Bowtie, an ultrafast, memory-efficient short read aligner for short DNA sequences (reads) from next-gen sequencers. Please cite: Langmead B, et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25.
An intuitive molecular editor and visualization tool
Avogadro is an advanced molecular editor designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science and related areas. It offers a flexible rendering framework and a powerful plugin architecture.
SciDAVis is a user-friendly data analysis and visualization program primarily aimed at high-quality plotting of scientific data. It strives to combine an intuitive, easy-to-use graphical user interface with powerful features such as Python scriptability.
JFreeChart is a free (LGPL) chart library for the Java(tm) platform. It supports bar charts, pie charts, line charts, time series charts, scatter plots, histograms, simple Gantt charts, Pareto charts, bubble plots, dials, thermometers and more. *** JFreeChart has moved to GitHub: https://github.com/jfree/jfreechart ***
A circuit simulator with graphical user interface (GUI)
Qucs is a circuit simulator with graphical user interface. The software aims to support all kinds of circuit simulation types, e.g. DC, AC, S-parameter, Transient, Noise and Harmonic Balance analysis. Pure digital simulations are also supported.
SAM (Sequence Alignment/Map) is a flexible generic format for storing nucleotide sequence alignment. SAMtools provide efficient utilities on manipulating alignments in the SAM format. The main samtools source code repository moved to GitHub in March 2012. For ongoing development since then, see http://github.com/samtools/samtools
Dedicated to computer-aided engineering Linux distribution
CAELinux is a live DVD Linux distribution dedicated to open source engineering with a focus on Computer Aided Engineering and Scientific Computing. Based on Ubuntu, it features a full software solution for open source production development with many CAD/CAM/CAE applications. It includes Freecad & LibreCad 2D/3D CAD systems, Salome & GMSH pre/post processors, Code_Aster & Calculix non-linear FE solver, Code-Saturne & OpenFOAM CFD solvers, Elmer multiphysics suite, Helyx-OS, Discretizer, EnGrid & Netgen 3D meshers, GEDA, KiCad & Arduin electronic design tools, PyCAM, OpenSCAM & Cura for CNC G-code generation, GNU Octave, Rkward, wxMaxima, Scilab, Scipy & Spyder for computationnal & mathematics modeling, and many more.
Gerbv is an open source Gerber file (RS-274X only) viewer. Gerbv lets you load several files on top of each other, do measurements on the displayed image, etc. Besides viewing Gerbers, you may also view Excellon drill files as well as pick-place file
SAGA - System for Automated Geoscientific Analyses - is a Geographic Information System (GIS) software with immense capabilities for geodata processing and analysis. SAGA is programmed in the object oriented C++ language and supports the implementation of new functions with a very effective Application Programming Interface (API). Functions are organised as modules in framework independent Module Libraries and can be accessed via SAGA’s Graphical User Interface (GUI) or various scripting environments (shell scripts, Python, R, ...). Please provide the following reference in your work if you are using SAGA: Conrad, O., Bechtel, B., Bock, M., Dietrich, H., Fischer, E., Gerlitz, L., Wehberg, J., Wichmann, V., and Boehner, J. (2015): System for Automated Geoscientific Analyses (SAGA) v. 2.1.4. Geosci. Model Dev., 8, 1991-2007, doi:10.5194/gmd-8-1991-2015. http://www.geosci-model-dev.net/8/1991/2015/gmd-8-1991-2015.html.
Technical Analysis Library
Technical analysis library with indicators like ADX, MACD, RSI, Stochastic, TRIX... This is not an end-user GUI trading or charting application. It is instead targeted to application developers using either Excel, .NET, Mono, Java, Perl, Python or C/C++.
Virastyar is an spell checker for Persian Language
Virastyar is a free and open-source (FOSS) spell checker for Persian. It stands upon the shoulders of many free/libre/open-source (FLOSS) libraries developed for Persian text processing. Contributors: Omid Kashefi Azadeh Zamanifar Masoumeh Mashaiekhi Meisam Pourafzal Reza Refaei (former member) Mohammad Hedayati (former member) Kamiar Kanani (former member) Mehrdad Senobari (former member) Sina Iravanin (former member) Mohammad Sadegh Rasooli (former member) Mohsen Hoseinalizadeh (former member) Mitra Nasri (former member) Alireza Dehlaghi (former member) Fatemeh Ahmadi (former member) Banafshe Bakhtiari (former member) Neda Pourmorteza (former member)
GeographicLib is a small set of C++ classes for converting between geographic, UTM, UPS, MGRS, and geocentric coordinates, for gravity (e.g., EGM2008), geoid, and geomagnetic field (e.g., WMM2010) calculations, and for solving geodesic problems. For documentation, visit https://geographiclib.sf.io
dcm4che is an implementation of DICOM and IHE actors in Java. Homepage: http://www.dcm4che.org, Google Group: http://groups.google.com/group/dcm4che?hl=en, Wiki: http://www.dcm4che.org/confluence, Issue Tracking: http://www.dcm4che.org/jira
JAGS is Just Another Gibbs Sampler. It is a program for the statistical analysis of Bayesian hierarchical models by Markov Chain Monte Carlo.
SkyChart is a software to draw chart of the night sky for the amateur astronomer from a bunch of stars and nebulae catalogs. See main web page for full download. This software is part of a full suite for astronomical observation: https://sourceforge.net/projects/ccdciel/ https://sourceforge.net/projects/indistarter/ https://sourceforge.net/projects/eqmodgui/ Requirement: https://sourceforge.net/projects/libpasastro/ See also: https://sourceforge.net/projects/indi/
utility to split mp3, ogg vorbis and FLAC files without decoding
mp3splt is a free utility to split mp3, ogg vorbis and FLAC files without decoding, selecting begin/end time; if file is an album, you can get splitpoints automatically from internet or a local cue, cddb file. It also splits Mp3Wrap and AlbumWrap archives. Supports splitting and trimming by silence detection. For mp3 files, both ID3v1 and ID3v2 are supported using original tags or user defined tags.
TinyCAD is a program for drawing electrical circuit diagrams commonly known as schematic drawings. It supports standard and custom symbol libraries. It supports PCB layout programs with several netlist formats and can also produce SPICE simulation netlists. It is also often used to draw one-line diagrams, block diagrams, and presentation drawings.
Open Source Solid Modeling CAD
BRL-CAD is a powerful cross-platform constructive solid geometry solid modeling system that includes an interactive geometry editor, ray-tracing for rendering & geometric analyses, network distributed framebuffer support, image & signal-processing tools.
Robocode is a programming tank game for Java and .NET
Robocode is a programming game, where the goal is to develop a robot battle tank to battle against other tanks in Java or .NET. The robot battles are running in real-time and on-screen. The motto of Robocode is: Build the best, destroy the rest!
The Open Source CFD Toolbox
OpenFOAM - The Open Source CFD Toolbox. OpenFOAM is a generic, programmable software tool for Computational Fluid Dynamics (CFD). For more information, see: - Main Website: https://openfoam.org - C++ Source Documentation: https://cpp.openfoam.org - Issue (Bug) Tracking: https://bugs.openfoam.org - User Guide: https://cfd.direct/openfoam/user-guide
Portable OS X FOSS applications
OS X FOSS portable applications are packaged so you can carry around on any portable device, USB thumb drive, iPod, portable hard drive, memory card, other portable device (or also on your internal hard disk), taking your preferences with you.
Expert System Tool
CLIPS is a forward-chaining rule-based programming language written in C that also provides procedural and object-oriented programming facilities.
FreeImage is a library project for developers who would like to support popular graphics image formats (PNG, JPEG, TIFF, BMP and others). Some highlights are: extremely simple in use, not limited to the local PC (unique FreeImageIO) and Plugin driven!
Qwt is a graphics extension to the Qt GUI application framework. It provides a 2D plotting widget and more.