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| The Taverna Knowledge Blog

The Taverna Knowledge Blog. Designing, Executing and Sharing Scientific workflows. The State of the Bioinformatics Nation. Components for Designing and Executing Workflows. Preface to the Taverna Knowledge-Blog. Provenance and Intermediate Results. Domain services and Shim Services. Identification of differentially-expressed genes from microarray data. Analysing Quantitative Trait Loci data. Case study: Which proteins are associated with my favourite protein? Functional Genomics in Taverna.

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| The Taverna Knowledge Blog | taverna.knowledgeblog.org Reviews
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The Taverna Knowledge Blog. Designing, Executing and Sharing Scientific workflows. The State of the Bioinformatics Nation. Components for Designing and Executing Workflows. Preface to the Taverna Knowledge-Blog. Provenance and Intermediate Results. Domain services and Shim Services. Identification of differentially-expressed genes from microarray data. Analysing Quantitative Trait Loci data. Case study: Which proteins are associated with my favourite protein? Functional Genomics in Taverna.
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1 table of contents
2 introduction
3 by admin
4 features of taverna
5 r scripts
6 parallel service invocations
7 looping
8 beanshell services
9 security in taverna
10 lists and iterations
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table of contents,introduction,by admin,features of taverna,r scripts,parallel service invocations,looping,beanshell services,security in taverna,lists and iterations,nested workflows,tools,taverna command line,taverna server,case studies,no comments,meta
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| The Taverna Knowledge Blog | taverna.knowledgeblog.org Reviews

https://taverna.knowledgeblog.org

The Taverna Knowledge Blog. Designing, Executing and Sharing Scientific workflows. The State of the Bioinformatics Nation. Components for Designing and Executing Workflows. Preface to the Taverna Knowledge-Blog. Provenance and Intermediate Results. Domain services and Shim Services. Identification of differentially-expressed genes from microarray data. Analysing Quantitative Trait Loci data. Case study: Which proteins are associated with my favourite protein? Functional Genomics in Taverna.

INTERNAL PAGES

taverna.knowledgeblog.org taverna.knowledgeblog.org
1

Domain services and Shim Services | The Taverna Knowledge Blog

http://taverna.knowledgeblog.org/2010/12/13/domain-services-and-shim-services

The Taverna Knowledge Blog. Designing, Executing and Sharing Scientific workflows. On December 13, 2010 by Katy Wolstencroft and Robert Stevens in Features of Taverna. Domain services and Shim Services. Conceptually, there are two different types of services used in Taverna; domain services and shim or helper services. Figure 1: a workflow showing Shim services and domain services. There are two ways of finding domain services:. Using the BioCatalogue, a registry of services for the Life Sciences. Decemb...

2

Identification of differentially-expressed genes from microarray data | The Taverna Knowledge Blog

http://taverna.knowledgeblog.org/2011/02/06/identification-of-differentially-expressed-genes-from-microarray-data

The Taverna Knowledge Blog. Designing, Executing and Sharing Scientific workflows. On February 6, 2011 by Peter Li in Case Studies. Identification of differentially-expressed genes from microarray data. Microarray data analysis workflow. The purpose of this workflow. Web service access to maxdBrowse. Use of Beanshell scripts for reconciling mismatches in data interoperability between services and implementing user interaction during workflow execution. Albeit basic, form of user interaction can also be i...

3

Case study: Which proteins are associated with my favourite protein? | The Taverna Knowledge Blog

http://taverna.knowledgeblog.org/2010/12/13/case-study-which-proteins-are-associated-with-my-favourite-protein

The Taverna Knowledge Blog. Designing, Executing and Sharing Scientific workflows. On December 13, 2010 by Marco Roos in Case Studies. Case study: Which proteins are associated with my favourite protein? These are the steps of the workflow:. Start with your favourite protein name. Find publications mentioning your favourite protein. Extract putative protein names mentioned in the abstracts. Check if the protein names are genuine proteins (i.e. have a uniprot reference). Creating an input in Taverna.

4

Analysing Quantitative Trait Loci data | The Taverna Knowledge Blog

http://taverna.knowledgeblog.org/2011/02/06/405

The Taverna Knowledge Blog. Designing, Executing and Sharing Scientific workflows. On February 6, 2011 by Paul Fisher in Case Studies. Analysing Quantitative Trait Loci data. Understanding the precise mechanisms, and identifying suitable candidate QTg, will help to provide insights that will surely enhance our knowledge of these genetically complex traits and may lead to the development of novel therapeutic treatments. In order to identify which genes lie within the QTL region of choice, the physical bou...

5

Taverna command line | The Taverna Knowledge Blog

http://taverna.knowledgeblog.org/2010/12/13/taverna-command-line

The Taverna Knowledge Blog. Designing, Executing and Sharing Scientific workflows. On December 13, 2010 by Stuart Owen in Tools. There are times when it becomes impractical to run workflows within the Taverna workbench. Examples of such scenarios are when running a workflow that is expected to take a long time to complete, or requires greater resources than that available on a typical desktop or laptop computer. The command line utility is available for Windows, Linux and Unix based platforms including M...

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knowledgeblog.org knowledgeblog.org

2011 June | Knowledge Blog

http://knowledgeblog.org/date/2011/06

Scientific Publishing for the Web Generation. Archive For June 2011. Introducing the Bioinformatics Knowledgeblog. On June 28, 2011 by Phillip Lord in Events. Last week (21st June), a small group of bioinformaticians gathered in a little room in the basement of a building on the campus of Newcastle University, and quietly bashed []. The Ontogenesis Knowledgeblog: Lightweight Semantic Publishing. On June 7, 2011 by Phillip Lord in Papers. Download resource as: [bib]. Knowledgeblog Table of Contents Plugin.

knowledgeblog.org knowledgeblog.org

Uncategorized | Knowledge Blog

http://knowledgeblog.org/category/uncategorized

Scientific Publishing for the Web Generation. Posts In Category Uncategorized. On August 19, 2013 by Lindsay Marshall in Uncategorized. Just added support to Greycite for some proprietary meta tags used by Walters Kluwer Health journals. These let us get a full set of metadata from the pages. On March 22, 2013 by Lindsay Marshall in Uncategorized. Phil Lord has been nagging me to post about the things that I have been changing and adding to the Greycite implementation, so : pubmed : if you pass [].

knowledgeblog.org knowledgeblog.org

2011 March | Knowledge Blog

http://knowledgeblog.org/date/2011/03

Scientific Publishing for the Web Generation. Archive For March 2011. On March 29, 2011 by Simon Cockell in Press. Phil Lord from the Knowledgeblog project has been at the JISCMRD International Workshop in Birmingham this week. There he gave a talk: Data linking with kblog View more presentations []. Please cite this resource as: Knowledge Blog http:/ knowledgeblog.org. Download resource as: [bib]. Knowledgeblog Table of Contents Plugin. Health and Public Health.

process.knowledgeblog.org process.knowledgeblog.org

Uncategorized | The Knowledgeblog Process

http://process.knowledgeblog.org/category/uncategorized

A knowledgeblog how-to knowledgeblog. Posts In Category Uncategorized. Proxying Pingbacks and Trackbacks. On July 26, 2011 by Simon Cockell in Uncategorized. Introduction Trackbacks and Pingbacks are both implementations of the linkback methodology for providing links between digital resources and things which hyperlink to those digital resources. This paradigm is most []. Please cite this resource as: The Knowledgeblog Process http:/ process.knowledgeblog.org. Download resource as: [bib].

process.knowledgeblog.org process.knowledgeblog.org

Process | The Knowledgeblog Process

http://process.knowledgeblog.org/category/all/process

A knowledgeblog how-to knowledgeblog. Posts In Category Process. Use of DOIs on Knowledgeblogs. On July 26, 2011 by Simon Cockell in Development. The Knowledgeblog project registers Digital Object Identifiers (DOIs) for posts using the Datacite service, in which the British Library is a partner. Datacite has an Application Programming Interface (API) which can []. Knowledgeblog types and peer-review levels. On August 10, 2010 by Simon Cockell, Daniel Swan and Phillip Lord in Process.

process.knowledgeblog.org process.knowledgeblog.org

How To | The Knowledgeblog Process

http://process.knowledgeblog.org/category/all/how-to

A knowledgeblog how-to knowledgeblog. Posts In Category How To. On September 7, 2012 by Phillip Lord in greycite. Greycite is a tool which extracts bibliographic metadata from a web page. It stores this metadata, and then makes it available for either computational use by tools such as []. Changing the Container Title. On August 23, 2012 by Phillip Lord in How To. Adding Multiple Authors to a Post. On August 22, 2012 by Phillip Lord in How To. Citing URLs with Kcite. The Kblog-metadata plugin (http:/ kno...

knowledgeblog.org knowledgeblog.org

2013 April | Knowledge Blog

http://knowledgeblog.org/date/2013/04

Scientific Publishing for the Web Generation. Archive For April 2013. On April 17, 2013 by Lindsay Marshall in tech. Greycite will now return citations in RIS format (http:/ en.wikipedia.org/wiki/RIS (file format) , though with the caveat that the Type record value is always set to be ELEC – it is difficult in []. Please cite this resource as: Knowledge Blog http:/ knowledgeblog.org. Download resource as: [bib]. Knowledgeblog Table of Contents Plugin. Health and Public Health.

knowledgeblog.org knowledgeblog.org

Who are we? | Knowledge Blog

http://knowledgeblog.org/who-are-we-3

Scientific Publishing for the Web Generation. The current knowledgeblog team is are all active scientists broadly coming from interdisciplinary biomedical and computing science backgrounds. We have developed knowledgeblog out of a desire to improve communication and the accessibility of knowledge both within and outside of science. Contributed to the development of the knowledgeblog platform. Currently, he is the manager of the Newcastle University Bioinformatics Support Unit, where he aids biologica...

knowledgeblog.org knowledgeblog.org

MathJax-Latex WordPress Plugin | Knowledge Blog

http://knowledgeblog.org/mathjax-latex-wordpress-plugin

Scientific Publishing for the Web Generation. The Knowledgeblog team have developed a plugin for WordPress that allows the easy inclusion of mathematical equations in blogposts. It leverages the MathJax. Javascript library to produce scalable, accessible, attractive graphical equations from standard LaTeX. Syntax embedded in posts. You can download the latest version of the plugin: Version 0.2 [wordpress.org]. The mathjax-latex settings page lets you configure how the plugin works. 8230;] the MathJax-LaT...

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| The Taverna Knowledge Blog

The Taverna Knowledge Blog. Designing, Executing and Sharing Scientific workflows. The State of the Bioinformatics Nation. Components for Designing and Executing Workflows. Preface to the Taverna Knowledge-Blog. Provenance and Intermediate Results. Domain services and Shim Services. Identification of differentially-expressed genes from microarray data. Analysing Quantitative Trait Loci data. Case study: Which proteins are associated with my favourite protein? Functional Genomics in Taverna.

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