 | |
| Developer(s) | The Bioclipse Project |
|---|---|
| Initial release | 17 November 2005 [1] |
| Stable release | 2.6.2 (November 4, 2016) [±] |
| Preview release | 2.6.2 RC (April 15, 2016) [±] |
| Type | Cheminformatics, bioinformatics |
| License | Eclipse Public License |
| Website | www |
The Bioclipse project is a Java-based, open-source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP). [2] [3]
Biclipse gained scripting functionality in 2009, [4] and a command line version in 2021. [5]
Like any RCP application, Bioclipse uses a plugin architecture that inherits basic functionality and visual interfaces from Eclipse, such as help system, software updates, preferences, cross-platform deployment etc. Via its plugins, Bioclipse provides functionality for chemo- and bioinformatics, and extension points that easily can be extended by other, possibly proprietary, plugins to provide additional functionality.
The first stable release of Bioclipse includes a Chemistry Development Kit (CDK) plugin to provide a chemoinformatic backend, a Jmol plugin for 3D-visualization of molecules, and a BioJava plugin for sequence analysis. Recently, the R platform, using StatET, [6] and OpenTox were added. [7]
Bioclipse is developed as a collaboration between the Proteochemometric Group, Dept. of Pharmaceutical Biosciences, Uppsala University, Sweden, the Christoph Steinbeck Group at the European Bioinformatics Institute, and the Analytical Chemistry Department at Leiden University, but also includes extensions developed at other academic institutes, including the Karolinska Institutet and Maastricht University. [8] The development is backed up by the International Bioclipse Association. [9]
The Bioclipse Scripting Language (BSL) is a scripting environment, currently based on JavaScript and Groovy. It extends the scripting language with managers that wrap the functionality of third party libraries, as mentioned above. These scripts thus provide means to make analyses in Bioclipse sharable, for example, on MyExperiment.org. Bioclipse defines a number of core data types that managers support, allowing information to be used between these managers.
Jmol is computer software for molecular modelling chemical structures in 3-dimensions. Jmol returns a 3D representation of a molecule that may be used as a teaching tool, or for research e.g., in chemistry and biochemistry. It is written in the programming language Java, so it can run on the operating systems Windows, macOS, Linux, and Unix, if Java is installed. It is free and open-source software released under a GNU Lesser General Public License (LGPL) version 2.0. A standalone application and a software development kit (SDK) exist that can be integrated into other Java applications, such as Bioclipse and Taverna.
JOELib is computer software, a chemical expert system used mainly to interconvert chemical file formats. Because of its strong relationship to informatics, this program belongs more to the category cheminformatics than to molecular modelling. It is available for Windows, Unix and other operating systems supporting the programming language Java. It is free and open-source software distributed under the GNU General Public License (GPL) 2.0.
The Chemistry Development Kit (CDK) is computer software, a library in the programming language Java, for chemoinformatics and bioinformatics. It is available for Windows, Linux, Unix, and macOS. It is free and open-source software distributed under the GNU Lesser General Public License (LGPL) 2.0.
Henry Stephen Rzepa is a chemist and Emeritus Professor of Computational chemistry at Imperial College London.
BALL is a C++ class framework and set of algorithms and data structures for molecular modelling and computational structural bioinformatics, a Python interface to this library, and a graphical user interface to BALL, the molecule viewer BALLView.
Apache Taverna was an open source software tool for designing and executing workflows, initially created by the myGrid project under the name Taverna Workbench, then a project under the Apache incubator. Taverna allowed users to integrate many different software components, including WSDL SOAP or REST Web services, such as those provided by the National Center for Biotechnology Information, the European Bioinformatics Institute, the DNA Databank of Japan (DDBJ), SoapLab, BioMOBY and EMBOSS. The set of available services was not finite and users could import new service descriptions into the Taverna Workbench.
JChemPaint is computer software, a molecule editor and file viewer for chemical structures using 2D computer graphics. It is free and open-source software, released under a GNU Lesser General Public License (LGPL). It is written in Java and so can run on the operating systems Windows, macOS, Linux, and Unix. There is a standalone application (editor), and two varieties of applet that can be integrated into web pages.
Fiji is an open source image processing package based on ImageJ2.
Blue Obelisk is an informal group of chemists who promote open data, open source, and open standards; it was initiated by Peter Murray-Rust and others in 2005. Multiple open source cheminformatics projects associate themselves with the Blue Obelisk, among which, in alphabetical order, Avogadro, Bioclipse, cclib, Chemistry Development Kit, GaussSum, JChemPaint, JOELib, Kalzium, Openbabel, OpenSMILES, and UsefulChem.
The Journal of Cheminformatics is a peer-reviewed open access scientific journal that covers cheminformatics and molecular modelling. It was established in 2009 with David Wild and Christoph Steinbeck as founding editors-in-chief, and was originally published by Chemistry Central. At the end of 2015, the Chemistry Central brand was retired and its titles, including Journal of Cheminformatics, were merged with the SpringerOpen portfolio of open access journals.
KNIME, the Konstanz Information Miner, is a free and open-source data analytics, reporting and integration platform. KNIME integrates various components for machine learning and data mining through its modular data pipelining "Building Blocks of Analytics" concept. A graphical user interface and use of JDBC allows assembly of nodes blending different data sources, including preprocessing, for modeling, data analysis and visualization without, or with only minimal, programming.
Computational Resources for Drug Discovery (CRDD) is one of the important silico modules of Open Source for Drug Discovery (OSDD). The CRDD web portal provides computer resources related to drug discovery on a single platform. It provides computational resources for researchers in computer-aided drug design, a discussion forum, and resources to maintain a wiki related to drug discovery, predict inhibitors, and predict the ADME-Tox property of molecules. One of the major objectives of CRDD is to promote open source software in the field of chemoinformatics and pharmacoinformatics.
WikiPathways is a community resource for contributing and maintaining content dedicated to biological pathways. Any registered WikiPathways user can contribute, and anybody can become a registered user. Contributions are monitored by a group of admins, but the bulk of peer review, editorial curation, and maintenance is the responsibility of the user community. WikiPathways is originally built using MediaWiki software, a custom graphical pathway editing tool (PathVisio) and integrated BridgeDb databases covering major gene, protein, and metabolite systems. WikiPathways was founded in 2008 by Thomas Kelder, Alex Pico, Martijn Van Iersel, Kristina Hanspers, Bruce Conklin and Chris Evelo. Current architects are Alex Pico and Martina Summer-Kutmon.
Christoph Steinbeck is a German chemist and has a professorship for analytical chemistry, cheminformatics and chemometrics at the Friedrich-Schiller-Universität Jena in Thuringia.
PathVisio is a free open-source pathway analysis and drawing software. It allows drawing, editing, and analyzing biological pathways. Visualization of ones experimental data on the pathways for finding relevant pathways that are over-represented in your data set is possible.
Pharmaceutical bioinformatics is a research field related to bioinformatics but with the focus on studying biological and chemical processes in the pharmaceutical area; to understand how xenobiotics interact with the human body and the drug discovery process.
Biocuration is the field of life sciences dedicated to organizing biomedical data, information and knowledge into structured formats, such as spreadsheets, tables and knowledge graphs. The biocuration of biomedical knowledge is made possible by the cooperative work of biocurators, software developers and bioinformaticians and is at the base of the work of biological databases.
