Archive For June 2011

A Survey of Metabolic Reconstruction Tools for Metagenomic Datasets

on June 21, 2011 by Matt Collison in Software Comparisons, Comments (3)

Matthew G. collison 1 1 Biopharmaceutical Bioprocess Technology Centre, Merz Court, Newcatle University, NE1 7RU Introduction Metagenomics is a rapidly expanding field and the ability to predict the metabolic […]

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review of “Downstream functional analysis of an ‘omics’ experiment using freely available tools” written by Simon Cockell

on by Bhushan Bonde in Reviews, Comments (0)

review of “Downstream functional analysis of an ‘omics’ experiment using freely available tools” written by Simon Cockell   The article describe an indetailed process of using DAVID a web […]

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

on by Simon Cockell in Reviews, Comments (0)

This post is a review of Differential Producibility Analysis (DPA) of transcriptomic data to help understand metabolic status of a cell or microorganism by Bhushan Bonde. This article describes […]

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Microbase Responder Tutorial

on 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 […]

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Review of “Analysing microarray data in BioConductor”

on by Colin Gillespie in Reviews, Comments (0)

This article describes a statistical analysis of the GSE20986 data set. This data set consists of four treatments, with each treatment having three replicates. The post takes the reader […]

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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 […]

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Review of “Volcano plots of microarray data”

on by Daniel Swan in Reviews, Comments (1)

This is a review for “Volcano plots of microarray data” by Colin Gillespie. The tutorial follows on from “Analysing Microarray data in BioConductor” and shows a widely-used visualisation technique […]

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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 […]

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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 […]

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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 […]

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