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.

MODELS Models in COPASI are based on reactions that convert a set of species into another set of species. Each species is located in a compartment, which is a physical location with a size (volume, area, etc). This maps directly to biochemical reaction networks, but can also represent other types of processes (for example, the species could be cell types). COPASI automatically converts the reaction network to a set of differential equations or to a system of stochastic reaction events — the user does not have to write down the math explicitly, the software does that. Models can also have: * Unlimited number of species, reactions, and compartments. * Arbitrary discrete events; these can be used to change the model, or just to monitor the progress of simulations. * Arbitrary differential equations; these have to be added explicitly by the user and can be mapped to species, compartments, or generic variables. * Compartments can have variable sizes (ie they can be variables of the model). * The rates of reaction can be picked from a set of predefined kinetic functions (the most common in biochemistry), or arbitrary functions defined by the user. Models can be visualized through * the GUI interface, with tables for reactions, species, compartments, etc.; * an arbitrary number of network diagrams (including an SBGN-compliant option); * the full set of differential equations; these can be exported in Latex or MathML formats. COPASI can import and export models in the SBML format (levels 1 to 3). Models can also be exported in XPP format, Berkeley Madonna format, and as C code (in addition to MathML and Latex). SIMULATION Simulation can be performed either with stochastic kinetics or with differential equations, and the software easily allows switching between them. The software provides an interface to create parameter scans (sweeps), parameter sampling and repeated simulations — including complex simulation scenarios mixing parameter samples with scans and repeats of simulations (or other analyses). Algorithms available for simulation: * LSODAR for ordinary differential equation modeling. * Gillespie's direct method for exact stochastic kinetics. * Gibson-Brooke's version of Gillespie's algorithm for exact stochastic kinetics. * τ-leap algorithm for faster (approximate) stochastic kinetics. * Adaptive SSA/τ-leap algorithm for faster (approximate) stochastic kinetics. * Hybrid Runge-Kutta/SSA for hybrid simulations with stochastic kinetics and differential equations. * Hybrid LSODA/SSA for hybrid simulations with stochastic kinetics and differential equations. Simulations can be of time courses or steady states. ANALISYS Models can be analyzed and modified with a large set of methods: * Stoichiometric analysis of the reaction network, including mass conservation analysis and elementary flux modes. * Optimization of arbitrary components of the model using a range of diverse algorithms. * Parameter estimation using a range of diverse optimization algorithms. This can be done over several different experiments simultaneously, including mixtures of steady-state and time course experiments. * Local sensitivity analysis. * Metabolic control analysis (a special form of sensitivity analysis). * Time scale separation analysis; this allows definition of fast and slow components of the model, in a time-dependent way. * Analysis of stochasticity using the linear noise approximation (allows estimating variances and co-variances even in the presence of large numbers of particles). * Cross sections, which allow to characterize non-linear dynamics properties, such as oscillations and chaos. * Lyapunov exponents, which allows to establish if the system dynamics are chaotic. DATA VISUALIZATION COPASI allows users to visualize data in various ways: * Network diagrams can be used to visualize time course simulations as movies; * Network diagrams can also be used to visualize mass conservation moieties, and elementary flux modes; * Arbitrary 2D plots of any model variables and parameters (including trajectories in phase space); * A series of plots that are most commonly used are already pre-defined; * Color-coded matrices, for easily identifying large and small values; * 3D bar chart representation of matrices DATA OUTPUT COPASI allows users to define report files where data is written to during simulations and analyses. These report files are useful for importing data onto other applications for further analysis and visualization.

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.

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.

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.

Classified ads is an attempt to re-produce parts of the functionality that went away when Usenet news ceased to exist. This attempt tries to fix the problem of disappearing news-servers so that there is no servers required and no service-providers needed for any operation ; data storage is implemented inside client applications that users are running. Features of the program currently include:

Colorful is a simple side-view shooter game, where the protagonist travels a maze of caves and corridors in order to collect color artifacts.

DayJournal is a minimalist digital journal that lets the content you create outlast DayJournal itself.

• Future proofs your journal entries by saving them as plain text and organizing them as you go. This means you can read or create entries when you don’t have DayJournal.
• Automatically saves as you write.
• Easily sync journals with cloud storage services because you choose where your journal folder is.
• Add pictures to your journal entries.
• Manage multiple journals.
• Keyboard shortcuts make it easy to navigate through entries.
• Create a journal archive file, an HTML page that looks great when printed so you can keep a physical journal too.
• Add to your journal from anywhere with Blip Journal for Android. DayJournal can automatically import entries synced to Dropbox from Blip Journal. On iOS? Now DayJournal can automatically import entries synced to Dropbox from the Day One app as well.

Simply put, DayJournal is the simple digital journal that finally does it right.

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.

The GFM is an application allowing for the manipulation of single/group/tigroup files from Texas Instruments handhelds. It can create a new file, open an existing file, save file, rename variables, remove variables, create folders, group files into a group/tigroup file, and ungroup a group/tigroup file into single files.

The GFM is intended to be used alongside TILP II, which can send and receive files from/to the handhelds.

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.

GSmartControl is a graphical user interface for smartctl, which is a tool for querying and controlling SMART (Self-Monitoring, Analysis, and Reporting Technology) data in hard disk and solid-state drives. It allows you to inspect the drive's SMART data to determine its health, as well as run various tests on it.

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.

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:

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.

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.

Psi is an instant messaging application for Windows, Linux, and Mac OS X that connects to the free, open XMPP network.

Features:

• Native look and feel on all supported OS
• Translated to many languages user interface
• Highly customizable
• Secure connections and end-to-end encryption

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

QtikZ is a small application helping you to create TikZ (from the LaTeX pgf package) diagrams for your publications.

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.

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.

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.

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.

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.

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.

Wireshark is an essential tool to capture and analyze the packets arriving or leaving the network interface. It is almost a GUI equivalent of the classic unix tool tcpdump.

Wireshark has a easy to use GUI to capture the packets matching the filter, on the mentioned interface and save them for later analysis.