Free computational biophysics software for mac

CogTool is an application to assist in the creation of design mockups and the calculation of predictions of skilled performance time for tasks on those designs. You are free to use this software for any purpose. However, it is provided as-is with no warrantee -- use at your own risk.
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.

A Carbonized version of the Parallel Fractal Demo, a numerically-intensive parallel graphics application, that uses the MacMPI_X.c library for communcations.

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.

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.

Folding@home Screensavers goal: to understand protein folding, misfolding, and related diseases

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.

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.

Adun is a new biomolecular simulator developed by the Computational Biophysics and Biochemistry Laboratory, a part of the Research Unit on Biomedical Informatics of the UPF.
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.

The Numerics osax augments AppleScript with computational commands.
The computational features now include five Suites: Linear algebra, FFT and convolution, Image files, 3D array handling, and Numerical data files.
Main features:
- linear algebra (eigenvalues, linear systems solving, etc.)
- signal processing (1d, 2d, and n-d FFT, cross- and self-correlations, convolution, interpolation)
- image processing (import/export, particle analysis)
- 3D arrays (handling by reference, extraction, isosurfaces, stream lines).
Enhancements:
- Linear algebra: transpose, multmatrix, invertmatrix, solve linear system, compute eigenvalues, LUdecomposition, pivot, determinant
- Basic linear algebra and basic commands for inverting, diagonalizing, and decomposing a matrix. These commands support complex matrices. multmatrix performs the product of matrices and/with vectors: M x M, M x v, v x M, v x v.
- FFT and convolution: fft1d, fft2d, filterarray, convolve, correlate, interpolate
- Fast Fourier transforms: 1d, grouped, n-dimensional, and 2d. Use algorithms which time like N.Log N. Not powers of 2-limited. Convolution and correlation of two arrays, support periodic boundary conditions. Interpolation, linear or spline, supports periodic boundary conditions.
- Image files: imagefile bounds, convert imagefile, create imagefile, create grayimagefile, particles
- Basic commands for doing image processing: getting an images bounds, importing it as a numerical matrix and back, and doing particles analysis (get statistical info and contours of particles of an image).
- 3D array handling: open3D, close3D, list3Darrays, info3D, contents3D, extract3D, isosurface, streamline
- This Suite is to cope with 3D data and visualize them conveniently. Instead of manipulating the data in your script, you load them into memory and specify a name for them. Using the name you can extract whatever fraction of the data you really need. You can produce isosurfaces of a scalar field, and the stream lines of a vectorial field (results are triangle lists).
- Numerical data files: XNFGetArray, XNFSave, XNFdelete, XNFtoc
- This Suite introduces a new extensible data format, XNF (eXtensible Numerical File format.), extension .xnf. XNF files store binary 1D, 2D, and 3D arrays. One XNF file may contain arbitrarily many arrays of various kinds, stored under a variety of formats: the XNF file manages a Table of contents which specifies the properties of each array. Access to arrays is simply by name. Since the Table of contents is a XML, you can apply XPaths to retrieve a particular set of data. XMLLib osax required.

Requirements:

• PowerPC: Mac OS X 10.4.7 or later.
• Intel: Mac OS X 10.5 or later.

Enhancements:
Version 1.8.7b5: Tagged/re-tagged all sources with final vmd-1-8-6 release tag.