| 1. |
- Bradley, Jean-Claude, et al.
(författare)
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Beautifying Data in the Real World
- 2009. - 1
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Ingår i: Beautiful Data. - Sebastol, USA : O'Reilly. - 9780596157111 ; , s. 259-278
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Bokkapitel (populärvet., debatt m.m.)
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| 2. |
- Spjuth, Ola, et al.
(författare)
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Bioclipse : an open source workbench for chemo- and bioinformatics
- 2007
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Ingår i: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 8, s. 59-
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND: There is a need for software applications that provide users with a complete and extensible toolkit for chemo- and bioinformatics accessible from a single workbench. Commercial packages are expensive and closed source, hence they do not allow end users to modify algorithms and add custom functionality. Existing open source projects are more focused on providing a framework for integrating existing, separately installed bioinformatics packages, rather than providing user-friendly interfaces. No open source chemoinformatics workbench has previously been published, and no successful attempts have been made to integrate chemo- and bioinformatics into a single framework. RESULTS: Bioclipse is an advanced workbench for resources in chemo- and bioinformatics, such as molecules, proteins, sequences, spectra, and scripts. It provides 2D-editing, 3D-visualization, file format conversion, calculation of chemical properties, and much more; all fully integrated into a user-friendly desktop application. Editing supports standard functions such as cut and paste, drag and drop, and undo/redo. Bioclipse is written in Java and based on the Eclipse Rich Client Platform with a state-of-the-art plugin architecture. This gives Bioclipse an advantage over other systems as it can easily be extended with functionality in any desired direction. CONCLUSION: Bioclipse is a powerful workbench for bio- and chemoinformatics as well as an advanced integration platform. The rich functionality, intuitive user interface, and powerful plugin architecture make Bioclipse the most advanced and user-friendly open source workbench for chemo- and bioinformatics. Bioclipse is released under Eclipse Public License (EPL), an open source license which sets no constraints on external plugin licensing; it is totally open for both open source plugins as well as commercial ones. Bioclipse is freely available at http://www.bioclipse.net.
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| 3. |
- Spjuth, Ola, 1977-, et al.
(författare)
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Bioclipse 2: A scriptable integration platform for the life sciences
- 2009
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Ingår i: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 10, s. 397-
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Tidskriftsartikel (refereegranskat)abstract
- Background: Contemporary biological research integrates neighboring scientific domains to answer complex ques- tions in fields such as systems biology and drug discovery. This calls for tools that are intuitive to use, yet flexible to adapt to new tasks. Results: Bioclipse is a free, open source workbench with advanced features for the life sciences. Version 2.0 constitutes a complete rewrite of Bioclipse, and delivers a stable, scalable integration platform for developers and an intuitive workbench for end users. All functionality is available both from the graphical user interface and from a built-in novel domain-specific language, supporting the scientist in interdisciplinary research and reproducible analyses through advanced visualization of the inputs and the results. New components for Bioclipse 2 include a rewritten editor for chemical structures, a table for multiple molecules that supports gigabyte-sized files, as well as a graphical editor for sequences and alignments. Conclusions: Bioclipse 2 is equipped with advanced tools required to carry out complex analysis in the fields of bio- and cheminformatics. Developed as a Rich Client based on Eclipse, Bioclipse 2 leverages on today’s powerful desktop computers for providing a responsive user interface, but also takes full advantage of the Web and networked (Web/Cloud) services for more demanding calculations or retrieval of data. That Bioclipse 2 is based on an advanced and widely used service platform ensures wide extensibility, and new algorithms, visualizations as well as scripting commands can easily be added. The intuitive tools for end users and the extensible architecture make Bioclipse 2 ideal for interdisciplinary and integrative research. Bioclipse 2 is released under the Eclipse Public License (EPL), a flexible open source license that allows additional plugins to be of any license. Bioclipse 2 is implemented in Java and supported on all major platforms; Source code and binaries are freely available at http://www.bioclipse.net.
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| 4. |
- Wagener, Johannes, et al.
(författare)
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XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services
- 2009
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Ingår i: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 10, s. 279-
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Tidskriftsartikel (refereegranskat)abstract
- BACKGROUND:Life sciences make heavily use of the web for both data provision and analysis. However, the increasing amount of available data and the diversity of analysis tools call for machine accessible interfaces in order to be effective. HTTP-based Web service technologies, like the Simple Object Access Protocol (SOAP) and REpresentational State Transfer (REST) services, are today the most common technologies for this in bioinformatics. However, these methods have severe drawbacks, including lack of discoverability, and the inability for services to send status notifications. Several complementary workarounds have been proposed, but the results are ad-hoc solutions of varying quality that can be difficult to use. RESULTS:We present a novel approach based on the open standard Extensible Messaging and Presence Protocol (XMPP), consisting of an extension (IO Data) to comprise discovery, asynchronous invocation, and definition of data types in the service. That XMPP cloud services are capable of asynchronous communication implies that clients do not have to poll repetitively for status, but the service sends the results back to the client upon completion. Implementations for Bioclipse and Taverna are presented, as are various XMPP cloud services in bio- and cheminformatics. CONCLUSION:XMPP with its extensions is a powerful protocol for cloud services that demonstrate several advantages over traditional HTTP-based Web services: 1) services are discoverable without the need of an external registry, 2) asynchronous invocation eliminates the need for ad-hoc solutions like polling, and 3) input and output types defined in the service allows for generation of clients on the fly without the need of an external semantics description. The many advantages over existing technologies make XMPP a highly interesting candidate for next generation online services in bioinformatics.
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| 5. |
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| 6. |
- Willighagen, Egon, et al.
(författare)
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Userscripts for the Life Sciences
- 2007
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Ingår i: BMC Bioinformatics. - : Springer Science and Business Media LLC. - 1471-2105. ; 8, s. 487-
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Tidskriftsartikel (refereegranskat)abstract
- Background The web has seen an explosion of chemistry and biology related resources in the last 15 years: thousands of scientific journals, databases, wikis, blogs and resources are available with a wide variety of types of information. There is a huge need to aggregate and organise this information. However, the sheer number of resources makes it unrealistic to link them all in a centralised manner. Instead, search engines to find information in those resources flourish, and formal languages like Resource Description Framework and Web Ontology Language are increasingly used to allow linking of resources. A recent development is the use of userscripts to change the appearance of web pages, by on-the-fly modification of the web content. This opens possibilities to aggregate information and computational results from different web resources into the web page of one of those resources. Results Several userscripts are presented that enrich biology and chemistry related web resources by incorporating or linking to other computational or data sources on the web. The scripts make use of Greasemonkey-like plugins for web browsers and are written in JavaScript. Information from third-party resources are extracted using open Application Programming Interfaces, while common Universal Resource Locator schemes are used to make deep links to related information in that external resource. The userscripts presented here use a variety of techniques and resources, and show the potential of such scripts. Conclusion This paper discusses a number of userscripts that aggregate information from two or more web resources. Examples are shown that enrich web pages with information from other resources, and show how information from web pages can be used to link to, search, and process information in other resources. Due to the nature of userscripts, scientists are able to select those scripts they find useful on a daily basis, as the scripts run directly in their own web browser rather than on the web server. This flexibility allows the scientists to tune the features of web resources to optimise their productivity.
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