Featured project

LibHPCII

In addition to stand-alone projects, we also carry out analysis as part of larger projects. We also participate in projects which don't fit the main categories, such as HPC and infrastructure projects, some examples of which are shown below,

Current projects

LibHPCII - A long-term solution for the usability, maintainability and sustainability of HPC software

Libhpc aims to provide a framework for building, running and maintaining future-proof, sustainable HPC applications. Lack of re usability and portability has been a major barrier to adoption in HPC code, leading to significant loss in what is often the most creative output of a research project and one with the greatest potential to benefit the wider res earch community and the general public. By providing a means for expressing application structure abstractly, libhpc enables HPC developers to share equivalent implementations for differing architectures via libhpc repositories. The same abstract structure also produces highly re-usable applications, which are easily adapted at and even during runtime to execute on widely different platforms, archite ctures and resource groups.

In libhpc2, we propose to create a production-ready environment from the prototype framework developed in libhpc. The libhpc 2 environment will include package-based installs, admin interfaces, a community component repository and DSL support; it will also support internet-scale networking. libhpc2 will also place a strong emphasis on stakeholder engagement, community building and skills development through responsive documentation, workshops and hackdays. LibHPC is aimed initially at  two target domains, fluid dynamics and bioinformatics. We will be working extensively with John Darlington’s group to produce robust workflows for a number of bioinformatics tasks including a variety of next generation sequencing applications.

PI: Prof. John Darlington

Funding body: EPRSRC

Grant reference: EP/K038877/1

BDSG contact: Dr. Sarah Butcher

Selected completed projects

Asperigillus fumigatus

Role of Aspergillus fumigatus gene clusters in mammalian niche-adaptation.

PI: Dr. Elaine Bignell

Funding body: BBSRC

Grant reference: BB/G009619/1

BDSG Contact: Geraint Barton

BGX/MMSEQ

Integrated Expression Analysis and E-support using Bayesian Models for Affymetrix Exon and Gene Arrays.

PI: Dr. Alex Lewin

Funding body: BBSRC

Grant reference: BB/G000352/1

BDSG contact: Geraint Barton

A distributed system for E-support of microarray data analysis and management

This was a collaborative project with the London E-Science Centre and the MRC Microarray Centre, to develop a novel system for microarray support taking advantage of recent advances in E-Science technology. The project developed a portal providing integrated access to microarray analysis software and a results database, with remote user support.

PI: Dr. S. Butcher

Funding body: BBSRC

Grant reference: BB/B/16488

BDSG Contact: Dr. Sarah Butcher

EpiCollect

EpiCollect is a mobile device based framework to enable the collection of data out in the field. It allows you to collect and submit geotagged data forms (along with photos) to a central project website from suitable mobile phones (Android or iPhone). For example, questionnaires, surveys etc. All data synchronised (ie a copy sent from the phone) from multiple phones can then be viewed / charted / filtered at the project website using Google Maps / Earth or downloaded. Furthermore, data can be requested and viewed/filtered from the project website directly on your phone using Google Maps.

Website: http://www.epicollect.net

Contact: Dr. David Aanensen

BDSG contact: Dr. Derek Huntley

Fowlpox

Correlation of immunogenicity with microarray analysis of vector mutants to improve live recombinant poxvirus vaccines in poultry.

PI: Dr. Mike Skinner

Funding body: BBSRC

Grant reference: BB/H005323/1

BDSG Contact: Geraint Barton

LabBook

LabBook was the first Android based electronic lab book. It is a fast, accurate and intuitive approach to recording, sharing and backing up experimental details. Hand written notes, photos, videos, barcodes and more can all be captured using a mobile device.

LabBook was developed by several members of the BDSG and in 2012 it won an Imperial Innovations IDEA prize. It is currently being rolled out in several departments across Imperial College and the team are looking for further collaborations.

Public website: http://labbook.cc/

BDSG contact: Geraint Barton

High Throughput Computing for Bioinformatics

 In collaboration with the London E-Science Centre, we developed a week long, intensive course on the use of high-throughput methodologies for bioinformatics. The course is targeted at post-MSc bio informaticians, and covers topics including parallel computing, the use of Grid Engine, CONDOR and GLOBUS, XML and Web Services in bioinformatics, and the Distributed Annotation System (DAS). Course delivery is split between lectures and hands-on practical sessions, and includes guest lecturers from The Wellcome Trust Sanger Institute and the National E-Science Centre.

PI: Dr. Sarah Butcher

Funding body: BBSRC

Grant reference: BB/D007232/1

BDSG Contact: Dr. Sarah Butcher

Rapport - Robust Application Porting for HPC in the Cloud

Cloud computing infrastructure is now widely used in many domains, but one area where there has been more limited adoption is research computing, in particular for running scientific high-performance computing (HPC) software. The Robust Application Porting for HPC in the Cloud (RAPPORT) project took advantage of existing links between computing researchers and application scientists in the fields of bioinformatics, high-energy physics (HEP) and digital humanities, to investigate running a set of scientific HPC applications from these domains on cloud infrastructure. 

PI: Prof. John Darlington

Funding body: EPSRC/JISC

Grant reference: EP/I034246/1

BDSG contact: Dr. Sarah Butcher