutinizer is a powerful program for capturing, generating, analyzing, importing and exporting infrared (IR) signals.

For capturing and sending IR signals several different hardware sensors and senders are supported. IR Signals can be imported not only by capturing from one of the supported hardware sensors (among others: IrWidget, Global Caché, and Arduino), but also from a number of different file formats (among others: LIRC, Wave, Pronto Classic and professional, RMDU (partially) and different text based formats; not only from files, but also from the clipboard, from URLs, and from file hierarchies), as well as the Internet IR Databases by Global Caché and by IRDB.

Imported signals can be decoded, analyzed, edited, and plotted. A collection of IR signal can thus be assembled and edited, and finally exported in one of the many supported formats.

The program contains the powerful IrpMaster IR-renderer, which means that almost all IR protocols known to the Internet community can be generated.

Jessie is an interface between why and Frama-C.

Why is a software verification platform that applies formal proving tools to annotated programs. The Jessie plugin provide the ability to analyze C programs by invoking Frama-C.

Key-mon is a Utility to show live keyboard and mouse status for teaching and screencasts. This tool will show the keyboard when doing a screen recording including: different key combinations, mouse wheel scrolling, support for 3 button mice, and touch tablet support.

NUT allows you to record what you eat and analyze your meals for nutrient composition. The database included is the USDA Nutrient Database for Standard Reference, Release 26.

This database of food composition tables contains values for calories, protein, carbohydrates, fiber, total fat, etc., and includes all the nutrient data in the USDA database, including the Omega-6 and Omega-3 polyunsaturated fatty acids. Nutrient levels are expressed as a percentage of the DV or Daily Value, the familiar standard of food labeling in the United States. The essential fatty acids, Omega-6 and Omega-3, are not currently mentioned in these standards, and a reference value has been supplied.

You may search this list of foods and view nutrient values for different serving sizes; you may also rank foods in order of level of a particular nutrient. You may change the daily calorie level to correspond to your personal metabolism, and the levels for fat, carbohydrates, fiber, and protein are automatically adjusted. You may customize the ratios of carbohydrates to protein to fat to suit your personal regimen. You may add your own recipes to the database, by creating them from the foods in the database. You can also add foods from the information on commercial food labels. The program is completely menu-driven and there are no commands to learn.

OnionShare lets you securely and anonymously share a file of any size with someone. It works by starting a web server, making it accessible as a Tor hidden service, and generating an unguessable URL to access and download the file.

It doesn't require setting up a server on the internet somewhere or using a third party filesharing service. You host the file on your own computer and use a Tor hidden service to make it temporarily accessible over the internet. The other user just needs to use Tor Browser to download the file from you.

Optical Ray Tracer is an application for analyzing the properties of lenses. You specify a single lens, or a series of lenses, then Optical Ray Tracer can simulate how light will behave when it passes through them.

Owncloud-client enables you to connect to your private ownCloud Server. With it you can create folders in your home directory, and keep the contents of those folders synced with your ownCloud server. Simply copy a file into the directory and the ownCloud Client does the rest.

Pingus is a Puzzle game where you need to save all your little penguins using the capabilities provided to you in the current level.

The basic game idea is to be like Lemmings game. This versions has some other cool stuff like a world map and some very cool secret levels.

Plater is a simple graphical tool for preparing plates for desktop 3D printers, such as RepRap.

It lets you load 3D models and manipulate them on XY plane. It is also possible to let Plater automatically arrange the files to fit. You can than export the prepared plate for later use or load it directly to Pronterface (if installed).

PyMOL is one of a few open-source visualization tools available for use in structural biology. The Py portion of the software's name refers to the fact that it extends, and is extensible by the Python programming language.

PyMOL has the ability to load, manipulate and visualize molecules from a variety of formats and sources. The program can easily be controlled using a menu-driven GUI, or from a large number of commands and/or scripts. A built-in raytracer is available to generate high-quality images of the views generated in the GL portion of the GUI.

PyMOL uses OpenGL Extension Wrangler Library (GLEW) and Freeglut, and can solve Poisson–Boltzmann equations using the Adaptive Poisson Boltzmann Solver (apbs).

Install this application to view, analyze, and prepare graphics images of proteins and experimental strucural data (e.g. crystallographic, NMR and electron microscopy based).

apitrace consists of a set of tools to:

• Trace OpenGL, OpenGL ES calls to a file
• Replay OpenGL and OpenGL ES calls from a file
• Inspect OpenGL state at any call while retracing
• Visualize and edit trace files

Quassel IRC is a modern, cross-platform, distributed IRC client, meaning that one (or multiple) client(s) can attach to and detach from a central core: much like the popular combination of screen and a text-based IRC client such as WeeChat, but graphical. In addition to this unique feature, we aim to bring a pleasurable, comfortable chatting experience to all major platforms, making communication with your peers not only convenient, but also available everywhere.

And the best of all: It's free - as in beer and as in speech.

This application is the client-only version of Quassel. You must first set up (or have been given an account on) the quassel core before using this.

QupZilla is a new and very fast QtWebKit browser. It aims to be a lightweight web browser available through all major platforms. This project has been originally started only for educational purposes. But from its start, QupZilla has grown into a feature-rich browser.

QupZilla has all standard functions you expect from a web browser. It includes bookmarks, history (both also in sidebar) and tabs. Above that, you can manage RSS feeds with an included RSS reader, block ads with a builtin AdBlock plugin, block Flash content with Click2Flash and edit the local CA Certificates database with an SSL Manager.

QupZilla's main aim is to be a very fast and very stable QtWebKit browser available to everyone. There are already a lot of QtWebKit browsers available, but they are either bound to the KDE environment, not actively developed or very unstable and miss important features. QupZilla, a multiplatform, modern and actively developed browser, is here to fill this gap by providing a very stable browsing experience.

Recoll finds keywords inside documents text as well as file names.

• It can search most document formats.
• It can reach any storage place: files, archive members, email attachments, transparently handling decompression.
• One click will open the document inside a native editor or display an even quicker text preview.

RemoteBox is a VirtualBox client which allows you to administer a server installation of VirtualBox and its guests over the network. Guests are launched in headless-mode which allows complete interaction with their displays from the client machine using RDP, which also supports sound and clipboard sharing. RemoteBox is compatible with VirtualBox on a server running Linux, Windows, Solaris or Mac OS X.

It supports most of the features of standard VirtualBox user interface with the advantage that all the guest resources are consumed on your server and not your client.

Screenruler is a program used to measure distances on your screen. You can change the ruler to apply to your zoomlevel. Different measurment units e.g. Centimeters can be chosen. It is easy to use and does what you would expect from a virtual ruler without any additional gimmicks.

Seafile is a next-generation open source cloud storage system, with advancedsupport for file syncing, privacy protection and teamwork.

Seafile allows users to create groups with file syncing, wiki, and discussion to enable easy collaboration around documents within a team.

The SELinux Troubleshooter provides a graphical user interface to help diagnose SELinux policy issues. When Access Vector Cache (AVC) denial messages are logged by SELinux, the SELinux Troubleshooter generates a desktop notification containing information about the problem and allows the user to launch the troubleshooting interface to help track down the cause of the denial.

Speed Dreams is a 3d cross-platform, open source motorsport simulation and racing game. It is a fork of the open racing car simulator Torcs, aiming to implement exciting new features, cars, tracks and AI opponents to make a more enjoyable game for the player, as well as constantly improving visual and physics realism.

Still being in costant development Speed-Dreams already has some unique feature as:

Tennix is a overhead view tennis simulator for one or two players. It features locations from all 4 Grand Slam tournaments in Australia, France, the USA and England.

TortoiseHg is a graphical front-end for the Mercurial version control system. TortoiseHg can visualize repository history and perform most repository operations.

TortoiseHg also plugs into the GNOME Files file manager.

Tor Browser Launcher is intended to make the Tor Browser Bundle (TBB) easier to maintain and use for GNU/Linux users. It downloads the same TBB from torproject.org that everyone else uses, and it doesn't alter it in any way. But it does make it much more usable, and it makes the task of keeping it up-to-date more secure.

You install torbrowser-launcher from your distribution's package manager and it handles everything else, including:

• Downloading the most recent version of TBB for you, in your language and for your architecture
• Automatically updating (while preserving your bookmarks and preferences)
• Verifying the TBB's GnuPG signature
• Includes AppArmor profiles to make a Tor Browser compromise not as bad (in some distros)
• Adding a Tor Browser application launcher to your desktop environment's menu
• Lets you set Tor Browser as your default browser
• Optionally playing a modem sound when you open Tor Browser (because Tor is so slow)

BitTorrent is a peer-to-peer file-sharing protocol that is commonly used to distribute large amounts of data between multiple users.

Transmission is a BitTorrent client with an easy-to-use frontend on top a cross-platform backend. Native frontends are available for OS X and Windows, as well as command line and web frontends.

Notable features of Transmission include Local Peer Discovery and Full Encryption, Full encryption, DHTµTP, PEX and Magnet Link support.

Trophy is a single-player racing game. Even though the goal is basically to finish the laps as the first, Trophy is an action game which offers much more than just a race.

Trophy has lots of extras, which are... er... 'untypical' for racing games. Some of these "unusual" features for races are: shooting other players, putting mines and many others.

Tuxguitar is a multitrack tablature editor and player. It provides the following features:

• Tablature editor
• Score Viewer
• Multitrack display
• Autoscroll while playing
• Note duration management
• Various effects (bend, slide, vibrato, hammer-on/pull-off)
• Support for triplets (5,6,7,9,10,11,12)
• Repeat open and close
• Time signature management
• Tempo management
• Imports and exports gp3,gp4 and gp5 files

TzClock is an analogue desktop Clock that can display the time around the world.

All the time zone information is read from the system, this means that as the time zone information is updated by the system repositories the clock is also updated. Once you have configured the clock as you like it all the settings can be saved.

Some of the features:

• Multiple faces showing different time zones
• An alarm that pops up a notification message
• Configurable date and time formats
• Customisable size, colours and fonts
• A simple analogue stopwatch

Uzbl is a webkit based web browser with a vi-like modal user interface. It has two modes, the command mode for running tasks such as opening a new URI ("o" on the keyboard) or opening a new window (the "w" command). Insert is the other mode, and is used for the input of text into the browser window itself.

xzgv is a simple image editor, with a focus on controlling all actions using keyboard input. It has a simple, two pane layout, with all the thumbnails of the current directory listed in the left pane, and the image viewed in the main pane. The menu in xzgv can be viewed in a context menu that is shown by right-clicking on the main image pane. This context menu also lists all the keyboard shortcuts if you are new to xzgv and need to know them.