Posts In Category Tutorials

Publishing information in the Linked Open Data cloud

on July 5, 2011 by Mikel Egana Aranguren in Data integration, Comments Off on Publishing information in the Linked Open Data cloud

Introduction Linked Data is a method for publishing structured data on the internet using current web technology. The core idea of Linked Data is to be able to use […]


Microbase Responder Tutorial

on June 21, 2011 by Keith Flanagan in Grid and Cloud Computing, Comments (2)

Introduction Microbase is a distributed computing platform that can be used to execute computationally intensive work in parallel, either on a single machine with multiple processors, or across a […]


Using standardized bioinformatics formats in Taverna workflows for integrating biological data

on by Peter Li in Bioinformatics APIs, Data integration, Tutorials, Comments (0)

The field of bioinformatics is replete with standard formats for representing biological data. Those standards that have been successfully adopted by the bioinformatics community are associated with software tools […]


The Ondex data integration back-end — Episode 1: The Ondex philosophy

on by Jochen Weile in Data integration, Tutorials, Comments (1)

Introduction Ondex (10.1093/bioinformatics/btl081) is a graph-based semantic data integration framework, which specializes on the integration of biological data. The Ondex project was originally started by Jacob Koehler and his […]


Making use of JSON – a primer for small-time scripters

on by Tim Booth in Bioinformatics APIs, Tutorials, Comments (0)

Making use of JSON – a primer for small-time scripters Here I’ll introduce the JSON data representation format, with a contrived situation where it might be useful and some […]


Determining the Effect of Genomic Variants Using the Ensembl Variant Effect Predictor

on by Bert Overduin in Tutorials, Comments (0)

Introduction The effect of newly discovered genomic variants on known transcripts is indispensable in prioritising and categorising such variants. The Ensembl Variant Effect Predictor (VEP) functionally annotates variants in […]


Using R: a guide for complete beginners

on by Alastair Kerr in Statistics, Tutorials, Comments (2)

This tutorial is intended to introduce users quickly to the basics of R, focusing on a few common tasks that  biologists need to perform  some basic analysis:  load a […]


Differential Producibility Analysis (DPA) of transcriptomic data to help understand metabolic status of a cell or microorganism

on by Bhushan Bonde in Metabolic modelling, Statistics, Systems Biology, Transcriptomics, Tutorials, Comments (2)

Bhushan Bonde Introduction While a vast amount of microarray data is now available freely at the various repositories at NCBI (GEO database) and EBI (ArrayExpress), there is currently no […]


Accessing Ensembl using Ruby – the Core database

on by Jan Aerts in Bioinformatics APIs, Comments (2)

This tutorial describes how to use the Ruby API to the Ensembl Core database. It is part of a collection of 3 tutorials on the Ruby API to Ensembl. […]


Kinetic modelling of metabolic pathways

on by Natalie Stanford and Kieran Smallbone in Metabolic modelling, Comments (2)

Authors Natalie J Stanford1,2 , Kieran Smallbone2,3 1. Integrative Systems Biology Doctoral Training Centre; 2. Manchester Centre for Integrative Systems Biology; and 3. School of Mathematics, University of Manchester, […]