Object-oriented equation-based modelling and optimisation software
DAE Tools is a cross-platform equation-based object-oriented modelling, simulation and optimisation software. It is not a modelling language nor a collection of numerical libraries but rather a higher level structure – an architectural design of interdependent software components providing an API for: - Model development/specification - Activities on developed models, such as simulation, optimisation, sensitivity analysis and parameter estimation - Processing of the results, such as plotting and exporting to various file formats - Report generation - Code generation, co-simulation and model exchange The following class of problems can be solved by DAE Tools: - Initial value problems of implicit form - Index-1 DAE systems - With lumped or distributed parameters - Steady-state or dynamic - Continuous with some elements of event-driven systems
Distributed and Parallel Computing with/for Python.
dispy is a comprehensive, yet easy to use framework for creating and using compute clusters to execute computations in parallel across multiple processors in a single machine (SMP), among many machines in a cluster, grid or cloud. dispy is well suited for data parallel (SIMD) paradigm where a computation (Python function or standalone program) is evaluated with different (large) datasets independently.
SQL DAL Maker is a generator of DTO and DAO classes. Target programming languages: PHP, Java, C++, Python, Ruby. To generate the class, you declare it in XML meta-program. Implemented as plug-ins for Eclipse, IntelliJ Platform, and NetBeans 8.+.
Model, simulate, and analyze biochemical systems using one tool.
Tellurium (te.) is a Python environment supporting Spyder2 IDE and Jupyter Notebook aimed for large-scale systems and synthetic biology simulation. It combines a number of existing libraries, including libSBML, libRoadRunner (including libStruct), libAntimony, and is extensible via telPlugins. In addition other tools kits such as matplotlib and NumPy are used to provide additional analysis and plotting support.
The application Bio7 is an integrated development environment for ecological modelling and contains powerful tools for model creation, scientific image analysis and statistical analysis. The application itself is based on an RCP-Eclipse-Environment (Rich-Client-Platform) which offers a huge flexibility in configuration and extensibility because of its plug-in structure and the possibility of customization.
Web based python-flask Queue management system
A web based management system developed for the purpose of easing the process of orgnizing queues and lines. Like many other (QMS)s Queue Management Systems, FQM does provide a basic dashboard to allow the users of the system and customers alike to interact with the system via a basic yet simple user interface . Brief user guide can be found on https://fqms.github.io/images/user_guide.pdf
Powerful command-line bookmark manager. Your mini web!
buku is a powerful bookmark manager written in Python3 and SQLite3. buku fetches the title of a bookmarked web page and stores it along with any additional comments and tags. You can use your favourite editor to compose and update bookmarks. With multiple search options, including regex and a deep scan mode (particularly for URLs), it can find any bookmark instantly. Multiple search results can be opened in the browser at once. Though a terminal utility, it's possible to add bookmarks to buku without touching the terminal! Refer to the section on GUI integration. If you prefer the terminal, thanks to the shell completion scripts, you don't need to memorize any of the options. There's an Easter egg to revisit random forgotten bookmarks too. Buku is too busy to track you - no history, obsolete records, usage analytics or homing. Demo: https://asciinema.org/a/8pm3q3n5s95tvat8naam68ejv
Processing and analysis of Small Angle X-ray Scattering (SAXS) data.
BioXTAS RAW is a program for analysis of Small-Angle X-ray Scattering (SAXS) data. The software enables: creation of 1D scattering profiles from 2D detector images, standard data operations such as averaging and subtraction, analysis of radius of gyration (Rg) and molecular weight, and advanced analysis using GNOM and DAMMIF. It also allows easy processing of inline SEC-SAXS data and data deconvolution using the evolving factor analysis (EFA) method. To install: Check the instructions available at: http://bioxtas-raw.readthedocs.io/en/latest/install.html and in the Files tab. User guides: RAW guides are available at: http://bioxtas-raw.readthedocs.io/ and in the Files tab. For requests, comments, and bug reports try our google group: http://bit.ly/rawhelp If that doesn't work, contact: soren (dot) skou (at) saxslab (dot) com and hopkins (dot) jesse (at) gmail (dot) com.
GUI designer for wxWidgets
wxGlade is a GUI designer written in Python with the popular GUI toolkit wxPython, that helps you create wxWidgets/wxPython user interfaces. It can generate Python, C++, Perl, Lisp and XRC (wxWidgets' XML resources) code.
Powerful desktop publishing software
Scribus is an Open Source program that brings professional page layout to Linux, BSD UNIX, Solaris, OpenIndiana, GNU/Hurd, Mac OS X, OS/2 Warp 4, eComStation, and Windows desktops with a combination of press-ready output and new approaches to page design. Underneath a modern and user-friendly interface, Scribus supports professional publishing features, such as color separations, CMYK and spot colors, ICC color management, and versatile PDF creation.
Altimetry profile visualizer
CycloGraph is an application to plot the gradient of roads using distances and heights. An open source alternative to Salitaker for plotting the profile of the roads your are planning to do with your bicycle. It also can import routes from kml.
Exploration and categorization of CREs and CRMs
Cis-regulatory elements (CREs) and cis-regulatory modules (CRMs) play an important role in temporal and spatial regulation of gene expression, which is a common process in eukaryotic organisms. We developed two programs that serve as exploratory tools in the analysis of CRM-mediated control of gene expression: “Exploration of Distinctive CREs and CRMs” (EDCC) and “CRM Network Generator” (CNG). EDCC correlates the presence and positions of CREs/CRMs with gene expression data and identifies candidate regulatory elements for further functional analysis. CNG provides an unbiased neural network approach to assess the importance of positional features that were determined by EDCC. To sustain a high computational performance even for large datasets, the mostly in Python 3 written programs use k-mer based indexing, parallelization and a neural network approach for categorization. For further information please refer to the publication: doi.org/10.1371/journal.pone.0190421
A collection of interactive educational exercises
eduActiv8 is a free Open Source multi-platform educational application that aims to assist in learning various early education topics - from learning the alphabet and new words, colours, time to a range of math related subjects. eduActiv8 is a continuation of the development of the pySioGame project just under a new name. It is being developed on GitHub at: https://github.com/imiolek-ireneusz/eduActiv8 but 'compiled' releases are published here. Currently, it is available for Windows, MacOS and Linux. Also ported to Android, however, its best used on tablets, mobile phone screens may prove a little bit too small to use certain activities: https://play.google.com/store/apps/details?id=org.eduactiv8.eduactiv8
Python Development Environment with all batteries included
Eric is a Python IDE written using PyQt and QScintilla. It provides various features such as any number of open editors, an integrated (remote) debugger, project management facilities, unit test, refactoring and much more.
Wapiti is a web-application vulnerability scanner
Wapiti is a vulnerability scanner for web applications. It currently search vulnerabilities like XSS, SQL and XPath injections, file inclusions, command execution, XXE injections, CRLF injections... It use the Python programming language.
Theoretical Density, Orbital Relaxation and Exciton analysis
The TheoDORE (Theoretical Density, Orbital Relaxation and Exciton analysis) package is a general purpose program suite for the analysis of excited states obtained from quantum chemical excited state calculations. Wavefunction analysis is based on state and transition density matrices, which provides a unified formalism applicable independent of the wavefunction model. TheoDORE is interfaced to a number of quantum chemical programs (Q-Chem, Columbus, Turbomole) and can be used for a wide range of excited state methods (MR-CI, ADC, CC, TDDFT). It is written in a modular fashion to allow for an easy extension of these capabilities.
Cellular manager for mobile phones/modems
Gammu is a cellular manager for mobile phones/modems. It contains libraries and functions for ringtones,logos,phonebook,SMS,etc. (used by external software), a command line version (with backup/restore) and SMS gateway (with MySQL and PostgreSQL supp
Video add-on for Kodi
Add-on for Kodi allowing to view video content provided by Garant TV Gomel
A Python package for CGNS
The package gathers various tools and libraries for CGNS end-users and Python application developpers. The main object of pyCGNS is to provide the application developpers with a Python interface to CGNS/SIDS, the data model. The MAP and PAT modules are dedicated to this goal: map the CGNS/SIDS data model the CGNS/Python implementation. The WRA module contains wrapper on CGNS/MLL and a MLL-like set of functions that uses the CGNS/Python mapping as implementation. See CGNS.NAV demo on: http://www.youtube.com/user/pyCGNS
Diffuse is a graphical tool for comparing and merging text files. It can retrieve files for comparison from Bazaar, CVS, Darcs, Git, Mercurial, Monotone, RCS, Subversion, and SVK repositories.
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
An open source framework for LC-MS based proteomics and metabolomics. OpenMS offers data structures and algorithms for the processing of mass spectrometry data. The library is written in C++.
EasyABC is an open source ABC editor
EasyABC allows the user to create, edit, view, play, convert music written in the ABC music notation language. The program was written in Python 2.7 and WxPython by Nils Liberg and runs on Windows, OSX, and Linux. Nils Liberg is no longer supporting this open source package, however I have volunteered to continue its support and development.
Exquisite Astrology Software
Astrology software for all.
PyMOL is an OpenGL based molecular visualization system
PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source PyMOL is free to everyone!