Olex2 is visualisation software for small-molecule crystallography developed at Durham University/EPSRC. It provides comprehensive tools for crystallographic model manipulation for the end user and an extensible development framework for programmers. The project has been supported by Olexsys Ltd since 2010.
Python module to interface with a Slocum glider dockserver
Dockserver-talk is a python module that provides an easy way to build custom clients that communicate with Teledyne Webb Research's dockserver software, used to control "Slocum" underwater gliders. The package comes with two applications built on top of dockserverTalk: BUGS: a program to monitor and display the position of gliders (as well as buoys and ships) with respect to a given GPS location (from an external source). Surfalarm: a program that can send text messages or make direct phone calls, acting upon a glider to surface and connect to a dockserver, being in a mission, or aborted. Serial2rudics: a helper program that lets a glider simulator connected to a serial port appear as a glider connecting and disconnection via rudics/iridium when at ther surface or underwater, respectively.
Generating cells for electronic structure calculations from CIF files
CIF2Cell is a tool to generate the geometrical setup for various electronic structure codes from a CIF (Crystallographic Information Framework) file. The program currently supports output for a number of popular electronic structure programs, including ABINIT, ASE, CASTEP, CP2K, CPMD, CRYSTAL09, Elk, EMTO, Exciting, Fleur, FHI-aims, Hutsepot, MOPAC, Quantum Espresso, RSPt, Siesta, SPR-KKR, VASP. Also exports some related formats like .coo, .cfg and .xyz-files. The program has been published in Computer Physics Communications 182 (2011) 1183–1186. Please cite generously.
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. For instructions and documentations, please refer to the wiki page. MAGeCK is developed and maintained by Wei Li and Han Xu from Dr. Xiaole Shirley Liu's lab at Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health. We thank the support from Claudia Adams Barr Program in Innovative Basic Cancer Research to develop MAGeCK.
PythonToolkit (PTK) is an interactive environment for python. It was designed to provide a python based environment similiar to Matlab for scientists and engineers however it can also be used as a general purpose interactive python environment.
Spheral++ provides a steerable parallel environment for performing coupled hydrodynamical & gravitational numerical simulations. Hydrodynamics and gravity are modelled using particle based methods (SPH and N-Body).
Python GUI program for Geiger counters like GMC-300/320/500/600
GeigerLog is a Python based GUI program to work with GQ Electronic's GMC-300 / 320 and GMC-500 /600 Geiger counters. Latest release 0.9.07 running on Python 3 with some new, improved handling of the Geiger counters; improved customization. Now supporting Radiation Maps even for non-WiFi counters. GeigerLog allows reading of Geiger counter data, logging to file, printing to screen and plotting as graph, showing Count Rate vs. Time, both in various, selectable units. The history stored on the Geiger counter's internal memory can be extracted, analyzed and graphed in the same way. The graph is live auto-updated and allows various customization. Time ranges for analysis can be set manually or per left/right mouse click. GeigerLog can control some functions of a connected counter. Quality control of the data is made possible with standard Statistics, Poisson Test on count rate histograms, and FFT & Autocorrelation analysis for any periodic signal hidden within the data.
A symbolic framework for C++, Python and Octave implementing automatic differentiation by source code transformation in forward and reverse modes on sparse matrix-valued computational graphs.
View and edit grids of meteorological values
Allows viewing and editing of weather data from weather models as two dimensional grids. Python scripting support hooks in the ingest, editing and product creation subsystems allow for customization. All network communication made through HTTP services. Enhanced version of the system used by national weather services.
Import your PCB boards to FreeCAD
[ENG] Mod FreeCAD-PCB allow you to import PCB boards to FreeCAD. Scope of mod: - support for many different layers, - possible to choose colours, transparency and names for each layer, - mod allows you to import IGES models with colours, - possible to show holes/vias independent. [PL] Moduł FreeCAD-PCB pozwala na importowanie płytek PCB do programu FreeCAD. Możliwości modułu: - wsparcie dla wielu różnych warstw, - wyświetlanie otworów, przelotek niezależnie od siebie, - możliwość wyboru koloru, przeźroczystości oraz nazwy dla poszczególnych warstw, - importowanie modeli zapisanych w formacie IGS wraz z kolorami. ***** Supported software: - Eagle (*.brd) - Razen (*.rzp) - FreePCB (*.fpc) - gEDA (*.pcb) - FidoCadJ (*.fcd) - KiCad (*.kicad_pcb) - IDF v2/v3 Requirements: FreeCAD >= 0.14 Project forum: https://sourceforge.net/p/eaglepcb2freecad/forum/
congruity is a GUI application for programming Logitech(R) Harmony(TM) remote controls. congruity builds upon the work of the concordance project, which provides the underlying communication. Please use the concordance project mailing lists.
Molecular dynamics by NMR data analysis
The software package 'relax' is designed for the study of molecular dynamics through the analysis of experimental NMR data. Organic molecules, proteins, RNA, DNA, sugars, and other biomolecules are all supported. It supports exponential curve fitting for the calculation of the R1 and R2 relaxation rates, calculation of the NOE, reduced spectral density mapping, the Lipari and Szabo model-free analysis, study of domain motions via the N-state model and frame order dynamics theories using anisotropic NMR parameters such as RDCs and PCSs, the investigation of stereochemistry in dynamic ensembles, and the analysis of relaxation dispersion data.
A simulation framework for production process modeling in Python
ACP is a simulation framework aimed to production processes modeling. Compared to its ancestor - jES - it is lightweight, more general and written in Python. The basic goal of the simulator is to find bottlenecks in production process which could be hard to detect with traditional approaches (e.g., top-down). In addition, it can be used to speculate about “what-if” scenarios in order to suggest solution strategies.
Text based timing diagram generator
This tool generates timing diagrams for documenting hardware design. It reads the description from a text file with a simple syntax. It generates vector graphic (EPS, SVG or EMF format). It can be used in command line mode or with a GUI. It is written in Python and works on any platform.
A software package for quantitative analysis in Panbiogeography
Croizat is a free, user-friendly, cross-platform desktop software package which biologists can use to integrate and analyze spatial data on species or other taxa and to explore geographical patterns in diversity under a panbiogeographic and graph-theoretic approach.
PyTom is a toolbox developed for interpreting cryo electron tomography data. All steps from reconstruction, localization, alignment and classification are covered with standard and improved methods. Please sign up to our mailing list to keep up with the most recent updates and versions.
The Geocanvas project aims to provide a very small and simple set of APIs to assist the developer in creating geographically referenced canvas applications within the GTK/Gnome environment.
The FMI++ PowerFactory FMU Export Utility
The FMI++ PowerFactory FMU Export Utility is a stand-alone tool for exporting FMUs for Co-Simulation (FMI Version 1.0) from DIgSILENT PowerFactory models. It is open-source (BSD-like license) and freely available. It is based on code from the FMI++ library and the Boost C++ libraries. The FMI++ PowerFactory FMU Export Utility provides a Python script that creates FMUs from certain PowerFactory models, including the XML model description and shared libraries. Additional files (e.g., time series files) and start values for exported variables can be specified. Currently, two types of simulations are supported: In quasi-static steady-state simulations a power system’s evolution with respect to time is captured by a series of load flow snapshots. RMS simulations allow to calculate the time-dependent dynamics of electromechanical models, including control devices (new in version v0.6).
open source python packages for X-ray MicroLaue Diffraction analysis
LaueTools is an open-source project for white beam Laue x-ray microdiffraction data analysis including tools in image processing, peaks searching & indexing, crystal structure solving (orientation & strain) and data & grain mapping visualisation.
Character animation system for games and simulations.
SmartBody is available for download for Windows, Linux and OSX users. SmartBody can also be used on Android and iOS platforms. SmartBody is a character animation platform that provides the following capabilities in real time: * Locomotion (walk, jog, run, turn, strafe, jump, etc.) * Steering - avoiding obstacles and moving objects * Object manipulation - reach, grasp, touch , pick up objects * Lip Syncing - characters can speak with simultaneous lip-sync using text-to-speech or prerecorded audio * Gazing - robust gazing behavior that incorporates various parts of the body * Nonverbal behavior - gesturing, head nodding and shaking, eye saccades - Online and offline retargeting of motion - Automatic skinning and rigging SmartBody is written in C++ and can be incorporated into most game engines. SmartBody is developed at the USC Institute for Creative Technologies from the Character Animation and Simulation group: http://cas.ict.usc.edu
Scanning probe microscopy data visualisation and analysis
A data visualization and processing tool for scanning probe microscopy (SPM, i.e. AFM, STM, MFM, SNOM/NSOM, ...) and profilometry data, useful also for general image and 2D data analysis.
Computer Assisted Proofs in Dynamics
Dynamical Systems and Homology Software. The CAPD library is a collection of flexible C++ modules which are mainly designed to computation of homology of sets and maps and nonrigorous and validated numerics for dynamical systems.
QtiPlot is a user-friendly, platform independent data analysis and visualization application similar to the non-free Windows program Origin.
The TRANSIMS Studio application is an integrated development environment for the TRansportation ANalysis and SIMulation System (TRANSIMS). Components include a run time environment to execute TRANSIMS in parallel, as well as a full featured GUI.
A Reduction software for SITELLE data
Reduction software for SITELLE and SpiOMM data. Don't forget to download and install ORB first (https://sourceforge.net/projects/orb-orb/) ::warning:: the official homepage is on github: https://github.com/thomasorb/orbs