Edinburgh Data-Intensive Research - powerNest

Statistical aspects of quantitative real-time PCR experiment design

Rob.Kitchen — Tue, 02 Feb 2010 15:45:47 +0000

powerNest 0.5.7 released

Jano.van.Hemert — Fri, 20 Nov 2009 14:48:53 +0000

Version:

0.5.7

This version contains minor UI tweaks to improve rendering on Windows platforms and an installer. Also improved handling of pre-allocated data.

Can now delete selections by right-clicking a node with the mouse.

Download:

http://www.powernest.net/PowerNest/Download.html

Projects:

powerNest

e-Science Research

Jano.van.Hemert — Thu, 24 Sep 2009 10:22:41 +0000

Speaker(s):

Jano.van.Hemert

Presentation Type:

invited

We explain how e-Science is essential to providing the context in terms of methods, tools and infrastructure for the development of a virtual fly brain. We show examples of steering computational processes, managing knowledge in the spatial context of an organism and formulation of models in developmental biology.

View more presentations from Jano van Hemert.

Date and time:

Monday, 21 September, 2009 - 14:00

Location:

Fly Brain Behaviour Workshop, Oxford, UK

Web site:

http://wiki.esi.ac.uk/See_details#Virtual_Fly_Brain_-_behaviour_workshop

Projects:

powerNest

Design and Optimization of Reverse-Transcription Quantitative PCR Experiments

Jano.van.Hemert — Tue, 18 Aug 2009 14:26:53 +0000

powerNest

Rob.Kitchen — Wed, 27 May 2009 11:36:58 +0000

Version:

0.5

PowerNest (www.powernest.net) is a software tool enabling experimenters to explore the effect of sampling on noise propagation throughout qPCR assays. The sampling process is assumed to be comprised of a number of levels; the acquisition of a sample and the preparation of extracted material, reverse-transcription of the mRNA, and the qPCR itself. Given a small set of data, representative of a larger assay, the error at each stage of the experiment is profiled using a nested-ANOVA.

Armed with this information, PowerNest allows the experimenter to explore the effects of modifications to the experimental design on the expected total error of the assay. When given the financial cost of replicates at each level, PowerNest will calculate a cost-optimal sampling-plan, delivering an experiment design that will minimise processing error and maximise the statistical resolution of the assay.

This is the first available powerNest beta. In the event of any bugs please contact the developers directly at support@powernest.net. This version contains minor UI tweaks and improved handling of pre-allocated data. Added the ability to delete selections by right-clicking a node with the mouse.

Download:

http://powernest.net

Projects:

powerNest

GeneE: Manage your microarray data more effectively

Jano.van.Hemert — Thu, 04 Sep 2008 09:34:45 +0000

Speaker(s):

Rob.Kitchen

Presentation Type:

demo

A 20-minute demonstration on the benefits of using GeneE to manage and analyse data acquired in gene expression studies.

Date and time:

Wednesday, 10 September, 2008 - 13:50

Location:

Appleton Tower Demo Room 2, e-Science All Hands Meeting 2008, Edinburgh, UK

Web site:

http://www.allhands.org.uk/

Projects:

powerNest

Microarrays in Minutes: Streamlining Gene Expression Data Analyses

Jano.van.Hemert — Fri, 15 Aug 2008 13:27:14 +0000

Speaker(s):

Rob.Kitchen

Presentation Type:

talk

The main aim of this project is to provide biologists with a compact, efﬁcient, and uncomplicated software platform for the robust analysis, intuitive representation, and reliable preservation of all data generated by high-throughput gene expression analysis techniques; such as quantitative real-time PCR (qPCR) or microarrays.

Date and time:

Wednesday, 10 September, 2008 - 11:00

Location:

e-Science All Hands Meeting 2008, Edinburgh, UK

Web site:

http://www.allhands.org.uk/

Projects:

powerNest

Wrapping Tools to Automate Workflows for Gene Therapy in Cystic Fibrosis

Jano.van.Hemert — Wed, 10 Oct 2007 13:07:38 +0000

NeSC Research Seminar Series

Speaker:

Rob Kitchen

Currently, the analysis of gene expression data generated by microarray and real-time PCR experiments is a slow process, often taking several weeks to properly process data from a small number of patients. In anticipation of a new clinical trial expected to involve 200 patients it is necessary to improve the efficiency of these analyses, through automation, in order to return meaningful biological data on a much shorter time scale.

The current procedures involve numerous stages of extracting small amounts of data from machine formatted, comma-separated text files. The useful data are identified, subjected to processing by established standard operating procedures, and passed to dedicated software for more complicated statistical analyses. Currently, all of these steps are performed manually using Excel spreadsheets and, due to the repetitive and time-consuming nature of the tasks, are vulnerable to errors. It has been recognised that the entire process would be very well suited to computer automation; through the creation of specialised wrapping scripts, databases, and a workflow of some kind to be invoked remotely via a web service, there is the potential to reduce the time required to perform each analysis by several orders of magnitude.

The aim of this project is to outline the analysis process then design, test, and implement the necessary scripts, databases, workflows, and web services as required by the end-user. A possible extension to this includes the option of providing a portal to facilitate interaction with the workflow. Furthermore it would be possible, given sufficient time, to provide a comparison of the data output from existing software, such as R or GeneSpring, in order to verify their suitability for these analyses.

Date and time:

Wednesday, 17 October, 2007 - 11:00

Length:

45 minutes

Location:

Cramond

Projects:

powerNest

Wrapping Tools to Automate Workflows for Gene Expression Analyses in Cystic Fibrosis

Jano.van.Hemert — Fri, 24 Aug 2007 13:37:08 +0000

NeSC Research Seminar Series

Speaker:

Rob Kitchen

Date and time:

Tuesday, 4 September, 2007 - 14:00

Length:

60 minutes

Location:

Newhaven

Projects:

powerNest