An object relational-mapping (ORM) library for Java
Hibernate is an Object/Relational Mapper tool. It's very popular among Java applications and implements the Java Persistence API. Hibernate ORM enables developers to more easily write applications whose data outlives the application process. As an Object/Relational Mapping (ORM) framework, Hibernate is concerned with data persistence as it applies to relational databases (via JDBC).
OpenJUMP is a community driven fork of JUMP the "Java Unified Mapping Platform" GIS software. The original JUMP was developed by Vivid Solutions, released under GPL2 in 2003 and discontinued in 2006. During 2004 already some enthusiastic developers joined together to enhance further the features of JUMP. They launched an independent development branch called OpenJUMP. The name gives credit to the original JUMP development, and at the same time describes the objectives of this project to be fully open to anyone wanting to contribute. These days OpenJUMP is developed and maintained by (some few) volunteers around the globe. If you need functionality or even better want to contribute you are very welcome to contact us at our mailing list.
The free computer aided translation (CAT) tool for professionals
OmegaT is a free and open source multiplatform Computer Assisted Translation tool with fuzzy matching, translation memory, keyword search, glossaries, and translation leveraging into updated projects.
A file format for exchanging computational models in systems biology
The Systems Biology Markup Language (SBML) is an XML-based description language for representing computational models in systems biology. Visit the project web site to learn more.
The Systems Biology Format Converter (SBFC) is a Java generic framework aiming to translate any systems biology model format into another. The SBFC Web Site providing detailed feature description and instructions for installing, using and developing new modules is: http://sbfc.sourceforge.net/ . Currently, SBFC allows the user to convert SBML models into the formats: BioPax, Matlab, Octave, XPP, DOT, and SBGN. Due to its modular design fast development and addition of new converters is highly facilitated. SBFC can be executed in two modes: 1. standalone executable downloading the package provided in this website; 2. web-service at http://www.ebi.ac.uk/biomodels/tools/converters . For general discussion about SBFC, please use the forum firstname.lastname@example.org . A mailing-list is also available for developers: email@example.com Thanks for using SBFC! The SBFC Team
Effectopedia is open knowledge aggregation and collaboration tool that provides a means of describing adverse outcome pathways in encyclopedic manner.
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.
TANGO is an object oriented control system for Linux and Windows. It provides a framework in C++, Java and Python for implementing distributed control objects an accessing them via a well-defined API. This sourceforge project a
Database replication tool based on XML Schema
xsd2pgschema is a Java application suite, which converts XML Schema 1.1 to PostgreSQL DDL and supports XML data migration into PostgreSQL based on the XML Schema without defects on information content. It also supports full text search via either Apache Lucene or Sphinx Search. File convesion from XML to CSV, TSV, or JSON is available as well as mapping XML Schema to JSON Schema. Obtained PostgreSQL database can be optimized at user's discletion. Moreover, XPath/SQL translation, direct XPath addressing and document order preservation are possible by option. Quite large XML file can be split and processed through xmlsplitter, a flexible XML splitter based on XPath and StAX.
Full-text index generator of OWL literals
owl-indexer generates full text index of OWL literal via either Apache Lucene or Sphinx Search. It is based on OWL API (https://github.com/owlcs/owlapi).
It's possible for machines to become self-aware.
We believe that it's possible for machines to become self-aware, but may not exhibit human-like thought processes. This project is a quest for conscious artificial intelligence. We will develop prototypes while we go for our main goal. Our steps will be 1) Develop a Learning/Predictive Module. 2) Develop a Planning Module based on the learning/predictive module. 3) Develop a Plan Optimization Module so plans built in the previous module can be optimized. 4) Develop a Decision Making Engine based on previous planning. 5) Develop prototypes of the artificial creature. 6) Publish some academic papers. And there is the video: http://www.youtube.com/watch?v=qH-IQgYy9zg Above video shows a popperian agent collecting mining ore from 3 mining sites and bringing to the base. At the time the agent is born, it doesn't know how to walk nor it knows that it feels pleasure by mining. He has tact only (blind agent). The video shows learning, planning, executing and optimizing plans.
Java code developed by the Australian ICGC team for operating on next-generation sequencing data. This code is currently being maintained and expanded by the QIMR Berghofer Genome Informatics team (http://www.qimrberghofer.edu.au/lab/genome-informatics/) More details and documentation can be found on the wiki: http://sourceforge.net/p/adamajava/wiki/Home/
BBMap short read aligner, and other bioinformatic tools.
This package includes BBMap, a short read aligner, as well as various other bioinformatic tools. It is written in pure Java, can run on any platform, and has no dependencies other than Java being installed (compiled for Java 6 and higher). All tools are efficient and multithreaded. BBMap: Short read aligner for DNA and RNA-seq data. Capable of handling arbitrarily large genomes with millions of scaffolds. Handles Illumina, PacBio, 454, and other reads; very high sensitivity and tolerant of errors and numerous large indels. Very fast. BBNorm: Kmer-based error-correction and normalization tool. Dedupe: Simplifies assemblies by removing duplicate or contained subsequences that share a target percent identity. Reformat: Reformats reads between fasta/fastq/scarf/fasta+qual/sam, interleaved/paired, and ASCII-33/64, at over 500 MB/s. BBDuk: Filters, trims, or masks reads with kmer matches to an artifact/contaminant file. ...and more!
Detection Classification and Localisation of marine mammals
The PAMGUARD project develops software to help detect, locate and classify marine mammals using Passive Acoustic Monitoring.
System for anonymous Web browsing
Our goal is to develop, implement, evaluate and provide a secure and scaleable technical infrastructure for anonymous communication. This project is supported by Deutsche Forschungsgemeinschaft (DFG).
The open source grid computing solution
JPPF makes it easy to parallelize computationally intensive tasks and execute them on a Grid.
A linguistic annotation store
LABB-CAT is a browser-based linguistics research tool that stores recordings and regular-expression searchable text transcripts of interviews. The search results, entire transcripts, and media, can be viewed or exported in a variety of format
High-speed, 3D-friendly, TightVNC-compatible remote desktop software
TurboVNC is a high-performance, enterprise-quality version of VNC based on TightVNC, TigerVNC, and X.org. It contains a variant of Tight encoding that is tuned for maximum performance and compression with 3D applications (VirtualGL), video, and other image-intensive workloads. TurboVNC, in combination with VirtualGL, provides a complete solution for remotely displaying 3D applications with interactive performance. TurboVNC's high-speed encoding methods have been adopted by TigerVNC and libvncserver, and TurboVNC is also compatible with any other TightVNC derivative. TurboVNC forked from TightVNC in 2004 and still covers all of the TightVNC 1.3.x features, but TurboVNC contains numerous feature enhancements and bug fixes relative to TightVNC, and it compresses 3D and video workloads much better than TightVNC while using generally only 5-20% of the CPU time of the latter. Using non-default settings, TurboVNC can also be made to compress 2D workloads as "tightly" as TightVNC.
SIMD-accelerated libjpeg-compatible JPEG codec library
libjpeg-turbo is a JPEG image codec that uses SIMD instructions (MMX, SSE2, NEON, AltiVec) to accelerate baseline JPEG compression and decompression on x86, x86-64, ARM, and PowerPC systems. On such systems, libjpeg-turbo is generally 2-6x as fast as libjpeg, all else being equal. On other types of systems, libjpeg-turbo can still outperform libjpeg by a significant amount, by virtue of its highly-optimized Huffman coding routines. In many cases, the performance of libjpeg-turbo rivals that of proprietary high-speed JPEG codecs. libjpeg-turbo implements both the traditional libjpeg API as well as the less powerful but more straightforward TurboJPEG API. libjpeg-turbo also features colorspace extensions that allow it to compress from/decompress to 32-bit and big-endian pixel buffers (RGBX, XBGR, etc.), as well as a full-featured Java interface.
Graph transformation, model transformation, object-oriented verification, behavioural semantics
Middleware for distributed applications
The purpose of the project is to develop a portable programming framework that facilitates distributed and multi-threaded programming for C++, Java, and Python. MADARA was originally developed as an agent-based middleware specifically for real-time, distributed artificial intelligence, but is now more general purpose for distributed timing, control, knowledge and reasoning, and quality-of-service. MADARA is composed of several tools and middleware, and the main entry point into the system is the Knowledge and Reasoning Language (KaRL) Engine, which provides a real-time scripting language for nanosecond execution times hooked into a flexible transport layer for distributed reasoning. The KaRL engine also supports object-oriented C++, Java, and Python programming through Containers, classes that provide abstractions and references for variable location within the KaRL Knowledge Base. This project is currently in process of being ported from http://madara.googlecode.com.
This is a maintenance project for the NMRShiftDB project (hosted on sf.net). Since development of NMRShiftDB has stopped, some interested people continue to maintain the software here and a public instance which can be reached at nmrshiftdb2.sf.net.
Data Analysis, Simulations and Visualization on the Sphere
Software for pixelization, hierarchical indexation, synthesis, analysis, and visualization of data on the sphere. Please acknowledge HEALPix by quoting the web page http://healpix.sourceforge.net and publication: K.M. Gorski et al., 2005, Ap.J., 622, p.759 Full software documentation available at http://healpix.sf.net/documentation.php Wiki Pages: https://sourceforge.net/p/healpix/wiki/Home GDL users should read https://sourceforge.net/p/healpix/wiki/HEALPix%20and%20GDL/
A modbus library implemented in Java.
JLibModbus is an implementation of the Modbus protocol v1.1b in java language. The library supports the most popular communication libraries (jssc, rxtx, jSerialComm, purejavacomm, java comm api); Maven dependency: <dependency> <groupId>com.intelligt.modbus</groupId> <artifactId>jlibmodbus</artifactId> <version>18.104.22.168</version> </dependency> Implemented MODBUS functions: 0x01 Read Coils 0x02 Read Discrete Inputs 0x03 Read Holding Registers 0x04 Read Input Registers 0x05 Write Single Coil 0x06 Write Single Register 0x07 Read Exception Status 0x08 Diagnostics 0x0B Get Comm Event Counter 0x0C Get Comm Event Log 0x0F Write Multiple Coils 0x10 Write Multiple Registers 0x11 Report Slave Id 0x14 Read File Record 0x15 Write File Record 0x16 Mask Write Register 0x17 Read Write Multiple Registers 0x18 Read Fifo Queue 0x2B Encapsulated Interface Transport (Read Device Identification interface)
Scaffold Hunter is a JAVA-based software tool for the analysis of structure-related biochemical data. It enables generation of and navigation in a scaffold tree hierarchy annotated with various data.