Controls any Robot in Python
Developed on Python to leverage state-of-the-art extensibility and easily integrated plugins Able to use low cost robots with the accuracy and dexterity of much more expensive robots, achieved in part by: a) Ability to drive movement by inexpensive DC gear head motors, including the inherent ability to specify movement by applied force rather than strict space/time control that steppers impose. b) Arms and linkages don't have to have super tight tolerances, because accuracy is achieved by tightly integrated visual feedback that's easy to program and low complexity processing. Ability to program easily with a GUI and visual interface that sees things from the robots' camera perspective. Flexible use of coordinate spaces that make programming arms with 6 or more degrees of freedom super easy. Got a bot arm with 13 linkages that can reach around corners? Easy. Simple arm with only 2 degrees of freedom, with one polar and one cartesian? Any arm geometry works.
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
Matplotlib is a python library for making publication quality plots using a syntax familiar to MATLAB users. Matplotlib uses numpy for numerics. Output formats include PDF, Postscript, SVG, and PNG, as well as screen display. As of matplotlib version 1.5, we are no longer making file releases available on SourceForge. Please visit http://matplotlib.org/users/installing.html for help obtaining matplotlib.
PyRPL turns your Red Pitaya into a powerful analog feedback device.
The Red Pitaya is a commercial, affordable FPGA board with fast analog inputs and outputs. This makes it useful for quantum optics experiments, in particular as a digital feedback controller for analog systems. Based on the open source software provided by the board manufacturer, PyRPL (Python RedPitaya Lockbox) implements many devices that are needed for optics experiments with the Red Pitaya. PyRPL implements various digital signal processing (DSP) modules (see features below). It allows to arbitrarily interconnect the available DSP modules and retrieve signal values on timescales below 1 ms. The graphical user interface (GUI) provides a realtime display of the various measurement instruments and allows the easy configuration of DSP signal chains and feedback controllers. At the highest abstraction level, arbitrary feedback sequences can be defined to fulfill tasks as complex as approaching and locking a resonance of a high-finesse Fabry-Perot cavity (tested up to finesse=100,000).
convert genome coordinates betweeen assemblies
CrossMap is a program for convenient conversion of genome coordinates and genomeannotation files between assemblies (eg. lift from GRCh36/hg18 to GRCh37/hg19 or vice versa).It support file in BAM, SAM, BED, Wiggle, BigWig, GFF, GTF format.
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.
Spectral - software for manipulating optical spectroscopy data
Spectral-SpecPro helps with the manipulation of optical spectroscopy data. Spectral takes files produced by Jasco instruments (uv-vis absorbance, fluorescence, circular dichroism readings as a function of wavelength, temperature, or time) and facilitates basic operations such as unit conversion (CD spectra), conversion into the format taken by CDPro (estimation of secondary structure; CD spectra), scatter correction (absorbance spectra), smoothing, re-sampling of the x-axis, and generic combination (sum, product, average, standard deviation) of multiple curves. Spectral-SpecPro is based on earlier software written by Stephen R Martin (MRC-NIMR London NW7 and Francis Crick Institute London NW1).
TI2BioP allows mainly the calculation of topological indices (spectral moments) derived from inferred and artificial 2D structures of DNA, RNA and proteins being possible to carry out a structure-function correlation irrespective of sequence alignments. TI2BioP version 2.1 is a python platform with a graphical interface designed for Linux OS.
TexGen is a geometric textile modelling software package to be used for obtaining engineering properties of woven textiles and textile composites.
This is a maths solving app and study guide for various levels..
Etchimaths is a Mathematics software, a helping tool for Mathematics simulation(solving) and study.It is a solving machine as well as a teaching machine, It involves Mathematics programs at various levels of studies;It exists as 1.Etchimaths(O'LEVEL) 2.Etchimaths(BAC) 3.Etchimaths(BEPC/BEPC+1) 4.Etchimaths(A'LEVEL) 5.Etchimaths(CAP) 6.Etchimaths(PROBATOIRE) 7.Etchimaths(UNIVERSITY) 8.Etchimaths(UNIVERSITE) 9.Etchimaths(IUT SPECIAL) 10.Etchimaths(ULTIMATE) and more to come
Space Science library for Python - contains superposed epoch classes, drift shell tracing, access to magnetic field models, streamline tracing, bootstrap confidence limits, time and coordinate conversions, etc.
A novel transcription factor complex prediction algorithm.
Eukaryotic gene expression is controlled through molecular logic circuits that combine regulatory signals of many different factors. Complexation of transcription factors and other regulatory proteins is a prevailing and highly conserved mechanism of signal integration within critical regulatory pathways and enable to infer controlled genes as well as the exerted regulatory mechanism. We developed DACO (domain-aware cohesiveness optimization), a novel algorithm that combines protein-protein interaction networks and domain-domain interaction networks with the cluster-quality metric cohesiveness. The metric is locally maximized on the holistic level of protein interactions while sophisticated connectivity constraints on the domain level are utilized to account for the exclusive and thus inherently combinatorial nature of the interactions within such assemblies. The original publication can be found on http://bioinformatics.oxfordjournals.org/content/30/17/i415 .
TCP Experiment Automation Controlled Using Python
TEACUP automates many aspects of running TCP performance experiments in a specially-constructed physical testbed. TEACUP enables repeatable testing of different TCP algorithms over a range of emulated network path conditions, bottleneck rate limits and bottleneck queuing disciplines. TEACUP utilises a text-based configuration file to define experiments as combinations of parameters specifying desired network path and end host conditions. When multiple values are provided (e.g. for TCP congestion control algorithm), an experiment is made up of multiple tests. For each experiment and test, TEACUP collects a range of data, such as tcpdump files of traffic seen or TCP stack information (e.g. using Web10G). TEACUP also collects a variety of metadata from the end hosts and bottleneck router, such as the actual OS/kernel version(s) used. TEACUP also provides some simple tools for analysing the results of experiments, such as plotting a flow's experienced RTT over time.
Lexico-grammatical/syntactical analyzer of sentences in English
"SayWhat?" is a natural language processing system for spell-checking, lexical, grammatical and syntactical analysis of simple sentences in English. Note that it is just an educational project, not even 50%-complete (there are still many problems to solve), so don't expect too much.
Portable bundle for Windows
This is a PORTABLE app bundle for WINDOWS. No installation required! (Uncompressed size is about 60Mb because of required libraries for all Windows versions from XP to 10. The application is incomparably small.) Unzip, run sumcalc.exe. That's it! You can put the folder wherever you want, except system folders with permissions (e.g. Program Files), and create a shortcut if needed. Cross-platform source and info: https://github.com/qandak/sumcalc Changelog: https://github.com/qandak/sumcalc/blob/master/CHANGELOG.md
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.
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.
The FMI++ TRNSYS FMU Export Utility
This open-source project provides a stand-alone tool for exporting FMUs for Co-Simulation from TRNSYS 17 models. The current release supports FMI version 1.0 and 2.0. Instructions on installation and usage are given in the documentation, which is provided as part of the download. This documentation also contains a tutorial on how to export a TRNSYS model as FMU for co-simulation and how to link it with a simple controller implemented in Modelica. The tool is based on code from the FMI++ library.
Software to processing and analyze of airborne measurements.
The Airborne Data Processing and Analysis (ADPAA) package is an open-source software package containing a collection of programs and scripts to process and analyze data from in-situ instruments deployed on airborne platforms. The ADPAA package was started to process data on the North Dakota Citation Research Aircraft but has been used to process data on many airborne platforms. The software methodology used in ADPAA is provided in the peer-review publication: Delene, D. J., Airborne Data Processing and Analysis Software Package, Earth Science Informatics, 4(1), 29-44, 2011, URL: http://dx.doi.org/10.1007/s12145-010-0061-4, DOI: 10.1007/s12145-010-0061-4.
Quality Assessment Tool for Genome Assemblies
QUAST performs fast and convenient quality evaluation and comparison of genome assemblies. QUAST computes a number of well-known metrics, including contig accuracy, number of genes discovered, N50, and others, as well as introducing new ones, like NA50 (see details in the paper and in the manual). A comprehensive analysis results in summary tables (in plain text, tab-separated and LaTeX formats) and colorful plots. The tool also produces web-based reports condensing all information in one easy to navigate file. QUAST has an intuitive command-line interface and a detailed manual to help users run it and understand its output. Furthermore, the Lab started a Beta version of web-QUAST at http://quast.bioinf.spbau.ru/ which makes quality evaluation even more simple. QUAST and MetaQUAST (extension for metagenomic assemblies) papers were published in Bioinformatics.
Scientific Visualisation Made Easy
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.
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.
GNU Health - The Free Hospital and Health Information System
GNU Health is the award-winning Free Hospital and Health Information System (HIS). GNU Health is the Hospital Information System by the United Nations .- International Institute for Global Health. GNU Health was chosen by Richard Stallman to be included in the GNU System, from the Free Software Foundation. GNU Health is brought to you by GNU Solidario, an Non-Profit Organization (NGO) that delivers Health and Education with Free Software.
Diffraction Contrast Tomography analysis code
Diffraction contrast tomography code base, as developed by researchers from beamline ID19 of the ESRF, Grenoble, France, and Manchester University, UK.