Open Source Scientific/Engineering Software - Page 4

Biological Annotation Tool is a general-purpose high speed environment for manipulating biological sequence annotations in multiple input and output formats. A plugin-style API permits much extensibility.

Tools for analysing the degree of folding in the human brain

The program implements a demo application which demonstrates using C++ stream-compatible sockets developed by Maciej Sobczak http://www.msobczak.com/

Cellicone is a project to develop an artificial life organism with the necessary components to make it comparable to biological life as we know it. This includes components ranging from proteins to cells to organs to limbs, and many steps between.

CircularLogo is a light-weighted, easy to use web application that visualizes the intra-motif dependencies of a DNA or RNA motif.

A tool written in C++ to generate very large Fibonacci numbers using the primary recursive formula: F(n) = F(n-1) + F(n-2) n > 1; F(1) = 1, F(0) = 0.

DRAMMS is a software package designed for 2D-to-2D and 3D-to-3D deformable medical image registration tasks. Released by Section of Biomedical Image Analysis (SBIA) at the University of Pennsylvania. Some typical applications of DRAMMS include, -- Cross-subject registration of the same organ (can be brain, breast, cardiac, etc); -- Mono- and Multi-modality registration (MRI, CT, histology); -- Longitudinal registration (pediatric brain growth, cancer development, mouse brain development, etc); -- Registration under missing correspondences (e.g., vascular lesions, tumors, histological cuts). DRAMMS runs in command line in UNIX/Mac OS, It accepts Nifti/ANALYZE/MetaImage image formats. It is fully-automatic --- takes two input images, and generates a registered image and (optionally) the deformation field. More information (installation, tutorial, manual, demonstration, FAQ, etc) can be found at http://www.rad.upenn.edu/sbia/software/dramms/ .

MathCAD-like math software. Planned features include graphs, equations and more.

Doceval is a software that allows to discover the documentation included in a tarball. Basically it serves to identify if a given software project has doc at all and helps with a report to evaluate how much documentation it has and how good it is.

This project introduces a kernel module "dnburstyloss" to enable dummynet emulate bursty packet loss by integrating some common theoretical loss models into Dummynet.

Displays text or information from a document by rapidly "flashing" short segments on the screen. This has also been called Rapid Serial Visual Presentation (RSVP), and is intended, experimentally, to aid with reading speed and comprehension.

FAST is an Analysis and Simulation Toolbox (FAST) for Fuel Cells (FC) FAST-FC is the doctorate work of David B. Harvey and was developed with support from the U.S. DOE, Ballard, and Queen's University. Derivative works of FAST-FC include FC-APOLLO which is a forked branch of this project intended to capture the code state at the exit of the funded DOE project. FAST-FC is the open and active community branch. FAST-FC is developed and maintained by the original creator and developer, David B. Harvey. Features of FAST-fc include transport of gases and liquids, multi-step reaction kinetics, transient and steady state operation for performance and durability, and scalable dimensionality from 1D - 3D domains. Future development work is on-going in FAST-fc and our strategic development schedule includes membrane degradation, improved liquid water transport models through the application of pore networks, and extension to stack-level simulation.

Fast calculator is fast and simple calculator with many functions on java.

G2C (Geospatial to Civil) The LandGML Interoperability Experiment initiated by Autodesk, U.S. Army Corps of Engineers Engineering Research and Development Center, and Galdos Systems. this open source tool transforms LandGML into LandXML documents.

The program allows to simulate and visualize the behaviour of monoatomic gas in 2D. The main feature of the programm is that simulation is performed using direct simulation of particles motion and collisions (i.e. all particles collisions are taken into account).

(We have migrated this project to github [June 1 2015)] http://github.com/msg-byu/enumlib). The source files have been removed from sourceforge. Go to github (link above) for the latest copy. <<<< OLD SUMMARY >>>> A Fortran 95 implementation of an algorithm for generating derivative structures of a parent lattice. The algorithm is discussed in detail in: Gus L. W. Hart and Rodney W. Forcade, "Algorithm for generating derivative structures," Phys. Rev. B 77 224115 (26 June 2008) http://msg.byu.edu/papers/GLWHart_enumeration.pdf Gus L. W. Hart and Rodney W. Forcade, "Generating derivative structures from multilattices: Application to hcp alloys," Phys. Rev. B 80 014120 (July 2009) http://msg.byu.edu/papers/multi.pdf Gus L. W. Hart, Lance J. Nelson, and Rodney W. Forcade, "Generating derivative structures at a fixed concentration," Comp. Mat. Sci. 59 101-107 (March 2012) http://msg.byu.edu/papers/enum3.pdf

H2O is a collection of C routines and applications designed for the optimization of multi-reservoir and multi-period hydrothermal power production scheduling. H2O is built upon nonlinear network algorithms and heuristic techniques for higher efficiency.

A high performance visualization tool for stars and particles able to run on Beowulfs. Rendering step is implemented separately and optimized for SSE, compatible with OpenGL. Navigation mechanism with quaternions. Ten color maps, sobel contour detect

IMMpractical implements various Markov chain model-based methods for analysis of DNA sequences. Please cite: Sparks, M.E., Brendel, V. and Dorman, K.S. (2007) Markov model variants for appraisal of coding potential in plant DNA. LNBI. 4463:394-405.

InterferenceSimulator is a program demonstrating quantal two-slit Fresnel interference patterns with one, the other, or both slits open. A magnetic flux situated between the two slits allows demonstration of the Aharonov–Bohm effect. Simulations with short de Broglie wavelengths illustrate the classical limit of quantum mechanics. Because of the universality of wave phenomena, this program can also demonstrate the geometrical-optics limit of wave optics for small wavelengths.

The "JTAG-GDB server" is a program for integrating the ARM-Embedded ICE logic with the GNU-Debugger GDB.

KSetiSpy is a KDE program for monitoring the SETI@home client and displaying information about the data it analyzes. It offers the same user interface as SETI Spy, a popular Windows utility.

Ksetiwatch monitors multiple SETI@home clients running on your computer or in your local network, and logs/manages completed work units. It is developed for the K Desktop Environment.

LAMMPS is a classical molecular dynamics simulator designed for parallel machines. It can model atomic, polymeric, biological, metallic, or mesoscale systems using a variety of force fields and boundary conditions and is easy to modify or extend.