Open Source Scientific/Engineering Software - Page 3

A simple and powerful interface for Tightvnc Server, written in python and developed with glade.

A C++ library for the computation of bifurcation diagrams: it provides tools for the integration of systems of ODEs that depend on parameters. A Python interface is included.

EDAS2 is a web-based environmental quality data management and decision support framework

Maui Scheduler is an advanced reservation HPC parallel batch scheduler for use with Linux and BSD clusters. Maui provides a complete scientific scheduling solution, supporting running custom parallel and MPI jobs over Myrinet and ethernet.

The PUMA Repository is a collection of Pascal units for medical informatics. It contains reusable source code for a wide field of health-care application development. The code includes a support engine for the European Data Format (EDF and EDF+), converting functions for units of measurement and an HL7 engine. PUMA is compatible with Lazarus and Free Pascal. Some of the units also support other Pascal implementations including Delphi, winsoft Pocket Studio and other compilers.

RASP uses structure-based chemical shift predictions to solve the backbone resonance assignment problem in protein NMR spectroscopy. This enables rapid determination of highly accurate assignments on the basis of minimal experimental datasets, even for spectroscopically challenging proteins. RASP takes as input spin systems assembled on the basis of an arbitrary set of conventional triple-resonance NMR experiments. Uniquely, RASP is capable of extensive assignments even in the abscence of Cbeta chemical shift information: over a test set of 154 proteins RASP assigns 88 % of residues with an accuracy of 99.7 %, using only information available from HNCO and HNCA spectra. RASP is described here: MacRaild and Norton (2014) RASP: Rapid and robust backbone chemical shift assignments from protein structure. J Biomol NMR doi:10.1007/s10858-014-9813-7

TIDAL is a collection of data acquisition and processing tools for research in respiratory physiology. It provides a high-level language for specifying experimental protocols and required computations.

TRURL is a suite of desktop calculators with reverse Polish notation (RPN) written in Object Pascal. Additionally, it comes with a free reusable class library (RPN Engine) as a toolbox for creating your own calculator. TRURL is an acronym for "TRURL is a Reusable Universal RPN Library". Class Libraries: • RPN Engine: Full-featured calculation engine for Pascal-based RPN calculators • Segmitator: Library for virtual seven-segment displays Applications: • TRURL A: Simple demo app for the RPN Engine • TRURL G: Desktop RPN calculator inspired by the UI of the DSKY unit of the Apollo Guidance Computer (AGC)

Viewmol is a graphical front end for computational chemistry programs. It is able to graphically aid in the generation of molecular structures for computations and to visualize their results.

clipsmm is a C++ interface to the CLIPS libray, a C library for developing expert systems.

Fast5 is a probabilistic file format for the storage of nucleotide and protein sequences based on hdf5.

mlpy is a Python module for Machine Learning built on top of NumPy/SciPy and of GSL. mlpy provides high-level functions and classes allowing, with few lines of code, the design of rich workflows for classification, regression, clustering and feature selection. mlpy is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License version 3. mlpy is available both for Python >=2.6 and Python 3.X.

zkcm library is a C++ library for multi-precision complex-number matrix calculations. It provides a number of functionalities including the LU decomposition, the singular value decomposition, tensor product calculation, tracing-out operations, etc.

An advanced calculator program that supports programming/scripting, a variety of mathematical functions, and a graphing utility.

ASSL (pronounced AY-sil), is a wrapper around CHP, an established async. process description language. This project provides a set of tools that aid the design, simulation, and synthesis of async. VLSI circuits. Common parser, independent tool projects

A small BOINC control script for Linux and the BSDs. Useful if there's no GUI on the crunching system yet you still want to easily monitor and control BOINC. Requires BOINC version 7.22 or higher.

See TTS demo at: http://rslp.racai.ro/index.php?page=tts This is an entirely written in JAVA project which includes a set of tools and methods designed to enable Multilingual Text-to-Speech (TTS) synthesis. We currently support English and Romanian but we will soon train more models and make them available for download. If you want to read more about our other NLP and TTS tools check out http://nlptools.racai.ro.

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

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.

An open-source corpus analysis class library written in C#. GUI of Tenka Text 0.1.3 comes with Wordlister - an advanced, extremely fast graphical wordlist tool and a simple regex concordance tool. Tenka Text - the open-source answer to WordSmith Tool

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.