Cross-platform DICOM implementation
Grassroots DiCoM is a C++ library for DICOM medical files. It is accessible from Python, C#, Java and PHP. It supports RAW, JPEG, JPEG 2000, JPEG-LS, RLE and deflated transfer syntax. It comes with a super fast scanner implementation to quickly scan hundreds of DICOM files. It supports SCU network operations (C-ECHO, C-FIND, C-STORE, C-MOVE). PS 3.3 & 3.6 are distributed as XML files. It also provides PS 3.15 certificates and password based mecanism to anonymize and de-identify DICOM datasets.
Moved to https://github.com/rdiankov/openrave An open-source, cross-platform, plugin-based robot planning environment for autonomous robotics. Includes services like collision detection, physics, (inverse) kinematics, sensors, robot controls, python bindings, and a network scripting environment.
Modelio-Open is a project hosting a set of open source extensions (SoaML, SysML and UML Testing Profile) for a previous version (1.2) of the Modelio Free tool . Currently, the lastest version (2.x) of Modelio modeling and generation tool is available at http://modelio.org/downloads/download-modelio.html. All extensions are downloadable at http://forge.modelio.org/projects.
Medical Image Registration Library
SimpleElastix is an extension of SimpleITK that comes with the elastix C++ image registration library. This makes state-of-the-art medical image registration really easy to do in languages like Python, Java, C# and R.
The Helsinki Finite-State Transducer toolkit is intended for processing natural language morphologies. The toolkit is demonstrated by wide-coverage implementations of a number of languages of varying morphological complexity.
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 tePlugins. In addition other tools kits such as matplotlib and NumPy are used to provide additional analysis and plotting support.
Libraries and command line tools for medical image processing.
This software provides libraries and command line tools for the processing and analysis of gray scale medical images.
Website2Pdf application helps to get offline form of webpages.
Favorite webpages can be made available offline as pdf files. Enter your favorite website url, with just one click pdf files will be created without loss of any css, styling of html. All the web files will be retained. Please make sure to use help button before you convert webpages to offline files.
MSTParser is a non-projective dependency parser that searches for maxi
MSTParser is a non-projective dependency parser that searches for maximum spanning trees over directed graphs. Models of dependency structure are based on large-margin discriminative training methods. Projective parsing is also supported. mstparser 0.5.1 is now available via Maven Central. If you use Maven as your build tool, then you can add it as a dependency in your pom.xml file: <dependency> <groupId>net.sourceforge.mstparser</groupId> <artifactId>mstparser</artifactId> <version>0.5.1</version> </dependency>
Neural Networks Collection
This project implements in C++ a bunch of known Neural Networks. So far the project implements: LVQ in several variants, SOM in several variants, Hopfield network and Perceptron. Other neural network types are planned, but not implemented yet. The project can run in two modes: command line tool and Python 7.2 extension. Currently, Python version appears more functional, as it allows easy interaction with algorithms developed by other people.
ScientificIcons is a central repository of icons for scientific programs, including molecular biology, lab automation, sample tracking, chemistry, biology, physiology, etc. Looking for an icon for a flask, chemical, gene, plate, robot, atom?
The CILogon project facilitates secure access to Cyberinfrastructure (CI) via the community-driven development and support of the MyProxy, GridShib, and GSI-OpenSSH software.
To retrieve obscure syntax of languages, or bookmark code comments.
Facilitates retrieval of personalized comments previously put into code. While writing new, (or reviewing old) code, user adds search-tag (the string "EGOF") to comments. Subsequently running Egof (followed by optional search words) retrieves them. Code can be in any programming language, or scripts used by applications, or HTML or LaTex files. Sounds like a combination of Unix find/grep, but has many more features. Searching is faster since database files are created, one per language. When creating them Egof goes through all (or specified subset of) user's folders/files, finds instances of the search-tag, and stores those lines of code plus some surrounding code. During running, Egof displays a prompt, and allows users to change options and modify the search, (using the same option-parsing software that was used to parse the command line.) Egof is command-line based. The documentation is comprehensive. Please invest <5 min to read the "Overview" section. Thank you.
A Python script for estimating the grain size from thin sections
Homepage & documentation: http://marcoalopez.github.io/GrainSizeTools/ GrainSizeTools script is a free, open-source, cross-platform script written in Python that provides several tools for visualizing and estimating grain size in polycrystalline materials. The script is able to estimate differential stress through paleopiezometers, implementing multiple piezometric relations for comparison, and to derive the actual (3D) grain size distribution from thin sections using the Saltykov and the two-step methods. The script only requires as input the areas of the grain profiles measured grain-by-grain in a thin section and does not require previous experience with Python programming language (see the documentation at the website). For users with coding skills, the script is organized in a modular way facilitating its reuse and code extension.
HPC cloud computing for OpenFOAM (R) users
SF2 is a generic framework for constructing cloud computing platform. The framework provides snapshot-based replication, virtual machine placement on multiple sites, and gossip-based physical machine discovery.
Simple program for artificial neural network users. Right now the program can manipulate with Feed forward back propagation network.
Biologic Institute's Stylus simulation software suite. (See the SVN repository for source code.)
Diffusion of Innovations Simulation
Energy and environmental monitoring of the server room
The solution GreenHop aims to perform energy and environmental (temperature, humidity, dew point and atmospheric pressure) monitoring of the Data Center server room, providing energy efficiency indicators through green metrics for Data Centers. The GreenHop solution is based on open source software and hardware. The approach of using open source solutions enables its deployment easier and independently of suppliers at the same time makes the solution scalable to the needs of each organization. Thus, we aim to provide ambiental monitoring of the Data Center server room while we keep the system to be customizable to implement and replicate.
IP Trace Analysis System Based on Code Moving
This Python project is a prototype for an application that does Kanji Hand-writing recognition. It uses a vector model to represent radicals and puts those together to full Kanji.
Lino is a suite of Python packages for IT professionals who offer business applications for small and medium-sized enterprises.
The Lunarc Application Portal (LAP) is a lightweight web based grid application portal implemented in Python, providing easy access to grid based resources and applications. The portal can easily be extended using a plugin architecture.
A mouse tracker for OS X. The tool should provide a simple way to log the user's mouse movements in the background for (later) analysis. Currently only for Mac OS X (ObjC & Cocoa), planned to make platform independent with Python. It consists out of two