The RDXplorer is a computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. CNV detection is based on the Event-Wise Testing (EWT) algorithm recently published by our group.
ThanCad is a 2dimensional cad, with limited 3d support and raster inclusion capability and emphasis in engineering. It is being written in Python and since it uses the Tkinter library, it is platform independent.
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.
Fast and sensitive variant-calling from sequencing data
QMForge reads output from various quantum mechanical calculations and provides tools for analyzing these results. Specifically, population (Mulliken and C-squared), fragment, and charge decomposition analyses are available. See https://qmforge.net for more info.
Arabic stop words list المستبعدات provide a classified word list and some tools to generate all forms of stops words, Youu can reuse it and select words by categories
plugin-based framework for systematic and reproducible experimentation
New version moved to http://github.com/ctuning/ck Collective Mind framework (cM) is an open-source plugin-based schema-free repository and infrastructure for collaborative, systematic and reproducible research and experimentation. This 3rd version (started in 2006) helps to implement, preserve, share and reproduce the whole experimental setup as connected modules and data. cM uses crowdsourcing to leverage knowledge and computational resources of multiple users. For example, it includes multi-objective GCC, LLVM and ICC auto-tuning scenarios using shared benchmarks, codelets, data sets, tools, and combined with classification and predictive models. cM includes OpenME interactive interface to open up and expose internals of various third-party tools such as GCC, LLVM, run-time systems, etc. and connect them to cM through dynamic plugins that allows online analysis and tuning of programs and architectures. Live repo: http://c-mind.org/repo
Python GUI program to work with Geiger counters like GMC-300/320/500
GeigerLog is a Python based GUI program to work with GQ Electronic's GMC-300 / 320 and now also GMC-500 Geiger counters. Available as "scripts" to run where a proper Python environment exists, or as "bundle", which brings its own Python environment (but currently runs on Linux only). 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 (limited to GMC-3xx counters!). Advanced analysis of the data now permits count rate histograms with Poisson fit for quality control of data, and FFT analysis for any periodic signal hidden within the data.
This project has moved to GitHub.
Designs primers on flanking constitutive exons for RT-PCR
A Python interface to the Wordnet database of word meanings and lexical relationships. allows the user to type expressions such as N['dog'], hyponyms(N['dog']), and closure(ADJ['red'], SYNONYM) to query the database for lexical relationships.
A high-level python to matlab(tm) bridge. Let's matlab look like a normal python library.
NGSolve is a general purpose Finite Element Library on top of Netgen. With the basic library one can solve heat flow equations, Maxwell equations, and solid mechanical problems. Several add-ons are available for particular application classes. New paper: J. Schöberl: "C++11 Implementation of Finite Elements in NGSolve", ASC Report 30/2014, Institute for Analysis and Scientific Computing, Vienna University of Technology, 2014 http://www.asc.tuwien.ac.at/~schoeberl/wiki/publications/ngs-cpp11.pdf
FramerD is a distributed semi-structured object database originally developed at MIT. It provides an internationalized Scheme-based scripting language, built-in text analysis tools, and special support for web scripting.
polyglot language framework to analyze genetic data
Framework for Systems Biology
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.
THIS PROJECT MIGRATED TO https://gitlab.com/mwetoolkit/mwetoolkit/
THIS PROJECT MIGRATED TO https://gitlab.com/mwetoolkit/mwetoolkit/ The Multiword Expressions toolkit aids in the automatic identification and extraction of multiword units in running text. These include idioms (kick the bucket), noun compounds (cable car), phrasal verbs (take off, give up), etc. Even though it focuses on multiword expresisons, the framework is quite complete and can also be useful in any corpus-based study in computational linguistics. The mwetoolkit can be applied to virtually any text collection, language, and MWE type. It is a command-line tool written mostly in Python. Its development started in 2010 as a PhD thesis but the project keeps active (see the SVN logs). Up-to-date documentation and details about the tool can be found on the mwetoolkit website: http://mwetoolkit.sourceforge.net/
RNNLIB is a recurrent neural network library for sequence learning problems. Applicable to most types of spatiotemporal data, it has proven particularly effective for speech and handwriting recognition. full installation and usage instructions given at http://sourceforge.net/p/rnnl/wiki/Home/
Space Time Analysis of Regional Systems: Combines a suite of geocomputational and dynamic visualization modules for the exploratory analysis of data measured for spatial and temporal units.
ScreenSifter is a unique tool for RNAi Screen analysis and management
ScreenSifter can help you in managing all your RNAi screens related projects in organized fashion. ScreenSifter, to perform the sequential, user friendly, guided, and advanced statistical analyses of RNAi screening results. User can upload their raw signal intensities and will avail complete quality control of screen, hit selection, plotting of hit genes with gene ontology, comparing of replicates or comparing of channels. In addition, ScreenSifter has visualization tools to plot specific genes or gene groups in the screen data. ScreenSifter also provides Gene Set Enrichment Analysis (GSEA), protein-protein interaction directly on the plot. Publication: ScreenSifter: analysis and visualization of RNAi screening data Pankaj Kumar, Germaine Goh, Sarawut Wongphayak, Dimitri Moreau and Frédéric Bard BMC Bioinformatics. 2013 Oct 3;14(1):290. http://www.biomedcentral.com/1471-2105/14/290/abstract
New online/touch-screen version: http://www.asymptopia.org/TuxMathScrabble-2015/ Encourages kids to construct compound equations and consider multiple abstract possibilities.
pyOBD-II (a.k.a. "pyobd2") is a Python library for communicating with OBD-II vehicles. Its goal is to make writing programs for vehicle diagnostics and monitoring vehicle data as easy as possible. Relies on pySerial to communicate with ELM scanners.
Python, Physics, PyQt, Software, Data adquisition, Spectroscopy, UV
Como técnico en informática en un Instituto de Física con el tiempo surgió la necesidad de tener que crear distintas piezas de software para ir resolviendo situaciones diarias. En este proyecto iré agregando pequeños programas en Python 2.7 que voy escribiendo para dar soluciones a algunos de los problemas que surgen día a día en el laboratorio, como ser comunicación con algunos dispositivos o rutinas para ordenar o modificar datos de forma recursiva algunos cálculos matemáticos, creación de gráficas etc. La finalidad principal del proyecto es poder poner a disposición de aquel que lo necesite mi trabajo tanto dentro del Instituto donde trabajo como fuera del mismo. Asi como tambien recibir la mayor cantidad de criticas, consejos e ideas posibles para poder mejorar mi trabajo. Podrán ver que parte de los programas están mas documentados que otros tratare de ir poniéndome al día comentando el código y escribiendo la documentación de los distintos scripts.
Pizza.py is a collection of Python tools that perform pre- and post-processing for the LAMMPS molecular dynamics package (or other simulators). Software wrapped by Pizza.py, so it can be invoked from Python, includes GnuPlot, MatLab, Raster3d, and RasMol
Python library for parsing, processing and linearising VRML97 files