Open Access
KNIME: The Konstanz Information Miner.
Michael R. Berthold,Nicolas Cebron,Fabian Dill,Thomas R. Gabriel,Tobias Kötter,Thorsten Meinl,Peter Ohl,Christoph Sieb,Kilian Thiel,Bernd Wiswedel +9 more
- pp 319-326
TLDR
Some of the design aspects of the underlying architecture of the Konstanz Information Miner are described and briefly sketch how new nodes can be incorporated.Abstract:
The Konstanz Information Miner is a modular environment, which enables easy visual assembly and interactive execution of a data pipeline. It is designed as a teaching, research and collaboration platform, which enables simple integration of new algorithms and tools as well as data manipulation or visualization methods in the form of new modules or nodes. In this paper we describe some of the design aspects of the underlying architecture and briefly sketch how new nodes can be incorporated.read more
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Fiji: an open-source platform for biological-image analysis
Johannes Schindelin,Ignacio Arganda-Carreras,Erwin Frise,Verena Kaynig,Mark Longair,Tobias Pietzsch,Stephan Preibisch,Curtis Rueden,Stephan Saalfeld,Benjamin Schmid,Jean-Yves Tinevez,Daniel J. White,Volker Hartenstein,Kevin W. Eliceiri,Pavel Tomancak,Albert Cardona +15 more
TL;DR: Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis that facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system.
Journal ArticleDOI
Big Data: A Survey
Min Chen,Shiwen Mao,Yunhao Liu +2 more
TL;DR: The background and state-of-the-art of big data are reviewed, including enterprise management, Internet of Things, online social networks, medial applications, collective intelligence, and smart grid, as well as related technologies.
Posted Content
ImageJ2: ImageJ for the next generation of scientific image data
Curtis Rueden,Johannes Schindelin,Johannes Schindelin,Mark Hiner,Barry E. DeZonia,Alison E. Walter,Alison E. Walter,Ellen T. Arena,Ellen T. Arena,Kevin W. Eliceiri,Kevin W. Eliceiri +10 more
TL;DR: The entire ImageJ codebase was rewrote, engineering a redesigned plugin mechanism intended to facilitate extensibility at every level, with the goal of creating a more powerful tool that continues to serve the existing community while addressing a wider range of scientific requirements.
Journal ArticleDOI
The ImageJ ecosystem: An open platform for biomedical image analysis
TL;DR: The ImageJ project is used as a case study of how open‐source software fosters its suites of software tools, making multitudes of image‐analysis technology easily accessible to the scientific community.
Journal ArticleDOI
A new bioinformatics analysis tools framework at EMBL–EBI
Mickael Goujon,Hamish McWilliam,Weizhong Li,Franck Valentin,Silvano Squizzato,Juri Paern,Rodrigo Lopez +6 more
TL;DR: A new framework aimed at both novice as well as expert users that exposes novel methods of obtaining annotations and visualizing sequence analysis results through one uniform and consistent interface is presented.
References
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The Chemistry Development Kit (CDK): An open-source Java library for chemo- and bioinformatics
Christoph Steinbeck,Yongquan Han,Stefan Kuhn,Oliver Horlacher,Edgar Luttmann,Egon Willighagen +5 more
TL;DR: The Chemistry Development Kit provides methods for many common tasks in molecular informatics, including 2D and 3D rendering of chemical structures, I/O routines, SMILES parsing and generation, ring searches, isomorphism checking, structure diagram generation, etc.
Parallel and Distributed Data Pipelining with KNIME
TL;DR: The parallel and distribution potential of pipelining tools is discussed by demonstrating several parallel and distributed implementations in the open source pipeline platform KNIME and verifying the practical applicability in a number of real world experiments.