Open Source Java Research Software
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Java Research Software
View 85 business solutionsBrowse free open source Java Research Software and projects below. Use the toggles on the left to filter open source Java Research Software by OS, license, language, programming language, and project status.
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Hypernomicon
Hypertext-infused philosophy personal database software
Hypernomicon is a personal productivity/database application for researchers that combines structured note-taking, mind-mapping, management of files (e.g., PDFs) and folders, and reference management into an integrated environment that organizes all of the above into semantic networks or hierarchies in terms of debates, positions, arguments, labels, terminology/concepts, and user-defined keywords by means of database relations and automatically generated hyperlinks (hence ‘Hyper’ in the name). Hypernomicon keeps track of all these things in a highly structured, thoroughly indexed and user friendly relational database, automatically generates semantic hyperlinks between all of them, and presents this information in many different forms so that you are constantly informed of ways all of your information is related that you had not realized. -
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DSpace
Open Source "turn-key" institutional repository application
Open Source Digital Asset Management system that enables services for access, provision, stewardship and re-use of digital assets with a focus on educational and research materials For Support, please see: https://wiki.lyrasis.org/display/DSPACE/Support RELEASES: The most recent releases are now distributed via GitHub: https://github.com/DSpace/DSpace/releases MAILING LISTS: Mailing lists have all been moved to Google Groups: https://wiki.lyrasis.org/display/DSPACE/Mailing+Lists -
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jMIR
Music research software
jMIR is an open-source software suite implemented in Java for use in music information retrieval (MIR) research. It can be used to study music in the form of audio recordings, symbolic encodings and lyrical transcriptions, and can also mine cultural information from the Internet. It also includes tools for managing and profiling large music collections and for checking audio for production errors. jMIR includes software for extracting features, applying machine learning algorithms, applying heuristic error error checkers, mining metadata and analyzing metadata. -
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Choco is not hosted on sourceforge anymore. Please now visit http://choco-solver.org/ !
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JaCoP is a Java Constraint Programming solver. It provides a significant number of (global) constraints to facilitate efficient modeling of combinatorial problems, as well as modular design of search. Documentation is available at project Web site. Please, note that the sources from version 4.0 are only available at GitHub.
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Docear
An Academic Literature Suite
Docear (pronounced dog-ear) is what we call an “academic literature suite”. It integrates everything you need to search, organize and create academic literature in a single application: a digital library, reference manager, PDF and file manager, note taking and mind mapping. And the best: Docear works seemlessly with many existing tools like Mendeley, Microsoft Word, and Foxit Reader. Docear is free and open source, based on Freeplane, funded by the German Federal Ministry of Technology and developed by scientists from around the world, among others from OvGU, and the University of California, Berkeley. -
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Ceka
Crowd Environment and its Knowledge Analysis
A knowledge analysis tool for crowdsourcing based on Weka. We also have a Python version of Crowdsourcing Learning: CrowdwiseKit on GitHub (https://github.com/tssai-lab/CrowdwiseKit). -
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CERCA
CERCA – Citation Extraction & Reference Checking Assistant
CERCA is an open-source research tool that supports the verification of bibliographic references in scientific manuscripts. It extracts references from PDF files and checks their existence and consistency against authoritative metadata sources, producing explainable diagnostics, audit logs, and reproducible reports. It is intended for: - Researchers performing final manuscript checks - Reviewers assessing reference consistency - Editors supporting editorial quality control - Meta-research and reproducibility workflows CERCA is an experimental tool. It does not replace manual verification. CERCA is a Java desktop application built with JavaFX. To run it, you need a JRE that includes JavaFX, such as Azul Zulu JRE. Developed by: Lidiany Cerqueira, PhD Computer Science Researcher -
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GUAJE FUZZY
Free software for generating understandable and accurate fuzzy systems
GUAJE stands for Generating Understandable and Accurate fuzzy models in a Java Environment. Thus, it is a free software tool (licensed under GPL-v3) with the aim of supporting the design of interpretable and accurate fuzzy systems by means of combining several preexisting open source tools, taking profit from the main advantages of all of them. It is a user-friendly portable tool designed and developed in order to make easier knowledge extraction and representation for fuzzy systems, paying special attention to interpretability issues. GUAJE lets the user define expert variables and rules, but also provide supervised and fully automatic learning capabilities. Both types of knowledge, expert and induced, are integrated under the expert supervision, ensuring interpretability, simplicity and consistency of the knowledge base along the whole process. Notice that, GUAJE is is an upgraded version of the free software called KBCT (Knowledge Base Configuration Tool). -
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MolMarker
Java software to evaluate the results obtained by molecular markers
Journal article to cite: Jahnke, G.; Smidla, J.; Poczai, P. MolMarker: A Simple Tool for DNA Fingerprinting Studies and Polymorphic Information Content Calculation. Diversity 2022, 14, 497. https://doi.org/10.3390/d14060497 Leave a review, please! Your opinion matters! :-) MolMarker is user-friendly software to help evaluate the research results obtained by molecular markers. The software can handle genetic (e.g. SSR) and biochemical (e.g. isozyme) data, can construct similarity matrices and UPGMA or NJ dendograms. It can calculate the frequencies of null alleles in the case of genetic data as well as H (heterosigosity) and PIC (polymorphic Information Content) values. Parentage analyses gives a list of possible parent-offspring combinations, and likelihood ratio statistics corresponding to the detected combinations. For details see MolMarker Manual.pdf -
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S-Match
S-Match is a semantic matching framework.
S-Match is a semantic matching framework. S-Match takes any two tree like structures (such as database schemas, classifications, lightweight ontologies) and returns a set of correspondences between those tree nodes which semantically correspond to one another. S-Match contains implementations of the semantic matching, minimal semantic matching and structure preserving semantic matching algorithms. S-Match applies as a solution in many fields, including: information integration, ontology evolution and alignment, peer-to-peer information sharing, digital libraries integration, web service composition, agent communication, and query answering on the web. S-Match is extendable to host new algorithms. -
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Navmol
Molecular structure navigator for Blind and Visually Impaired people
Navmol is a software that allows people that are blind or visually impaired to navigate and edit molecular structures in a simple and intuitive way. -
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OrthoInspector is a new software system for orthology/paralogy analysis. Its purpose is to facilitate the installation and the maintenance of a database describing orthology/inparalogy relations and to provide tools to exploit these data.
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REPEATS is a bioinformatics software designed to help biologists to analyze sequence - either nucleotide or protein - for interspersed repeats. It offers functionalities to manage sequence data, analyze and store search results for further analysis.
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AFE-Web
Antike Fundmünzen Europa
Cooperation project between Goethe-University and Römische-Germanische Kommission. Will bring numismatic data online and tries to link the data with existing ones. ... resulting project code is planed to be open source! -
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AMPdoc
Apache, MySQL, PHP package for library, archive, museum automation
AMPdoc mblazquez edition is a portable package with Apache, MySQL, PHP, and Perl which includes a selection of documentary software applications for libraries, archives, museums, publishers, conferences and documentation centers. AMPdoc mblazquez edition enables to perform workflow management duties, publication of contents, web positioning, among others. Usually, difficulty in installing and configuring of necessary applications has limited the access to technologies to information professionals. With AMP doc mblazquez edition any information professional can use different documentary software in accordance with his needs, without requiring installation. In addition, it can run on any computer running Windows. This package seeks to democratize Documentary Technologies, providing support and contributes to moving towards modernization and the update of knowledge in this area. -
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AMPdoc Black Sun
Apache, MySQL, PHP package for manage syndication channels feeds
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BPMN extension for Cloud computing
java project for modifying jBPM models into cloud aware models
Program based on created BPMN 2.0 Cloud extension. It reads a model *.bpmn, which was created using jBPM BPMN 2.0 modeling tool. Then user is able to define a sensitivity of data elements. After that an Ontology is created and filled in with model elements. Special logical rules process the data. User is able to additionally define the security level. The resulting model is created and can be opened in the jBPM. -
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Babel Software is an exploratory implementation within the localisation space. It takes advantage of a concept called Micro Crowdsourcing.
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Biomedical Information Management System (BIMS) is a modular multilayer object - oriented software architecture, which provides a flexible computational solution to capture and manage a heterogeneous biomedical data: textual and visual information.
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Bracer
Repository has been moved to: http://dtitov.github.com/bracer
Java library for parsing and evaluating math expressions. Javadoc is available at http://bracer.sourceforge.net/javadoc/ P.S. This library depends on Apache Commons Math, so don't forget to include commons-math-2.2.jar to your project. -
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This is a Content Based Image Retrieval Interface with only color features implemented. This is part of a thesis work to analyze the different color features and observe the performance on mainly corel5k images.
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Centre d'informations (CI)
Not a search engine but navigation routes within a research domain.
The Centre d'Informations (CI) aim is to articulate and display whatever type of knowledge available on a given field (see screenshots examples for various fields). The software is built as a network of information articulated using concepts (figure). The website should not be understood as a conventional search engine but as different ways to navigate within this knowledge (information and concept) network. Each information is thoroughly formalized; the aim is not exhaustivity or information amount but rather information quality so as to ensure the best possible articulation within the existing network (quality of the network) and ensure the subject diversity so as to cover the field with robustness. -
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Graphical editor using HTML5 canvas for input of chemical structures, molecule interactions, as well as protein sequence and 3D structural motifs. Facilitates searches in chemo-informatics, bioinformatics and structural biology .
