Open Source Scientific/Engineering Software - Page 57

BioWord, a Microsoft Word add-in, allows instant access to most sequence manipulation needs, such as reverse-complementing, translating or FASTA formatting, and features a full suite of sequence search methods, pair-wise alignment and motif discovery.

Thiis is .NET library for CANopen master and slave devices. It is based on C open source CANopen stack - CanFestival. For details about CanFestival, see www.canfestival.org

CFDTool - "CFD Simulation Made Easy" CFDTool is a fluid dynamics toolbox for modeling and simulation of flows with coupled heat transfer. Based on FEATool Multiphysics (https://www.featool.com), CFDTool is specifically designed to make advanced fluid mechanics and heat transfer simulations both easy and enjoyable. - Completely stand-alone and cross-platform self-contained toolbox - Optionally use as MATLAB Add-On toolbox - Fully integrated and easy to use MATLAB GUI - Modeling and simulation in 1D, 2D, 3D, and axisymmetric/swirl/cylindrical coordinate systems - Seamless OpenFOAM GUI and SU2 CFD solver integrations (https://www.featool.com/Easy-to-Use-OpenFOAM-GUI) - Built-in geometry and CAD tools - Automatic mesh and grid generation - Pre-defined equations and boundary conditions for: + Incompressible viscous fluid flows (Navier-Stokes equations) + Compressible, supersonic, trans-sonic, and turbulent flows + Heat conduction with conjugate heat transfer

COPE (Connecting Overlapped Pair-End reads) is a method to align and connect the illumina sequenced Pair-End reads of which the insert size is smaller than the sum of the two read length.The connected reads can be used in genome assembly, resequencing and transcriptome research. The full citation: COPE: An accurate k-mer based pair-end reads connection tool to facilitate genome assembly Binghang Liu; Jianying Yuan; Siu-Ming Yiu; Zhenyu Li; Yinlong Xie; Yanxiang Chen; Yujian Shi; Hao Zhang; Yingrui Li; Tak-Wah Lam; Ruibang Luo Bioinformatics (2012) 28(22): 2870-2874; doi: 10.1093/bioinformatics/bts563

CRF++ is a simple, customizable, and open source implementation of Conditional Random Fields (CRFs) for segmenting/labeling sequential data. CRF++ is designed for generic purpose and will be applied to a variety of NLP tasks.

DACPEI is a WYSIWUG Software for Conceptual design of Light Fixed Wing aircraft. It is specifically designed to be intuitive and easy to use by engineering students (not necessary aerospace/aeronautics). DACPEI is divided in 9 modules, for analyzing mission profile, Aircraft performance, propulsion and layout design, as well as sketch component for developing aircraft drawings. DACPEI enable users to export their design to the FlightGear flight simulator software, enabling the designer to "test-drive" their designs while they are on the drawing board. Designers will get an immediate feel for the performance and handling qualities of their designs in less than 7 minutes.

The DC Water Design Extension integrates the EPANET hydraulic analysis software with ArcView GIS

Evoker is a graphical tool for plotting genotype intensity data in order to assess quality of genotype calls. It implements a compact, binary format which allows rapid access to data, even with hundreds of thousands of observations. PLEASE NOTE: This source repository is no longer active. See the github link above for the latest version.

GPL-licensed Electronic Medical Record and Practice Management system for medical providers that runs in any web browser in multiple languages. It provides an XML-RPC backend and multiple import and export formats, as well as reporting and other features

A cross-platform Java program to turn a simple Geiger counter into the equivalent of a state-of-the art digital model, plus some – using your laptop computer.

Ghawwas (previously known as Khawas) is an open source system for Arabic corpora processing. Ghawwas V4.0 provides the following main functions: a. Frequency list for single word and N-Grams b. Concordance c. Collocation (MI, CHI Squared, LL, T-Score, Z Score, Dice, Log Dice, Weirdness Coefficient) d. Lexical patterns search e. Two corpora frequency profile comparison based on MI, CHI, LL, T-Score, Z Score, Dice, Log Dice, Weirdness Coefficient f. Accept Windows and UTF-8 character encoding g. Accept TXT, DOC, DOCX, RTF and HTML formats h. Export the processing results in CSV file format

HexTool is a simple yet effective calculator/tool; invaluable for people who work with Hex and Binary. Now you can convert between Hex, Binary and Decimal on the fly. No install needed: just unzip and run it!

Version 2.5 is available! The latest changes are in TFastList class. It is the secondary class intended for fast string managment. The newest TGraph component is available as well. The new ParseUtils.FindFormula method allows searching any of possible formulas within some text. Parse components are intended for Delphi developers and perform high-speed (about 10 million evaluations per second) mathematics and boolean calculations. All components are available for Delphi 6, Delphi 7, Delphi 2005, Delphi 2006, Delphi 2007, Delphi 2009, Delphi 2010, Delphi XE, Delphi XE2, Delphi XE3, Delphi XE4, Delphi XE5, Delphi XE6, Delphi XE7, Delphi XE8, Delphi 10 Seattle, Delphi 10.1 Berlin. Please note that the samples do not require components installation (however installation is possible and in case when installed you find the components on "Samples" page of the pallete). You may open the Delphi project file (*.dpr) in the sample folder and simply run it. Fully functional TGraph component

A basic and easy java program to make black and white identikit drawing ,with a library of face elements that you can also modify and expand without limit !Source code available. Also available a very rough base for a 3D construction of the face.

A collection of astronomy tools written in java: sky map, astronomical events, ephemerides, planet visibility, moon calendar and galilean moons.

The LaTeX Equation Compiler is a preprocessor for LaTeX files that enables numeric and symbolic calculations. It reads equations specified by special keywords in the LaTeX file, manipulates them and calculates numeric values of variables. If your OS can install .deb packages, have a look at my PPA http://launchpad.net/~jrheinlaender/+archive/ppa

Parser for mathematical expressions written in Java. Expressions may contain variables, functions and constants. The parser turns a string argument into an expression tree, which then can be evaluated.

Motofit co-refines Neutron and X-ray reflectometry data, using the Abeles matrix / Parratt recursion and least squares fitting (Genetic algorithm or Levenberg Marquardt). It works in the IGOR Pro environment (TM Wavemetrics).

Motorola HC08 (especially MC68HC908JB8) monitor-mode programmer project. Includes hardware part (RS-232 programmer design in Eagle) and software part (in C++ for KDE/Qt).

This program was designed mainly for preconditioning and analysis of electrophysiological data, including patch-clamp and 2-electrode voltage clamp recordings. The program includes tools both for basic analysis of whole-cell recordings or analysis of single channel properties. Program can display and analyse long traces incuding many sweeps, series and even groups simultaneously. Current amplitudes or time intervals are easily measured. Single channel conductance, kinetics, NPo, as well as number of channels in a patch and their open probability may be estimated with the analysis of dwelling time at each conductance level. The program directly reads files, created by Pulse and PatchMaster software (HEKA Elektronik Dr. Schulze GmbH) as well as ASCII files. However, the program may be useful in various applications when editing and measurements in a 2-dimentional (for example time-current) wave are required.

This program is a soundcard based signalgenerator and oscilloscope for low frequency and low voltage signals written for linux using the alsa api. It uses the internal DAC/ADC of the soundcard (PCM) to capture signals or generate them. Depending on the available PCM device, it's possible to generate or capture signals up to 96 Khz.

OVATION Prime is a seasonal model of the diffuse, monoenergetic, proton, and wave aurora. The OVATION Prime model is written in IDL and was developed at the Johns Hopkins Applied Physics Laboratory (JHU-APL) by Patrick Newell and co-workers. This current version includes updates to the retrospective and real time components, several efficiency enhancements and a user configuration as implemented by Rob Redmon and Janet Machol of NOAA. This is a community model. Users are invited to suggest and provide improvements. Documentation includes a model description and instructions for running the software. The README is available here: http://sourceforge.net/p/ovation-prime/code/HEAD/tree/trunk/README.pdf?format=raw A web interface for running the model for historical periods is available here: http://sd-www.jhuapl.edu/Aurora/ovation_prime/prime_display.html Realtime versions are running here: http://www.ngdc.noaa.gov/stp/ovation_prime/ http://www.swpc.noaa.gov/ovation/

Programming language designed to simplify the development of small and large-scale networked applications. PROSE includes an execution engine and language that compiles into platform-independent bytecode. Bytecode can also be assembled directly.

Fast and efficient 3D pharmacophore search developed by the Camacho Lab (http://smoothdock.ccbb.pitt.edu) at the University of Pittsburgh. Source code is available through the svn repository.

PyEPL (Python Experiment-Programming Library) is a library for coding psychology experiments in Python. It supports presentation of both visual and auditory stimuli, and supports both manual (keyboard/joystick) and sound (microphone) input as responses.