Virtual Screening software for Computational Drug Discovery
PyRx is a Virtual Screening software for Computational Drug Discovery that can be used to screen libraries of compounds against potential drug targets. PyRx enables Medicinal Chemists to run Virtual Screening from any platform and helps users in every step of this process - from data preparation to job submission and analysis of the results. While it is true that there is no magic button in the drug discovery process, PyRx includes docking wizard with easy-to-use user interface which makes it a valuable tool for Computer-Aided Drug Design. PyRx also includes chemical spreadsheet-like functionality and powerful visualization engine that are essential for Rational Drug Design. Please visits PyRx home page to learn more about PyRx and watch videos on how to use it.
Jena is Java toolkit for developing semantic web applications based on W3C recommendations for RDF and OWL. It provides an RDF API; ARP, an RDF parser; SPARQL, the W3C RDF query language; an OWL API; and rule-based inference for RDFS and OWL. Jena is now an Apache project: http://jena.apache.org/
Graphical Interface for Medical Image Analysis and Simulation
GIMIAS is a workflow-oriented environment for solving advanced biomedical image computing and individualized simulation problems, which is extensible through the development of problem-specific plug-ins. In addition, GIMIAS provides an open source framework for efficient development of research and clinical software prototypes integrating contributions from the Physiome community while allowing business-friendly technology transfer and commercial product development.
Avalon Toolkit for SMILES-based cheminformatics services
The Avalon Cheminformatics Toolkit contains tools to render and canonicalize SMILES and manipulate MOL file and related formats as well as structure fingerprinting.
A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.
The goal of PyTables is to enable the end user to efficiently and easily manipulate large datasets (both homogenous, i.e. arrays, and heterogenous, i.e. tables) on a persistent, hierarchical way.
A framework and runtime environment for exploring agent-based models designed to support the definition of models using an expressive, high-level and extensible Java API and to support the exploration of these models in both interactive and batch mod
mpiP is a lightweight profiling library for MPI applications.
SNFaceCrop, face detection and cropping software
SNFaceCrop is a Windows-based application to detect and crop faces from an image file. The detected faces can be automatically saved into files or copied into the Windows clipboard. SNFaceCrop is open source and using OpenCV library for face detection.
A speech synthesis and recognition library that is cross-platform, accessible from Java and C++, and has a very small API. Uses CMU Sphinx4 and FreeTTS internally.
Oscill8 is a suite of tools for analyzing dynamical systems which concentrates on understanding how the dynamical behavior depends on the parameters using bifurcation theory and reaction network theory.
Open-Source Cheminformatics and Machine Learning
A collection of cheminformatics and machine-learning software written in C++ and Python. NOTE: the RDKit source code and downloads are now in github: https://github.com/rdkit/rdkit The core algorithms and data structures are written in C++. Wrappers are provided to use the toolkit from either Python or Java. Additionally, the RDKit distribution includes a PostgreSQL-based cartridge that allows molecules to be stored in relational database and retrieved via substructure and similarity searches.
A real-time graph plotter. While your application is computing and logging results to a CSV file using the LiveGraph Writer API, the plotter lets you visualise and monitor the results live - by instantly plotting charts and graphs of the data.
CRF++ is a simple, customizable, and open source implementation of Conditional Random Fields (CRFs) for segmenting/labeling sequential data. CRF++ is designed for generic purpose and will be applied to a variety of NLP tasks.
UNFS3 is a user-space NFSv3 server
UNFS3 is a user-space implementation of the NFSv3 server specification. It provides a unified mountd and nfsd program and so far runs under Linux, NetBSD, and Solaris.
Nice looking calculator using Reverse Polish Notation (RPN) written for Windows. It supports DEC, HEX, BIN, OCT numbers, GRAD, RAD and DEG.
jamod is an object oriented implementation of the Modbus protocol, realized 100% in Java. It allows to quickly realize master and slave applications in various transport flavors (IP and serial).
The Modular toolkit for Data Processing (MDP) is a Python data processing framework. From the user's perspective, MDP is a collection of supervised and unsupervised learning algorithms and other data processing units that can be combined into data processing sequences and more complex feed-forward network architectures. From the scientific developer's perspective, MDP is a modular framework, which can easily be expanded. The implementation of new algorithms is easy and intuitive. The new implemented units are then automatically integrated with the rest of the library. The base of available algorithms is steadily increasing and includes signal processing methods (Principal Component Analysis, Independent Component Analysis, Slow Feature Analysis), manifold learning methods ([Hessian] Locally Linear Embedding), several classifiers, probabilistic methods (Factor Analysis, RBM), data pre-processing methods, and many others.
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout
Model-based Analysis of Genome-wide CRISPR-Cas9 Knockout (MAGeCK) is a computational tool to identify important genes from the recent genome-scale CRISPR-Cas9 knockout screens technology. For instructions and documentations, please refer to the wiki page. MAGeCK is developed and maintained by Wei Li and Han Xu from Dr. Xiaole Shirley Liu's lab at Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute and Harvard School of Public Health. We thank the support from Claudia Adams Barr Program in Innovative Basic Cancer Research to develop MAGeCK.
Educational Linux Distribution
Main goals: * Prepare operating system based on Linux kernel and free software for use at home from scratch by building sources. Binary packages/images are also available. * Each package is installed in separate directory, so you can use different versions of applications and libraries by design. * There is only one user 'kanapi' with root permissions, so you don't have to login, remember passwords, etc. * Simple configuration * Automatic compilation.
OpenPR stands for Open Pattern Recognition project and is intended to be an open source library for algorithms of image processing, computer vision, natural language processing, pattern recognition, machine learning and the related fields.
Spglib is a C-library written for finding crystal symmetry. Symmetry operation, space group, etc, can be obtained using this symmetry finder. It is easy to include this library to your code. For more information, See, http://spglib.sourceforge.net/
SmartWin++ is a C++ template GUI library written to give the flexibility of the Windows API without the hassle and lack of typesafety that MFC/WTL delivers. A flexible, expandable abstraction of the Windows API (formerly Win32 API).
MARF is a general cross-platform framework with a collection of algorithms for audio (voice, speech, and sound) and natural language text analysis and recognition along with sample applications (identification, NLP, etc.) of its use, implemented in Java.
SIVIC is an open-source, standards-based software framework and application suite for processing and visualization of DICOM MR Spectroscopy data. Through the use of DICOM, SIVIC aims to facilitate the application of MRS in medical imaging studies.