Open Source Python Scientific/Engineering Software for BSD - Page 9

QDC (quick direct-method controlled) is an optimized exact implementation of the Gillespie's direct-method. It is designed for biochemical simulations when there is the need of dynamic parameters whose values can change during the simulation.

The Systems Biology Workbench(SBW) is a framework for application intercommunications. It uses a broker-based, distributed, message-passing architecture, supports many languages including Java, C++, Perl & Python, and runs under Linux,OSX & Win32. It comes with a large number of modules, encompassing the whole modeling cycle: creating computational models, simulating and analyzing them, visualizing the information, in order to improve the models. All using community standards, such as SED-ML, SBML and MIRIAM.

Mapnik is an OpenSource C++/Python toolkit for developing GIS (Geographic Information Systems) applications. At the core is a C++ shared library providing algorithms/patterns for spatial data access and visualization.

mod_openopc is a full featured implementation of the OpenOPC library for Python. It is cross platform compatible (full Python 2.5 and up). We used to recommend running it on a POSIX platform (Unix / Linux), but thanks to modest efforts since 2014, performance in Windows OS environments is excellent.

pyGerber2Gcode is a Pyhon based simple Gerber to G-code converter.

Software oscilloscope using Python and tkinter. Supports multiple sources: socket, file, audio, USB. Displays data by samples, time or frequency. Scales the input automatically or manually. It has been renamed "pdatascope" to avoid a name-clash with Pyscope, a scoping package on PyPi. See https://sourceforge.net/p/pydatascope/ for the latest code.

WeeWX is a free, open source, software program, written in Python, which interacts with your weather station to produce graphs, reports, and HTML pages. Downloads can be found at http://weewx.com/downloads Development happens at https://github.com/weewx/weewx

We here present a novel computer algorithm, called AutoClickChem, capable of performing many click-chemistry reactions in silico. In silico modeling of click-chemistry products may prove useful in rational drug design and drug optimization.

A three-step approach towards experimental brain-computer-interfaces, based on the OCZ nia device for EEG-data acquisition and artificial neural networks for signal-interpretation.

A web-based LIMS (Laboratory Information Management System) · Built in Plone · Professionally supported · Making waves · bi:ka (Zulu): tell it as it is More information and links to manuals, user forums, support and translations are available at https://www.bikalims.org/support-and-service-provision Bika community: www.bikalims.org Main project sponsor, Bika Lab Systems: www.bikalabs.com Inquiries: lemoene@bikalabs.com

BrennerMD is a public domain Fortran molecular dynamics program by Donald Brenner and other people. This project is to maintain the original source code and to build a Python interface on top of it.

That project aims at studying and comparing typical airline IT methods, for instance RM-related algorithms. It works from a Unix/Linux/Mac command-line, and exposes basic APIs. It is being developed in C++, with Python wrappers for some components.

FreePM is an opensource physicians practice management / electronic medical record application. The company providing support for FreePM nolonger exists. You may consider TORCH http://sourceforge.net/projects/op-torch/ or one of the other FOSS EMR's.

GluCat is a generic library of C++ templates that implement universal Clifford algebras over the field of real numbers. The PyClical extension module for Python gives users an easy Python scripting interface for calculations in Clifford algebras. The name PyClical is an homage to Pertti Lounesto's CLICAL.

Liegkat-Archiv delivers ALK converters for spatial data formats (EDBS, BGRUND, SQD, DFK, HK) and coordinate systems used in German cadastral agencies before ALKIS into KML and JML. It delivers Python packages and XSL files.

Not a whole lab, just a small bench ! **Feel free to contact me via https://sourceforge.net/sendmessage.php?touser=1865508 if you want to take over this project** Mathbench is intended for the development of short scripts such as those daily used when doing research in applied mathematics and physics. Simple widgets and a strong plugin system make it useful and extensible. ANNOUCEMENT: Mathbench's purpose is still relevant and could also benefit from the latest improvements of the wxPython toolkit. However, for lack of time, it is not actively developped anymore. Feelf you want to take over this project, I'd be happy to let it evolve in other hands. I might ask a few questions on what you intend to do before giving up all control on it though :)

A programmable signal generator and RF synthesizer for scientific experiments, especially quantum computing and quantum information processing. It includes hardware, firmware, software, and documentation, all under an open source license.

Py3DN, is an open-source solution providing innovative tools to analyze 3D data collected with the widely used commercial system Neurolucida (MBF). It allows the construction of mathematical representations of neuronal topology, visualization and a variety of morphometric analysis on the neuronal structures. Above all, it provides a flexible environment where new types of analyses can be easily set up allowing total freedom to test new hypotheses. The application was developed in Python and uses Blender (an open source program) to produce detailed 3D representations of raw and processed data. Py3DN is described in the paper: Aguiar P et al, "Versatile morphometric analysis and visualization of the three-dimensional structure of neurons", Neuroinformatics, 2013, 11(4):393-403 doi: 10.1007/s12021-013-9188-z

This project delivers Linux support (USB driver and Tools) for a Digital Signal Processor (DSP) cards of the Signal Ranger series, see http://www.softdb.com/product_dsp.shtml for details) connected to a Linux host via USB.

A tool to calculate atoms exposition to a probe in a three dimensional molecule structure.

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

Tandem mass spectral peptide identification and validation software, similar to X!Tandem, OMSSA, MyriMatch. Suitable for single hosts through large clusters. Written in Python for simplicity, with performance-critical sections in C++.

pyLPCTools is a replacement for the Flash Programming Tools use with the Philips(tm)/NXP(tm) LPC2xxx series of ARM based microcontrollers. pyLPCTools is a script together with some ARM assembly language and a Python user interface. Please Donate !!

A Python interface to the GSL library. The wrapper covers nearly everything GSL provides.

ART is a flexible simulation framework for wind instruments. It includes a growing library of modelling elements. So far bore discontinuities, branches, tone holes, cylindrical and conical tubes, Bessel horns and bent tubes are available for frequency domain modelling. In the time domain generic bidirectional propagation elements, scattering elements, fractional delays, convolution with reflection functions and general z-domain networks are available and can be described using MuParserX expressions. Cylindrical and conical ducts can also be defined based on their geometry. Available models and their parameters can be enumerated and combined to form simulators for complex acoustical structures. Parameters can be specified symbolically by expressions containing other parameter values or global variables. Dependencies between parameters are resolved at run time. However, MuParserX expressions are compiled at design time. Zero-delay loops are detected and reported.