Open Source Python Scientific/Engineering Software for Linux

Arabeyes is a Meta project that is aimed at fully supporting the Arabic language in the Unix/Linux environment. It is designed to be a central location to standardize the Arabization process. Arabeyes relies on voluntary contributions.

An update to Python package to perform comprehensive analysis of small RNA sequencing data, including miRNA annotation, A-to-I editing, novel miRNA detection, isomiR analysis, visualization through IGV, processing Unique Molecular Identifieres (UMI), tRF detection and producing interactive graphical output. miRge3.0 is developed in python v3.8 and is a recent update of our previous version miRge2.0. This build includes command line interface (CLI) and cross-platform Graphical User Interface (GUI). For more details refer to documentation link below.

This is a collection of software modifications created to integrate NanoEngineer-1, PACKMOL and MSI2LMP for the purpose of easily creating molecular dynamics cells. NanoEngineer-1 is a molecular CAD software written by Nanorex and provides the user an easy way to create molecules, while the software modifications allow the user to type atoms using multiple force fields. PACKMOL can generate a random collection of molecules using the molecule templates from NanoEngineer-1 thus providing the initial MD cell. Modifications to PACKMOL allow the atom type data to be passed through to the MSI2LMP software. MSI2LMP creates a LAMMPS input file based on class I or class II force fields. MSI2LMP was modified to use numerically coded force field data generated by NanoEngineer-1. The MMP file format was extended and integrated into all three software applications. http://www.nanoengineer-1.net http://www.ime.unicamp.br/~martinez/packmol/ http://lammps.sandia.gov/

This project is for maintaining a linux system that concentrates on math, logic, and geometry related softwares.

Libre Mechanics it’s an Open Knowledge project created to offer a useful platform of information related with the development and research of Mechanical Engineering themes and similar fields, higly related with the use of Open Source and Software Libre tools. Here you will find a wide variety of projects, publications and scientific material available as references for developing their own projects, also guides and tutorials that allow you to take advantage of free software tools available today. The four principal lines of work are: Design Analysis and Simulation Automation and Robotics Development

Febrl (Freely Extensible Biomedical Record Linkage) does data standardisation (segmentation and cleaning) and probabilistic record linkage ("fuzzy" matching) of one or more files or data sources which do not share a unique record key or identifier.

niftilib is a collection of i/o routines for the nifti1 neuroimage data format. C (nifticlib), Java (niftijlib), Matlab (niftimatlib), and Python (pynifti) code is available. For nifti format info see: http://nifti.nimh.nih.gov/

This project aims to provide software usefull in automation tasks like building automation. Different backends are supported like KNX or OpenHAB. Note: The project has moved to GitHub. Please consult: https://github.com/CometVisu/CometVisu - for the CometVisu https://github.com/OpenAutomationProject - for the different OpenAutomation subprojects

ZMapServer is a Zope Product that provides a clean interface to the MapServer (http://mapserver.gis.umn.edu) web mapping application.

The Simple Medical Imaging Library Interface (SMILI), pronounced 'smilie', is an open-source, light-weight and easy-to-use medical imaging viewer and library for all major operating systems. The main sMILX application features for viewing n-D images, vector images, DICOMs, anonymizing, shape analysis and models/surfaces with easy drag and drop functions. It also features a number of standard processing algorithms for smoothing, thresholding, masking etc. images and models, both with graphical user interfaces and/or via the command-line. See our YouTube channel for tutorial videos via the homepage. The applications are all built out of a uniform user-interface framework that provides a very high level (Qt) interface to powerful image processing and scientific visualisation algorithms from the Insight Toolkit (ITK) and Visualisation Toolkit (VTK). The framework allows one to build stand-alone medical imaging applications quickly and easily.

MaxFem is an open software package for electromagnetic simulation by using finite element methods. The package can solve problems in electrostatics, direct current, magnetostatics and eddy-currents. Since version 0.4.0, MaxFEM requires Python 3. We have moved the installers to the MaxFEM website (see below). In order to improve MaxFEM, we will require you to fill out a simple form before downloading them.

PROJECT HAS MOVED! ROS is now hosted at https://code.ros.org/gf/project/ros/

This is a Computer Aided Electronic Design tool. It features schematic capture, simulation and PCB layout for both analog and numerical componants with the help of Gnome.

PyGeo is a dynamic 3d geometry framework written in Python, rendered with VPython.

Mathpad is a command line utility. It will later have a GUI, but not at this time.

The BladeDesigner package is a CAD/CAE tool providing classes for turbomachine blade design. So far it is optimized to be useful in the aerodynamic design process. It comes with a GUI but is most powerful with user defined python scripts.

Dowser is a research tool for the web. It clusters results from search engines, associates words that appear in previous searches, and keeps a local cache of all the results you click on in a searchable database. It helps you keep track of what you find.

Voice keyboard/dictation. Aims to be a total substitute for a keyboard. Spell out words letter by letter (using code: alpha, bravo, ..). Arrow keys, modifiers work. Speak whole words (but whole word accuracy is not good). Attach commands to some word

a transmission line impedance calculator

JLink lets users author flow charts based on ISO 5807 and IBM standards. Developers can use JLink to add flowcharts to applications, serve a flow chart over the web in PDF or PNG, or dynamically create a flowchart with Javascript, Python or Ruby scripts

The OpenVCT project is designed to provide a common platform for performing Virtual Clinical Trials of medical imaging. OpenVCT provides tools for simulation of patient accrual and reader studies of medical imaging devices, simulating by simulating cohorts of patients and readers. OpenVCT uses common data standards, such as DICOM, to ensure inter-compatibility.

ReconstructIt is a program to assist accident reconstruction specialists with calculations, graphs, and related tasks. It currently runs on MS Windows; one project goal is to port it to other platforms.

Multiplayer framework for flight simulators. Based on M&S HLA 1.3 standards. Provides a 3D air traffic visualization tool and HLA plug-ins for FlightGear, Microsoft Flight Simulator X and X-Plane.

Python script that was originally intended for use in forensic examinations that parses WTMP files from Unix-like operating systems and generates a CSS-styled HTML report containing login terminal, username, log start date and login time/date in a table. Good for postmortem forensic examinations or as a way of getting "last" like information where you don't have the ability to boot the machine in question but can grab the wtmp.

A web-based repository of plasmids and biobricks (see http://parts.mit.edu) plus related utility programs that support synthetic biology research. Note: This project is not updated any longer. A completely re-written and much better version of this web server can be found here: http://www.rotmic.org