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Genetic Code 1.2.1

Genetic Code 1.2.1


Genetic Code - Widget displays standard genetic code in a simple table more>>
The Genetic Code widget displays the standard genetic code in a simple table showing the 64 codons and the amino acids each codon codes for.
This widget is free for all users. Download it now !
Enhancements:
- The one-letter code for GGT is now correct (G and not C).
- The GTT codon was missing.
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Download (111KB)
Added: 2006-01-26 License: Freeware Price:
1381 downloads
Geneious 4.6.2

Geneious 4.6.2


Aligns sequences, visualizes 3D structures, builds trees. With many other core bioinformatics functions. more>>


An automatically-updating library of genomic and genetic data; that provides a fully integrated, visually-advanced toolset for
- Sequence alignment and phylogenetics
- Sequence analysis, Contig assembly,
- primers, restriction analysis
- BLAST. Protein structure viewing, NCBI, UniProt, Pubmed auto-find and more
- API for creating you own plug-ins

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Download (32.2MB)
Added: 2009-04-23 License: Freeware Price:
42 downloads
Encog 2.1.0

Encog 2.1.0


Encog functions as an effective neural network and bot programming library. more>>

Encog 2.1.0 functions as an effective neural network and bot programming library. Encog can be used independently either to create neural networks or HTTP bot programs. Encog also includes classes that combine these two advanced features. Encog contains classes for Feedforward Neural Networks, Hopfield

Neural Networks, and self organizing maps. Training can be accomplished using backpropagation, simulated annealing, and genetic optimization. Additional classes are provided for pruning neural networks.
Encog also includes advanced HTTP bot programming features. A multithreaded spider that can store its workload either in memory on a database is provided. HTML parsing is provided, as well as advanced form and cookie handling.

If you are looking for a Java or C# neural network or bot API, Encog is a great choice. Encog is currently at version 2.0.

Major Features:

  1. Neural Network Architectures
    • ADALINE Neural Network
    • Adaptive Resonance Theory 1 (ART1)
    • Bidirectional Associative Memory (BAM)
    • Boltzmann Machine
    • Counterpropagation Neural Network (CPN)
    • Elman Recurrent Neural Network
    • Feedforward Neural Network (Perceptron)
    • Hopfield Neural Network
    • Jordan Recurrent Neural Network
    • Radial Basis Function Network
    • Recurrent Self Organizing Map (RSOM)
    • Self Organizing Map (Kohonen)
  2. Training Techniques
    • Backpropagation
    • Resilient Propagation
    • Manhattan Update Rule Propagation
    • Competitive Learning
    • Hopfield Learning
    • Genetic Algorithm Training
    • Instar Training
    • Outstar Training
    • ADALINE Training
  3. Training Data Models
    • Supervised
    • Unsupervised
    • Temporal (Prediction)
    • Financial (downloads from Yahoo Finance)
    • SQL
    • XML
    • CSV
    • Image Downsampling
  4. Activation Functions
    • Competitive
    • Sigmoid
    • Hyperbolic Tangent
    • Linear
    • SoftMax
    • Tangential
    • Sin Wave
    • Bipolar
    • Gaussian
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Download (2.6MB)
Added: 2009-10-06 License: GPL Price: FREE
downloads
 
Other version of Encog
Encog 2.0.0can be accomplished using simulated annealing, back-propagation, and genetic optimization. Additional classes are provided for pruning neural networks. Encog also includes advanced HTTP
Price: FREE
License:GPL
Download (2.4MB)
11 downloads
Added: 2009-07-09
Encog 1.0.0Training can be accomplished using simulated annealing, back-propagation, and genetic optimization. Additional classes are provided for pruning neural networks. Encog also includes advanced
Price: FREE
License:GPL
Download (5.7MB)
290 downloads
Added: 2008-10-07
Punnet Square Calculator

Punnet Square Calculator


Calculate punnet squares for genetic traits more>> SnapTalk is the cross-platform private chat and file-transfer utility for your office. Instantly send messages and files on your local network.
More powerful than other chat programs, SnapTalk includes full featured archiving and search of transcripts. In addition, SnapTalk includes customizable "SnapBacks" that let you reply with a single click of the mouse.
SnapTalk uses peer-to-peer technology and unlike public chat systems, does not rely on Internet servers. This keeps SnapTalk up and running even if the Internet is down. It also increases security and productivity because all messages are kept in-house. You can be sure that everything in SnapTalk is company business. SnapTalk seamlessly connects Mac and Windows computers!
SnapTalk is plug and play software. It installs in a minute and is immediately usable. SnapTalk configures itself and finds other users on the network without system administration.
Features:
Create private virtual LANs across a WAN
No Administration necessary. Ability to administrate other computers on the network. This feature is secured and requires access to the product registration code). Capabilities include transmitting of defined AutoReplies, groups, general preferences, templates, networking settings, SnapBacks, user lists and templates.
Send attachments and folders with your messages
Keep transcripts of your conversations in the searchable archives
Spell-check your messages as you type
Design SnapBacks that let you respond to calls with a single button-click
Create groups, which allow you to talk to multiple people with one easy selection
Decide how you will be notified with sounds and alerts
Activate an auto-reply message when you are out of the office
Use password protection to restrict program access
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Download (783KB)
Added: 2009-06-02 License: Freeware Price: FREE
200 downloads
JBeagle 0.1

JBeagle 0.1


A highly extensible toolkit for creating and running evolutionary algorithms more>>

JBeagle 0.1 offers you a very useful and highly extensible toolkit which is designed for creating and running evolutionary algorithms such as genetic algorithms and genetic programming.

JBeagle aims to provide support for parallel processing, configuration and tracking via the GUI or command line.

Enhancements: Initial release.

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Download (349KB)
Added: 2009-05-06 License: GPL Price: FREE
14 downloads
breve 2.5.1

breve 2.5.1


breve - 3D behaviors simulation environment more>>
breve is a simulation environment which allows users to define the behaviors and interactions of different types of agents in a simulated 3D world and observe the emergent behaviors. breve is conceptually similar to packages such as Swarm and StarLogo, but simulates objects in a continuous 3D world with continuous time.
breve thus allows simulation involving realistic collision detection and physics.
Agent behaviors are written in a simple object oriented language called "steve".
Users define an agents behavior by specifying how the agent interacts with the world at each timestep and how the agent interacts when it collides with other agents. breve includes full collision detection and experimental support for real physical simulation of rigid bodies.
Enhancements:
- Universal PPC/Intel build for Mac OS X
- New garbage collection system for improved stability and memory management
- Enhanced support for genetic algorithms and evolutionary computation.
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Download (25.8MB)
Added: 2007-01-23 License: GPL Price:
1005 downloads
PlantGrowth 1.0

PlantGrowth 1.0


PlantGrowth - generate 3D plants based on a genetic code more>>
PlantGrowth generates 3D plants based on a genetic code in realtime and renders them in OpenGL.

C++ source code using OpenGL / GLUT is included.

PlantGrowth controls :

Click and drag to rotate camera
+ / - to zoom in / out.


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Download (107KB)
Added: 2005-11-11 License: Freeware Price:
1444 downloads
H2 Database Engine 1.1.113

H2 Database Engine 1.1.113


An SQL database engine written in Java more>> An SQL database engine written in Java

H2 is an SQL database engine written in Java (but also available as a native binary). JDBC and ODBC APIs are supported.
Embedded and server modes are available. A Web console application is included. Clustering is supported.
H2 Database Engine is a web based java database engine.

Main features:
- Fast database engine
- Free, source code is included
- Supports standard SQL
- Written in Java
- Disk based or in-memory databases
- Browser base Console application
- JDBC API
- Limited ODBC support
- Embedded and client/server (network) mode
- High availablility support (clustering / failover)
- Wide range of data types including large objects (BLOB/CLOB)
- Strong security features (SSL, users, roles, encrypted files)
- Multiple connections, table level locking
- Cost based optimizer, using a genetic algorithm for complex queries
- Transaction support (serializable transaction isolation)
- Zero-administration, automatic recovery
- Large resultset, external sorting
- Scrollable and updatable resultset support
- Read only views and inline views
- Inner and outer joins, subqueries
- Many functions already built-in
- Triggers and Java functions / stored procedures
- Referential integrity / foreign key constraints with cascade, check constraints
- Multiple schema support
- Compatibility modes for HSQLDB, MySQL and PostgreSQL
- Sequence and autoincrement columns
- Well tested (high code coverage, randomized stress tests)
- Small footprint (smaller than 1 MB)
- Uses a small number of database files
- Can be compiled to native code using GCJ
- Primary keys, multiple index types (b-tree, linear hash, tree, hash)
- ORDER BY, GROUP BY, HAVING, UNION, LIMIT
- Information Schema
- Multiple connections
- Collation support
- EXPLAIN PLAN support
- The database can generate SQL script files
- Support for linked tables, and a built-in virtual range table
- Automatic re-compilation of prepared statements
- Sophisticated trace options
- Low memory requirements
- Easy to understand exception messages
- Standard handling of NULL values
- Multilanguage console application (at this time, English and German).

Enhancements
- Shell tool: the built-in commands EXIT, HELP, ?, LIST, and so on didnt work with a semicolon at the end.
- JDK 1.5 is now required to build the jar file. However it is still possible to create a jar file for Java 1.4. For details, see buildRelease.sh and buildRelease.bat. As an alternative, compile using JDK 1.5 or 1.6 and use Retrotranslator to create a Java 1.4 version http://retrotranslator.sourceforge.net/).
- When deleting or updating many rows in a table, the space in the index file was not re-used in the default mode (persistent database, b-tree index, LOG=1). This caused the index file to grow over time. Workarounds were to delete and re-created the index file, alter the table (add a remove a column), or append ;LOG=2 to the database URL. To disable the change, set the system property h2.reuseSpaceBtreeIndex to false.
- Identifiers with a digit and then a dollar sign didnt work. Example: A1$B.
- MS SQL Server compatibility: support for linked tables with NVARCHAR, NCHAR, NCLOB, and LONGNVARCHAR.
- Android: Workaround for a problem when using read-only databases in zip files (skip seems to be implemented incorrectly on the Android system).
- Calling execute() or prepareStatement() with null as the SQL statement now throws an exception.
- Benchmark: the number of executed statements was incorrect. The H2 database was loaded at the beginning of the test to collect results, now it is loaded at the very end. Thanks to Fred Toussi from HSQLDB for reporting those problems. However the changed do not affect the relative performance.
- H2 Console: command line settings are no longer stored in the properties file. They are now only used for the current process, except if they are explicitly saved.
- Cache: support for a second level soft-references cache. To enable it, append ;CACHE_TYPE=SOFT_LRU (or SOFT_TQ) to the database URL, or set the system property h2.cacheTypeDefault to "SOFT_LRU" / "SOFT_TQ". Enabling the second level cache reduces performance for small databases, but speeds up large databases. It makes sense to use it if the available memory size is unknown. Thanks a lot to Jan Kotek!

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Download (4.9MB)
Added: 2009-05-24 License: Freeware Price: FREE
218 downloads
 
Other version of H2 Database Engine
H2 Database Engine 0.9connections, table level locking - Cost based optimizer, using a genetic algorithm for complex queries - Transaction support (serializable transaction isolation) - Zero-administration
License:Freeware
Download (5.2MB)
1413 downloads
Added: 2005-12-15
CLC Sequence Viewer 6.2

CLC Sequence Viewer 6.2


CLC Sequence Viewer is a freeware that creates a software environment enabling users to make a large number of bioinformatics analyses, combined with smooth data management, and excellent graphical viewing and output options. more>>

CLC Sequence Viewer 6.2 is a freeware that creates a software environment enabling users to make a large number of bioinformatics analyses, combined with smooth data management, and excellent graphical viewing and output options.

Major Benefits:

  • You will have easy access to a large number of integrated research tools:
    • Creating and editing alignments
    • Interactive restriction site analysis
    • Phylogenetics
    • Integrated GenBank searches
    • Advanced DNA to Protein translation
  • You can get easy access to hardware accelerated database searches
    • Plug in the Bioinformatics Cube and increase your search speed up to 200 times
  • Your research work will be easy to carry out
    • The program is graphically based, intuitive, and user-friendly
  • You will have a bioinformatics solution that continuously evolves
    • The frequent program updates keep you up to date with the latest scientific developments. Your ideas for future improvements will have top priority.
  • You will get superior customer service
    • Free support to all users.

Major Features:

  1. Bioinformatics features in CLC Sequence Viewer
    • Multiple alignment of DNA, RNA, and proteins
      • Two proprietary algorithms
      • ClustalW
      • Muscle
      • T-Coffee
      • MAFFT
      • Kalign
    • Consensus sequence determination and management
    • Conservation score along alignments
    • Open reading frame determination
    • Easy access to web-based protein and nucleotide search in GenBank, including download facilities and full graphical overview of sequence annotations of your choice
    • Translation from DNA to proteins (all genetic translation tables)
    • Reports with residue composition, molecular weight and iso electric point (for proteins)
    • Neighbor-joining and UPGMA phylogenies
    • Restriction site analysis and viewing
    • Create reverse complement
    • Shuffle sequence
    • Option of viewing and graphical manipulation of bioinformatics analyses made in commercial workbenches from CLC bio
  2. Other features in CLC Sequence Viewer
    • Full integration of data input, data management, calculations results, and data export. This eliminates time spent on manual data transfers between different programs and databases
    • All types of files can be saved in local projects and launched from the program
    • Detailed history log
    • User-friendly graphical tools used in order to find and work with relevant regions of DNA, RNA and protein sequences
    • Text-based sequence view
    • Easy printing of reports and graphics
    • Export of user-defined figures to various graphics file formats
    • Import and export of data in a large number of file formats
    • Option of working with different files and in different file projects at the same time
    • Option of working in several active workspaces at a time, enabling simultaneous work on multiple projects

Enhancemnets:

  • New features:
    • Import list of sequences in csv format: each line in the file represents a sequence with name, optional description, and sequence. Typically useful for importing lists of oligos.
    • Advanced view of elements in a folder including batch editing.
    • Extract sequences improvements
    • You can now drag results from NCBI searches into the view area to open directly (previously you could only drag into a folder to save)
    • "Find" in text view now accepts Enter as command to find the next hit
    • Importing VectorNTI archives previously resulted in a sequence list. Now it imports as single sequences.
    • Export of annotations in GFF format (note that annotations with joined regions are not supported)
  • Bug fixes:
    • Problem rendering scatter plots without lines
    • DNA strider files could loose name upon import
    • Rare misplacement of annotations when editing very large sequences
    • Various bug-fixes
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Download (21.8MB)
Added: 2009-08-17 License: Freeware Price: Notavailable
downloads
 
Other version of CLC Sequence Viewer
CLC Sequence Viewer 6.1Translation from DNA to proteins (all genetic translation tables) Reports with residue composition, molecular weight and iso electric point (for proteins) Neighbor-joining and UPGMA phylogenies
License:Freeware
Download (21.7MB)
20 downloads
Added: 2009-05-31
CLC Sequence Viewer 6.1Translation from DNA to proteins (all genetic translation tables). - Reports with residue composition, molecular weight and iso electric point (for proteins). - Neighbor-joining and UPGMA
Price: FREE
License:Freeware
Download (21.7MB)
208 downloads
Added: 2009-06-02
Price: FREE
License:Freeware
Download (35.8MB)
408 downloads
Added: 2008-10-04
CLC Free Workbench 4.0.1

CLC Free Workbench 4.0.1


CLC Free Workbench - Bioinformatics program for DNA, RNA, and protein sequence analysis more>>
CLC Free Workbench creates a software environment enabling users to make basic bioinformatics analyses and smooth data management, combined with nice graphical viewing and output options.
CLC Free Workbench is a tool that enabling users to make basic bioinformatics analyses by create a software environment.
Main features:
- GenBank searching and viewing (linear and circular views)
- Multiple alignment of DNA, RNA and proteins (2 alignment algorithms)
- Advanced alignment editing and sequence editing
- Joining multiple alignments and multiple sequences into one
- Open reading frame determination
- Translation from DNA to proteins (all genetic translation tables)
- Reports with residue composition, molecular weight and iso electric point (for proteins)
- Neighbor-joining and UPGMA phylogenies
- Interactive restriction site analysis and viewing
- Other reporting facilities
- Import/export to a number of data formats
- Launch of external files
- Detailed History Log
- Batch runs of analyses such as DNA to protein translation.
Enhancements:
- Fixed error in conversion of old sequence data with lowercase characters
- Old data can now be converted through the help menu
- Fixed error when trying to save an element to non-selected location
- A few help updates
- Better license handling on Windows Vista
- Fixed error in alignment editing
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Download (26.8MB)
Added: 2007-07-06 License: Freeware Price:
852 downloads
breveWalker 1.5

breveWalker 1.5


breveWalker - Physically simulated creature learns to walk more>>
breveWalker is a screensaver in which a physically simulated creature learns to walk using a genetic algorithm.
Starting with random walking behaviors, the system learns over time by selectively breeding and mutating these behaviors.
The behaviors are saved from run to run, so evolution continues where it left off every time the screensaver runs.
Enhancements:
- improved speed
- improved graphics
- all behaviors are saved from one run to the next (as opposed to saving just one individual)
- built with the 1.5 version of the breve simulation engine.
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Download (686KB)
Added: 2006-05-16 License: Freeware Price:
725 downloads
Return to Castle Wolfenstein 1.41beta

Return to Castle Wolfenstein 1.41beta


Single player demo of the popular 1st person shooter. more>>


You are B.J. Blazkowicz, an Army Ranger recruited into the Office of Secret Actions (OSA) tasked with escaping and then returning to Castle Wolfenstein in an attempt to thwart Heinrich Himmler?s occult and genetic experiments.
Himmler believes himself to be a reincarnation of a 10th century dark prince, Henry the Fowler, also known as Heinrich. Through genetic engineering and the harnessing of occult powers, Himmler hopes to raise an unstoppable army to level the Allies once and for all.
Game Demo 1.0
Download from MacGameFiles (108MB)
View QuickTime Trailer
Game Feature: Return to Castle Wolfenstein: Mac OS X Meets WWII
Other Resources
- Enemy Territory: A free, stand-alone, downloadable multiplayer MOD in which players wage war as Axis or Allies in team based combat (players will also want to download the security patch).
- True Combat: Elite: A MOD set against the backdrop of modern urban warfare.
- CyberExtruder: Cyberx-3D game skins compatible.

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Download (17MB)
Added: 2002-12-16 License: Update Price:
5946 downloads
AssociationViewer 1.5.1

AssociationViewer 1.5.1


Easily view SNPs in a generic context more>>

AssociationViewer 1.5.1 is a mighty efficacious Java application used to display SNPs in a genetic context. Supplementary data (such as genes or LD plots) is downloaded from various public data sources on the fly and saved locally in a cache. Custom data can be added as supplementary tracks.

Major Features:

  1. Display SNPs and their p-values in a genetic context, similar to usual genome browsers
  2. Automatically download supplementary information from Ensembl/Biomart
  3. Display Hapmap LD plots (currently coming from CEU population)
  4. Create reports (made of one or several regions of interest), which can be reloaded later
  5. Print and export the display to various data formats
  6. Import external data file such as BED or Wiggle as supplementary tracks
  7. Does not require to have a local copy of any data or data source, except for the primary file of SNPs and their respective p-values
  8. Users can scroll and browse through their data in real time
  9. Small in size (AssociationViewer itself is less than 500 KB, less than 5 MB with the required libraries)
  10. Downloaded data is kept in a cache locally for faster access
  11. Due to the cache, memory requirement is reasonable and should be constant over time (from the moment SNPs are loaded to the moment the application is closed)

Requirements:

  • Java plugin version 1.6 (aka Java6) or more recent, which is usually already installed on most computers and OS (Operating System). If it is not the case, it can be downloaded from the Java official web site.
  • A reasonable screen resolution (minimum 1024 x 768, more is recommended)
  • A working Internet connection
  • Enough free memory, AssociationViewer uses by default 256 MB of memory.
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Download (4.1MB)
Added: 2009-07-16 License: GPL Price: FREE
11 downloads
Return to Castle Wolfenstein Updater 1.3.2

Return to Castle Wolfenstein Updater 1.3.2


Return to Castle Wolfenstein Updater 1.3.2 is an interesting in which you play the part of B.J. Blazkowicz, a highly decorated Army Ranger recruited into the Office of Secret Actions (OSA), tasked with escaping and then returning to Castle Wolfenstein to stop Heinrich Himmlers occult and genetic experiments. more>>

Return to Castle Wolfenstein Updater 1.3.2 is an interesting in which you play the part of B.J. Blazkowicz, a highly decorated Army Ranger recruited into the Office of Secret Actions (OSA), tasked with escaping and then returning to Castle Wolfenstein to stop Heinrich Himmler's occult and genetic experiments. Blast your way through hidden crypts, forests, air bases, secret weapons facilities, genetic labs, villages overrun by the occult, and other locations while avoiding monstrous Nazi creations and agents of evil.

This update installs the 1.32 patch for Return to Castle Wolfenstein, adding the PunkBuster anticheating software, several new multiplayer maps, improved support for ATI's TruForm technology, and many multiplayer fixes and optimizations. In addition, Mac users will now be able to see many more servers in the in-game browser.

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Download (17MB)
Added: 2002-06-10 License: Freeware Price:
434 downloads
PongWars 2.0

PongWars 2.0


PongWars essentially merges the game of more>>
PongWars essentially merges the game of "Pong" with the sci-fi classic "Star Wars" into one grotesquely twisted abonination.
PongWars has highly optimized genetic algorithm for computer AI.
It features 640x480 graphics and animation, multiple channels of paddle-blasting sci-fi sound, an in-game MOD music soundtrack, and great 1 or 2 player action promising many hours of nostalgic revery for any 1970s geek,
Main features:
- Customizable gameplay settings
- Anachronistic 8-bit 640x480 graphics
- Nerdy Star Wars themed MOD music
- Deftly incorporated audio samples from certain copyrighted works
- Highly optimized genetic algorithm for computer AI.
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Download (1.4MB)
Added: 2006-06-26 License: Freeware Price:
1947 downloads
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