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GEneral NEural SImulation System 2.2.1

GEneral NEural SImulation System 2.2.1


GEneral NEural SImulation System is a neural network simulator. more>>
GENESIS (short for GEneral NEural SImulation System) is a general purpose simulation platform that was developed to support the simulation of neural systems ranging from subcellular components and biochemical reactions to complex models of single neurons, simulations of large networks, and systems-level models.

GENESIS has provided the basis for laboratory courses in neural simulation at Caltech, the Marine Biological Laboratory, the Crete, Trieste, Bangalore, and Obidos short courses in Computational Neuroscience, and at least 49 universities of which we are aware.

Most current GENESIS applications involve realistic simulations of biological neural systems. Although the software can also model more abstract networks, other simulators are more suitable for backpropagation and similar connectionist modeling.

Installation

1. Pick the place where you want to install the "genesis" directory tree. If you are making a system-wide installation as "root" user, /usr/local is a good choice. For a personal installation, without root privileges, you can use your home directory ("~"). Change to this directory and extract the genesis directory from the archive file genesis2.2.1-linux-bin.tar.gz. For example,

cd /usr/local
tar xvzf /mnt/cdrom/genesis2.2.1-linux-bin.tar.gz

or from wherever you have it (e.g.~/downloads/genesis2.2.1-linux-bin.tar.gz).

2. Change to the "genesis" directory and run the setup script that creates the ".simrc" GENESIS initialization file". Then copy .simrc to your home directory.

cd genesis
./binsetup
cp .simrc ~

3. Finallly, add the genesis directory to your search path, so that "genesis" can be found from any directory that you are in. If your login shell is bash, you can do this by editing the .bashrc file in your home directory to add the line

PATH=$PATH:/usr/local/genesis

at the end of the file. If you are using tcsh or csh as your command shell, add

set path=($path /usr/local/genesis)

to your .tcsh or .csh file.

At this point, you are ready to try running GENESIS. Change into the directory genesis/Scripts and try some of the tutorials suggested in the README file.
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Added: 2005-04-01 License: BSD License Price:
1667 downloads
Particle Simulation 0.9.1

Particle Simulation 0.9.1


Particle Simulation is a simulation of spraying up to 60k particles in realtime. more>>
Particle Simulation project is a simulation of spraying up to 60k particles in realtime.
Particle Simulation is a playful simulation game which allows you to spray particles into the "air". The number of simulated particles is only limited by the speed of your computer.
The particles dont interact with each other, but will bounce back from the ground and accelerate depending on a gravity constant.
This constant can be changed (along with a number of other parameters) in the source code or via commandline parameters.
Enhancements:
- Colors were adjusted and a new animation mode was introduced.
- Segmentation fault was fixed.
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Added: 2007-01-10 License: GPL (GNU General Public License) Price:
1057 downloads
Noble Ape Simulation 0.686

Noble Ape Simulation 0.686


The Noble Ape Simulation creates a random environment and simulates the ape inhabitants cognitive processes. more>>
The Noble Ape Simulation has been developed (as the Nervana Simulation) since 1996 and is a biological simulation software. The aim of the simulation is to create a detailed biological environment and a cognitive simulation.
The Simulation is intended as a palette for open source cross-platform development. It provides a stable means of simulating large-scale environments and cognitive processes on Windows, Mac and Linux.
The Simulation includes a detailed scripting language for user-implemented movement and cognitive-process development.
Enhancements:
- This release fixes a bug in displaying only the seen Noble Apes, and has code simplification towards OpenGL implementation.
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Added: 2007-07-30 License: Freeware Price:
816 downloads
Ikaros Simulation Framework 1.0

Ikaros Simulation Framework 1.0


Ikaros is a framework for writing and running component-based simulators. more>> <<less
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Added: 2007-06-02 License: GPL (GNU General Public License) Price:
877 downloads
Mars Simulation Project 2.80

Mars Simulation Project 2.80


Mars Simulation Project is a simulation of a human settlement on Mars. more>>
Mars Simulation Project is a free software Java project to create a simulation of future human settlement of Mars.
The simulation is a multi-agent artificial society set in a detailed virtual world.
XML configuration files allow the user to modify the simulation properties.
The Mars Simulation Projects main window contains the following components:
- Menu Bar
- Search Tool
- Time Tool
- Mars Navigator
- Monitor Tool
- Rover Info Window
- Settlement Info Window
- Person Info Window
- Unit Bar
The Mars Simulation Project can be configured with a number of XML configuration files located in the "conf/" directory. It is recommended that you save a backup copy of a configuration file before modifying it in case there is an error and the simulation cannot read the modified configuration file.
Here are the configuration files you can modify for the simulation. You will need to start a new simulation for any changes to be loaded in.
- buildings.xml
- crops.xml
- landmarks.xml
- malfunctions.xml
- medical.xml
- people.xml
- settlements.xml
- simulation.xml
- vehicles.xml
Enhancements:
- This release includes the new mission tool for viewing, creating, and editing missions as well as plenty of bugfixes.
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Added: 2007-03-30 License: GPL (GNU General Public License) Price:
941 downloads
Arithmetic Operations Simulation Library 0.01

Arithmetic Operations Simulation Library 0.01


Arithmetic Operations Simulation Librarys aim is to develop an open source library to simulate heavy arithmetic operations. more>>
Arithmetic Operations Simulation Librarys aim is to develop an open source library to simulate heavy arithmetic operations efficiently.
Finding different ways to solve a problem has been an interesting way to relax for many people. Not only they derive some kicks out of it, but as a side effect they develop much deeper insight into the problems enabling them to work out solutions under different constraints easily.
Here you will find discussion/hints to solve some common programming problems in efficient ways, supported with code that you can try.
DSP Programming Tricks
Often support for many heavy arithmetic operations goes missing to reduce the chip cost for marketability reasons, or during chip development stages. And we programmers have to make for the lack of these.
Accessing recent N items in history
This problem attracted my attention during DSP guest lectures by Mr. Ganesh Bhokare at PUCSD in later half of 2005. Various programming solutions to this problem would be.
Maintain a circular buffer in an array of N (or N+1) items. This will require support for MOD operation.
In case N is a power of 2, bitwise-anding with (N-1) can be used in place of MOD.
If neither N is a power of 2, nor MOD support is available?
Enhancements:
- This version supports finding the first 1/0 bit from left/right (lsb/msb), 16-bit unsigned numbers multiplication, division and mod operations, and also special cases of division by 3.
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Added: 2006-05-15 License: GPL (GNU General Public License) Price:
1258 downloads
Multi-Simulation Interface 0.14.0

Multi-Simulation Interface 0.14.0


Multi-Simulator Interface, in shrot MSI, is a simulation interconnection engine. more>>
Multi-Simulator Interface, in shrot MSI, is a simulation interconnection engine. In other words it is a program that connects simulations together by synchronizing their clocks and data. Multi-Simulation Interface serves the same purpose as HLA and supports most of HLAs functionality (and more).
The MSI is an HLA alternative. The major motivating factors in the design of the MSI are speed, interoperability, and ease of use.
The MSI was written as a cutting edge distributed simulation component to connect multiple instances of ATLs premiere simulation software, CSIM, and it can be used to interface any compatible simulations.
How does the MSI compare to HLA?
The MSI was originally created to be just a light weight HLA RTI. However, as it was written, limitations in HLA were discovered. The MSI is an improvement on both the design and implementation of HLA. Some highlights include:
A 1,536 to 1 reduction in size over the publicly available (until late 2002) HLA RTI.
At least one order of magnitude of bandwidth consumption less than the publicly available (until late 2002) HLA RTI.
The ability to subscribe to an object name in addition to a type.
Time synchronization that allows for proper causality when used with discrete event simulators.
Support for systems-of-systems (SoS) and hierarchically organized simulations.
Availability for many platforms.
MSI Concept - A Synchronized Data Broker
The concept behind MSI is the synchronized data broker. There are many connected software systems that posses state data that changes over the life of that system. In the case where these systems need to exchange this changing data with other systems and the other systems will exhibit the effects of this data on their own state, the synchronization of this data may need to be managed.
Historically the management of this data has been as simple as tagging it with the time of its release. If there is any conflict in the data the most recent version of the data is used. If the data is late an extrapolation can potentially be used. In SQL relational databases transactions and locking are used to ensure data integrity. Most data brokering services offer little or no sychronization, only delivery.
MSI Setup and Use
The MSI uses a XML stream through a direct socket connection for communications. This enables the MSI to be used from any programming language that can use sockets (C, C++, Java, Ada, Lisp, Perl, etc.). Also, the MSI was written with cross-platform libraries that make it portable to all the major OS platforms (Linux, Solaris, Mac OS X, Microsoft Windows, IRIX, HPUX, etc.).
The MSI is a single executable file and is distributed with example code for the simulator/federate side interface.
MSI Time Synchronization
The MSI time synchronizer can mix unconstrained with time constrained simulations. Each constrained simulation reports the time of the next event that will occur in that simulation/federate. This time may be artificially inflated to cause loose synchronization (less overhead but less guarantee of accuracy). The simulations/federates will advance to the announced time.
MSI Data Synchronization
The MSI implements a publish/subscribe data broker. The MSI is presently not validating, therefore it does not require a separate data format specification (like the HLA FOM). When data format validation is implemented, it will be an optional feature and not written in Lisp. This greatly reduces MSIs setup time. Also, not being locked to a predetermined data format allows for dynamic data types.
There are five commands associated with the MSI data broker: publish, subscribe, update, unsubscribe, destroy (destroy is not implemented yet). Simulations/federates may subscribe to object names in addition to object types. This allows simulations to subscribe to specific objects of a type without needing to receive updates of all objects of that type. The update command is both an incoming and outgoing command. When a simulation/federate receives an update command, it is expected to reflect the new values of that object.
The MSI has a very flexible publish and subscribe system. A federate may subscribe to an object type or an object name. In addition a federate may specify particular attributes of an object or object type. For example, if an object has attributes name, x, y, and z, a federate that only considers two dimensions may choose to subscribe only to name, x, and y.
The MSI also supports systems of systems and object hierarchy in simulations. A publishing federate may designate a parent object. Subscribers may then subscribe to the objects children.
MSI Messaging
The MSI allows simulations/federates to send messages (interactions in HLA) to each other. These messages can contain multiple attributes and be multicast to a specific group of simulations.
Recently Added Features
Removed external library dependencies to improve the portability and fragility of the MSI.
Added a better client library.
Improved documentation.
Enhancements:
- An XML parsing bug in the utilities library was fixed.
- The socket library was enhanced with more protocols, Win32 tricks, and the ability to key off of addresses as well as names.
- The --wait-for command line argument was added.
- Several internal bugs were fixed.
- More of the client library and the CSIM interface were flushed out.
- All standard functionality was tested.
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Added: 2006-05-26 License: GPL (GNU General Public License) Price:
1254 downloads
Natural Language Toolkit 0.8

Natural Language Toolkit 0.8


Natural Language Toolkit is a suite of Python libraries and programs for symbolic and statistical natural language processing. more>>
Natural Language Toolkit is a suite of Python libraries and programs for symbolic and statistical natural language processing. NLTK includes graphical demonstrations and sample data.
It is accompanied by extensive documentation, including tutorials that explain the underlying concepts behind the language processing tasks supported by the toolkit.
Documentation:
A substantial amount of documentation about how to use NLTK is available from the nltk home page:
< http://nltk.sourceforge.net >
In particular, the NLTK home page contains three types of documentation:
- Tutorials teach students how to use the toolkit, in the context of performing specific tasks. They are appropriate for anyone who wishes to learn how to use the toolkit.
< http://nltk.sourceforge.net/tutorial/ >
- The toolkits reference documentation describes every module, interface, class, method, function, and variable in the toolkit. This documentation should be useful to both users and developers.
< http://nltk.sourceforge.net/ref/nltk.html >
- A number of technical reports are available. These reports explain and justify the toolkits design and implementation. They are used by the developers of the toolkit to guide and document the toolkits construction. Students can consult these reports if they would like further information about how the toolkit is designed and why it is designed that way.
< http://nltk.sourceforge.net/tech/ >
Enhancements:
Code (major):
- changed package name to nltk
- import all top-level modules into nltk, reducing need for import statements
- reorganization of sub-package structures to simplify imports
- new featstruct module, unifying old featurelite and featurestructure modules
- FreqDist now inherits from dict, fd.count(sample) becomes fd[sample]
- FreqDist initializer permits: fd = FreqDist(len(token) for token in text)
- made numpy optional
Code (minor):
- changed GrammarFile initializer to accept filename
- consistent tree display format
- fixed loading process for WordNet and TIMIT that prevented code installation if data not installed
- taken more care with unicode types
- incorporated pcfg code into cfg module
- moved cfg, tree, featstruct to top level
- new filebroker module to make handling of example grammar files more transparent
- more corpus readers (webtext, abc)
- added cfg.covers() to check that a grammar covers a sentence
- simple text-based wordnet browser
- known bug: parse/featurechart.py uses incorrect apply() function
Corpora:
- csv data file to document NLTK corpora
Contrib:
- added Glue semantics code (contrib.glue, by Dan Garrette)
- Punkt sentence segmenter port (contrib.punkt, by Willy)
- added LPath interpreter (contrib.lpath, by Haejoong Lee)
- extensive work on classifiers (contrib.classifier*, Sumukh Ghodke)
Tutorials:
- polishing on parts I, II
- more illustrations, data plots, summaries, exercises
- continuing to make prose more accessible to non-linguistic audience
- new default import that all chapters presume: from nltk.book import *
Distributions:
- updated to latest version of numpy
- removed WordNet installation instructions as WordNet is now included in corpus distribution
- added pylab (matplotlib)
Enhancements:
Code:
- changed nltk.__init__ imports to explicitly import names from top-level modules
- changed corpus.util to use the rb flag for opening files, to fix problems reading corpora under MSWindows
- updated stale examples in engineering.txt
- extended feature stucture interface to permit chained features, e.g. fs[F,G]
- further misc improvements to test code plus some bugfixes
Tutorials:
- rewritten opening section of tagging chapter
- reorganized some exercises
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Added: 2007-07-03 License: GPL (GNU General Public License) Price:
850 downloads
ACT-RBOT + MRS 1.0 (Documentation)

ACT-RBOT + MRS 1.0 (Documentation)


ACT-RBOT + MRS project is a cognitive agent-based social simulation toolkit. more>>
ACT-RBOT + MRS is a cognitive agent-based social simulation toolkit (RBOT+MRS) and production system based on ACT-R for modelling single actor cognitive experiments (RBOT) and multiple actors in a simulated (semiotic) world (RBOT + MRS).
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Added: 2006-11-23 License: GPL (GNU General Public License) Price:
1066 downloads
 
Other version of ACT-RBOT + MRS
ACT-RBOT + MRS Alpha 0.8.2ACT-RBOT + MRS project is a cognitive agent-based social simulation toolkit. a cognitive agent-based social simulation toolkit (RBOT+MRS) and production system based on
License:LGPL (GNU Lesser General Public License)
Download (5.7MB)
1116 downloads
Added: 2006-10-03
ACT-RBOT + MRS 0.1 (Tools)ACT-RBOT + MRS is a cognitive agent-based social simulation toolkit. ACT-RBOT + MRS 0.1 ... ACT-RBOT + MRS is a cognitive agent-based social simulation toolkit (RBOT+MRS). ACT-RBOT
License:LGPL (GNU Lesser General Public License)
Download (MB)
1004 downloads
Added: 2007-01-24
Cell Electrophysiology Simulation Environment 1.4.6

Cell Electrophysiology Simulation Environment 1.4.6


Cell Electrophysiology Simulation Environment is a simulation environment for electrophysiology. more>>
Cell Electrophysiology Simulation Environment (CESE) is a comprehensive framework specifically designed to perform computational electrophysiological simulations, for example, simulations of cardiac myocyte electrical activity.
Cell Electrophysiology Simulation Environment is useful for simulations of action potentials, individual ionic currents, and changes in ionic concentrations.
CESE is a cross-platform program, it runs on any system that has Java runtime environment (JRE) version 1.4 or above. It was tested on Windows, Linux, Solaris, MacOS X, and AIX.
CESE users
CESE is an integrated environment for performing computational simulations using a variety of electrophysiological models.
At this stage CESE allows creation and execution of the single-cell models (containing both Hodgkin-Huxley (HH) and Markovian current formulations). Models of electrical activity of cardiac myocytes with source code are included in the CESE distribution. We hope to extend the number of available models, and add certain neuronal models in the future.
The main strength of CESE is in its uniformity ? a program interface remains the same for different types of models. You can easily switch between models and compare simulation outputs. Model parameters can be modified, selected for output and/or clamped in the same, standard way.
CESE extends the conventional electrophysiological meaning of the "voltage clamp". You can clamp virtually any model variable, including voltage (membrane potential), total or individual ionic currents, ionic concentrations, temperature, gating variables, etc. The clamping commands can be complex piece-wise functions, individually set for the model variable of interest. This opens endless possibilities for the exploration of complex model behavior.
CESE provides simple, but efficient data visualizations. Simulation results can be presented in the graphic and tabulated forms. Plots can be customized, and regions of interest zoomed.
Even though CESE was not designed to be a data analysis tool, you can generate current-voltage relationships (I-Vs) and calculate statistical parameters for a given signal within the program. You can export your data to ASCII, Axon Text File (ATF), and NetCDF formats to continue analysis in your favorite package.
CESE developers
CESE was created from the ground up to incorporate the best programming practices available to Java developers, both in terms of user interface consistency and code clarity and reuse. Wherever possible, CESE rely on available Java APIs (for example Java2D, JavaBeans, JAXP) to simplify the code.
Model creation requires a number of house-keeping functions to be coded ? these include ODE integrators, routines for handling model parameters, saving/restoring model state, visualizing simulation results, etc. CESE provides you with implementation for these routines, hence, you can concentrate on writing the code for concrete ionic current(s), and CESE will handle the rest.
CESE is not trying to create complicated programming frameworks on its own ? rather, it utilizes core Java APIs. For example, models are Java components conforming to the JavaBeans specification. We use XML to specify clamping commands, and Java object serialization to save/restore model parameters.
Enhancements:
- This release improves results printing, adds export to the scalable vector graphics (SVG) format, improves support for continuous simulations, and fixes many bugs in plot rendering and model switching.
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Added: 2007-02-12 License: GPL (GNU General Public License) Price:
587 downloads
Strobe Light 1.0

Strobe Light 1.0


Simple utility that turns your monitor into a configurable strobe light. more>>
Simple utility that turns your monitor into a configurable strobe light.

Source code is included alongside the executable "strobelight" in the archive.
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Added: 2005-09-16 License: GPL (GNU General Public License) Price:
878 downloads
The breve simulation environment 2.5.1

The breve simulation environment 2.5.1


Tthe breve simulation environment is a 3D simulation environment for decentralized systems and artificial life. more>>
breve is a free, open-source software package which makes it easy to build 3D simulations of decentralized systems and artificial life.
Users define the behaviors of agents in a 3D world and observe how they interact. breve includes physical simulation and collision detection so you can simulate realistic creatures, and an OpenGL display engine so you can visualize your simulated worlds.
breve simulations are written in an easy to use language called steve. The language is object-oriented and borrows many features from languages such as C, Perl and Objective C, but even users without previous programming experience will find it easy to jump in. More information on the steve language can be found in the documentation section.
breve features an extensible plugin architecture which allows you to write your own plugins and interact with your own code. Writing plugins is simple and allows you to expand breve to work with existing projects. Plugins have been written in breve to generate MIDI music, download web pages, interact with a Lisp environment and interact with the "push" language.
Enhancements:
- An experimental Python language bridge is now available.
- There were also fixes related to Push language support and fixes for broken demos.
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Added: 2007-01-23 License: Free To Use But Restricted Price:
1004 downloads
Light 1.4.12

Light 1.4.12


Light is yet another Mozilla-based browser. more>>
Light is yet another Mozilla-based browser. Features very simple non-bloated GTK+ interface, familiar Netscape 4.x keyboard shortcuts, context menus, etc. Tested with Mozilla 0.9.6 and newer. Supports Java/SSL/downloads/queue downloads to an external download manager.

The goal of this project is to have a usable, fast browser for reading news, searching bugzilla, etc. There are no binary packages, and I do not plan to provide them anytime soon. Compiling Light from source requires Mozilla 0.9.6+ and Mozilla headers.

Carefully read README and INSTALL, and read manual.html in the doc/ directory for explanation of how things are done and why. may work but this is unsupported. Bug reports are welcome, but requests to implement a Cookie Editor are not.
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Added: 2006-10-19 License: GPL (GNU General Public License) Price:
640 downloads
LinuxSSN 0.0.pre_alpha3.0

LinuxSSN 0.0.pre_alpha3.0


LinuxSSN is an undersea combat simulation. more>>
LinuxSSN project is an undersea combat simulation.

LinuxSSN is a naval combat simulation. It is based on the operations of a nuclear submarine.

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Added: 2007-01-09 License: GPL (GNU General Public License) Price:
1020 downloads
Hogwash Light BR 1.1

Hogwash Light BR 1.1


Hogwash Light BR is an IPS (Intrusion Prevention System). more>>
Hogwash Light BR is an Intrusion Prevention System that can filter packets directly in the layer 2 of the OSI model (so the machine doesnt need even an IP address).
Detection of malicious/anomalous traffic is done by rules based in signatures, and the user can add more rules. It is an efficient and versatile IPS, and it can even be used as bridge to honeypots and honeynets.
Since it doesnt make use of the operating systems TCP/IP stack, it can be "invisible" to network access and attackers.
Enhancements:
- New rules were added.
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Added: 2006-05-19 License: GPL (GNU General Public License) Price:
1256 downloads
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