computational
CogTool 1.0b18
CogTool - application to assist in the creation of design mockups and the calculation of predictions of skilled performance time more>>
Detailed information is provided in the CogTool User Guide. We strongly recommend that you read the guide to get the most out of the CogTool system.
To help you get started quickly with CogTool, we have also provided a Tutorial. This document walks you through an example in detail, but it is not as comprehensive as the CogTool User Guide and it refers to the CogTool User Guide, so you need both.
The installation procedure differs depending on the platform being used for modeling. The software is currently available for the Mac OS X (10.4 or higher, including IntelMacs) and Windows (Windows 98 or higher) platforms. Follow the instructions below for the appropriate platform.
The ability to execute task models integrated with driving is not available in the current version. If your primary interest is models integrated with driving, you may still use the old version, which requires a Mac OS X system (but does not run on Intel Macs).
Enhancements:
- New features in CogTool 1.0b17 include support for some new widgets, faster importing of background images from a folder, improved performance all around, new properties panes, the ability to export storyboard and scripts to various formats, a visualization of what the underlying computational cognitive engine (ACT-R) is doing to produce the human performance predictions, and re-written users guide and tutorial.
FractionAction X 0.9.1
FractionAction is free a program converting among rational fractions, decimals (with periodicity) and simple continued fractions within programs computational limits. more>>
FractionAction X 0.9.1 is a free program converting among rational fractions, decimals (with periodicity) and simple continued fractions within program's computational limits. Also shows factors for fraction's top and bottom (in reduced form with GCD [greatest common divisor]).
Results not guaranteed (i.e. don't use results to help build your rocket ship, etc.): reports of errors welcomed. Not a tutorial on the functions.
) and simple continued fractions within programs computational limits. FractionAction X 0.9.1 is a useful software that can convert between rationalOpenBabel 1.99r1
OpenBabel - Molecular modeling file converter more>>
OpenBabel is a project designed to pick up where Babel left off, as a cross-platform program and library designed to interconvert between many file formats used in molecular modeling and computational chemistry.
Open Babel includes two components, a command-line utility and a C++ library.
The command-line utility is intended to be used as a replacement for the original babel program, to translate between various chemical file formats.
The C++ library includes all of the file-translation code as well as a wide variety of utilities to foster development of other open source chemistry software.
CUDA 2.3
CUDA offers you a common purpose parallel computing architecture leveraging the parallel compute engine in NVIDIA graphics processing units (GPUs) to solve many complex computational problems in a fraction of the time required on a CPU. I more>> <<less
SphinxReport 1.0 Alpha 3
A report generator written in python using sphinx and matplotlib more>>
Once the pipeline settles down, SphinxReport permits an easy transition towards the automatic report generation needed when the pipeline is run on new data sets. SphinxReport is easy to use and powerful enough to give all the flexibility needed during the development of computational pipelines and robustness during the production use of a pipeline. It is intended for developers and computational scientists with python scripting experience.
Major Features:
- Uses simple markup in the form of restructured text
- Supports both automated and narrative analysis
- Keeps code, data and text together
- Takes care of indexing and formatting to produce something presentable
- Produces static html, latex, ps and pdf.
STARS 0.7.2a
STARS - Space Time Analysis of Regional Systems more>>
The views support several types of dynamic visualization:
- Linking different views to examine a given observation across different dimensions (spatial, temporal, distributional)
- Conditioning (brushing) one or more destination views on the selection of a set of observations on an origin view
- Animations of of maps, distributions, box plots, scatter plots, parallel coordinate plots and other views over time
- Spatial traveling
- Roaming windows
- View generated views (creating new views from existing views)
STARS includes a suite of computational modules:
- Classic descriptive statistics
- Exploratory Spatial Data Analysis (Local and Global Spatial Autocorrelation)
- Inequality Analysis
- Distributional mixing and mobility
- Classic Markov and Spatial Markov methods
STARS also includes utility methods for creating different types of geographical weight matrices, variable transformations, and for reading ArcView shapefiles to develop STARS projects.
Enhancements:
- Bug fix in ProjectMaker Application
- Bug fix in example project data (California).
Maple 11.0.1
Maple is the essential computational tool that accelerates and enhances your analytical work more>> <<less
EvoJava 0.9.0
EvoJava - Software for exploring computational models of biological systems more>>
I have developed and tested EvoJava using Gentoo Linux on Opteron and Pentium systems; Ive also tested with Microsoft Internet Explorer and Firefox for Windows XP SP2 (where I have Suns Java installed.)
This is a preliminary beta version of EvoJava. It contains only four "universe" types, and lacks significant documentation. Im releasing this code "as is", hoping users will help me improve the final program. Keep an eye on these pages for updates. I make no promises about schedules or about what the final program will include; all I can say is that EvoJava is moving along nicely. The final release will include full, documented source code, released under the GPL.
Fura 1.7.0 Build 090601
Provides grid enablement and distribution of applications on heterogeneous computational resources more>> Provides grid enablement and distribution of applications on heterogeneous computational resources
Fura is an open source self-contained grid middleware that allows the grid enablement and distribution of applications on heterogeneous computational resources.
Fura features a wizard-guided installation and configuration, web-based GUI, and Web Services compliance.
Furas component based plug-in architecture allows grid services to be extended or replaced, and new services can be developed reusing existing components.
Fura is for developers or highly technical enthusiasts who want the open and latest grid technology early and often to use it in non-critical computing environments.
Fura is not recommended to use Fura where support options, maintenance, and software/hardware certifications are valued. For such environments, you must use either Fura Open Enterprise Edition (GPL Licensed) or Fura Commercial Enterprise Edition (Commercial EULA).
Enhancements
- Fixed a portal error when trying to start a task that its already running.
- Fixed an issue when using read-only files with the agent.
- When the agent (re)starts it cleans up their directories, even if they contain read-only files.
- Fixed a portal error when trying to delete a task without having permissions to do it.
- Fixed a portal error when trying to reset a task.
Avogadro 0.9.5
Advanced molecular editor designed for use in computational chemistry, molecular modeling, bioinformatics and others more>> Advanced molecular editor designed for use in computational chemistry, molecular modeling, bioinformatics and others
Avogadro is a free and open source advanced molecular editor designed for cross-platform use in molecular modeling, computational chemistry, bioinformatics, materials science, and related areas. It offers flexible rendering and a powerful plugin architecture.
The main concept behind Avogadro is to enable a strong framework for molecular visualization and editing. Each community has their own needs and goals for an ideal tool.
So Avogadro seeks to allow users to easily provide their own scripts and plugins for rendering, commands, tools... etc.
Avogadro is based on top of existing chemistry software, including Open Babel. In the future, it will offer strong scripting abilities to allow for automated demos, submission of calculations to local computational resources, and user-defined customization.
NOTE: This release is an early beta release and is intended to gain feedback and interest in the project.
Main features:
- Cross-platform molecular builder/editor.
- Plugin architecture for developers, including rendering, interactive tools, commands, and Python scripts.
- Built-in molecular mechanics (including MMFF94 and UFF).
- Input generation for Gaussian and GAMESS-US, with more packages to come.
- Support for crystallographic unit cells.
- Visualization of iso surfaces and orbitals, including Gaussian cubes, OpenDX, and Gaussian fchk files.
- Translations into French and German.
System requirements:
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- OpenBabel 2.2.0 or later.
- Eigen 2.0.0 Beta 3 or later.
Enhancements
- General
- More build system improvements - external plugins can easily be built against libavogadro on Linux and Mac.
- Includes a standard Mac "app bundle" -- completely relocatable disk image
- Added a check for updated versions of Avogadro on the network (e.g., when 0.9.6 or 1.0 is released)
- Includes improved translations and localization, including localized numbers everywhere and a full translation in Indonesian
- More bugs found and fixed.
- Interface
- Updated interface allows more screen space for drawing / viewing
- Tools moved to a new toolbar
- Tool and Display Settings appear on demand
- Updated keyboard shortcuts for switching tools
- Keyboard shortcuts for switching elements in the Draw tool: type the element symbol (e.g., Fe for iron)
- Visual cues can now be disabled for the navigation tool
- Moved "insert fragment" to Build menu
- Rendering
- Significantly improved protein "Cartoon" display type
- Added a custom color option
- Display of forces from geometry optimization is fixed (was broken in previous 0.9 releases)
- Extensions
- Added "Insert Peptide" builder for oligopeptides.
- Added visualization of NMR spectra.
- Atom, bond, angle, and torsion property tables now allow editing. This means you can now set a bond length, angle or dihedral exactly.
- Allow sorting of property tables for each column.
- Improved vibration plugin, fixing many bugs, and smoothing the animation.
- Added syntax highlighting for GAMESS-US.
- Now can run local Gaussian 03 jobs.
Singular 3.0.2
Singular - a Computer Algebra System for polynomial computations more>>
Important features of SINGULAR:
- Main computational objects: ideals/modules over very general polynomial rings over various ground fields.
- Large variety of algorithms implemented in kernel (written in C/C++).
- Many more algorithms implemented as SINGULAR libraries.
- Intuitive, C-like programming language.
- Extensive documentation: Manual (info, ps, and html), Publications.
- Available for most hard- and software platforms: Unix (HP-UX, SunOS, Solaris, Linux, AIX), Windows, Macintosh.
Enhancements:
- factory, libfac updated for gcc 4.1.x
- configure/speed improved for 64bit architectures
- new library: dmod.lib ( dmod_lib)
- new library: perron.lib ( perron_lib)
- improved center.lib ( center_lib): revised implementation, new functions (sa_reduce etc.)
- revised ncalg.lib ( ncalg_lib): new algebras, U(sl_n) and U(g_2) changed to conform GAP.
- new algorithms in primdec.lib ( primdec_lib): radical et al.
- improved version of slimgb, incorporated into groebner
- improved module generator (modgen)
- experimental: new type bigint
- more architectures: Solaris on x86/opteron, ...
- build process improved: builds automatically without patches on 64bit architectures
Note:
Singular for Mac OS X 10.3 and 10.4 is available via the fink project (which aims at bringing the full world of Unix Open Source software to Darwin and Mac OS X).
Ideally, after installing fink, type:
fink selfupdate
fink install singular singular-doc
Madagascar 0.9.8
Software package for geophysical data processing and reproducible numerical experiments Madagascar is an open-source software package for multidimensional data analysis and reproducible computational more>> Software package for geophysical data processing and reproducible numerical experiments
Madagascar is an open-source software package for multidimensional data analysis and reproducible computational experiments.
Madagascar aims to provide:
- a convenient and powerful environment
- a convenient technology transfer tool
for researchers working with digital image and data processing in geophysics and related fields. Technology developed using the Madagascar project management system is transferred in the form of recorded processing histories, which become "computational recipes" to be verified, exchanged, and modified by users of the system.
Main features:
- Madagascar is a modern package. Started in 2003, and publicly released in 2006 it was developed entirely from scratch. Being a relatively new package, it follows modern software engineering practices such as module encapsulation and test-driven development. A rapid development of a project of this scope (more than 300 main programs and more than 3,000 tests) would not be possible without standing on the shoulders of giants and learning from the 30 years of previous experience in open packages such as SEPlib and Seismic Unix. We have borrowed and reimplemented functionality and ideas from these other packages.
- Madagascar is a test-driven package. Test-driven development is not only an agile software programming practice but also a way of bringing scientific foundation to geophysical research that involves numerical experiments. Bringing reproducibility and peer review, the backbone of any real science, to the field of computational geophysics is the main motivation for Madagascar development. The package consists of two levels: low-level main programs (typically developed in the C programming language and working as data filters) and high-level processing flows (described with the help of the Python programming language) that combine main programs and completely document data processing histories for testing and reproducibility. Experience shows that high-level programming is easily mastered even by beginning students that have no previous programming experience.
- Madagascar is an open-source package. It is distributed under the standard GPL open-source license, which places no restriction on the usage and modification of the code. Moreover, access to modifying the source repository is not controlled by one organization but shared equally among different developers. This enables an open collaboration among different groups spread all over the world, in the true spirit of the open source movement.
- Madagascar uses a simple, flexible, and universal data format that can handle very large datasets but is not tied specifically to seismic data or data of any other particular kind. This "regularly sampled" format is borrowed from the traditional SEPlib. A universal data format allows us to share general-purpose data processing tools with scientists from other disciplines such as petroleum engineers working on large-scale reservoir simulations.
System requirements:
-
Enhancements
- New reproducible papers, several structural changes, and numerous bug fixes.
Parallel Fractal Carbon 1.0
Parallel Fractal Carbon - Experiment with and learn parallel programming more>>
This code is meant as a tool for helping people experiment with and learn parallel programming. You may try different parallelization techniques or substitute different computational routines, if you wish.
Folding@home Screensaver 5.02
Folding@home Screensaver - distributed application screensaver more>>
What is protein folding and how is folding linked to disease? Proteins are biologys workhorses -- its "nanomachines." Before proteins can carry out these important functions, they assemble themselves, or "fold." The process of protein folding, while critical and fundamental to virtually all of biology, in many ways remains a mystery.
Moreover, when proteins do not fold correctly (i.e. "misfold"), there can be serious consequences, including many well known diseases, such as Alzheimers, Mad Cow (BSE), CJD, ALS, Huntingtons, Parkinsons disease, and many Cancers and cancer-related syndromes.
You can help by simply running a piece of software. Folding@Home is a distributed computing project -- people from through out the world download and run software to band together to make one of the largest supercomputers in the world. Every computer makes the project closer to our goals.
Folding@Home uses novel computational methods coupled to distributed computing, to simulate problems thousands to millions of times more challenging than previously achieved.
Adun 0.71
Adun is a new biomolecular simulator developed by the Computational Biophysics and Biochemistry Laboratory more>>
Enhancements:
New Features and Improvements
- Minimisation
- BFGS, Conjugate Gradient and Steepest Descent algorithms available
- Initial short minimisation step added before initial production loop.
- Improved handling of exploding simulations
- On detecting an exploding simulation AdunCore transparently
- Rolls back the simulation to a previous state
- Performs a minimisation
- Restarts the simulation from the rolled back state.
- Improved container functionality
- Van der waals radius used to define exclusion volume on insertion of a system.
Bug Fixes
- Fixed critical bug that affected temperature stability.
- Fixed critical bug preventing use of Charmm & Amber.
- As a result of this fix its no longer necessary to specify the type of of Lennard-Jones function used by a force field.
