NBAF-Wallingford

NBAF-Wallingford

Introduction
Examples of NBAF Wallingford Services
Scientific Remit of Projects
How to Apply for NBAF-W Services
Contacts

Introduction

NBAF-Wallingford provides bioinformatics services at a variety of levels to suit the needs of researchers in the NERC community.

NBAF-Wallingford can be engaged in:

• fully collaborative projects, where NBAF-Wallingford staff will undertake bioinformatics planning and analyses in co-operation with NERC researchers,
• a service role, where data is sent to NBAF-Wallingford with a defined set of analyses required; we would then return your results after these are carried out.
• support role, providing advice and informatics support at a level appropriate to your project,
• a training role, where you, or your colleagues, including NERC-funded Ph.D. students and post-doctoral researchers, visit NBAF-Wallingford to learn techniques or get assistance with your research projects.

Examples of NBAF-Wallingford services

Examples of the expertise NBAF-Wallingford can provide are listed below. We will work in collaboration with other nodes of the NERC Biomolecular Analysis Facility to co-ordinate bioinformatics processing with them where relevant.

Please contact us to discuss your interests and requirements. We are, of course, happy to discuss other possible bioinformatics activities beyond those listed here.

• Guidance on experimental design for microarray and next-generation transcriptomic experiments.
• Sequence Analysis e.g. sequence assembly, homology searching, genomic and metagenomic annotation, in silico microsatellite detection
• Microarray analysis using R, and other packages, as deemed appropriate.
  
• Programming in languages such as  R, Perl, Perl-CGI, PHP, Java, Javascript. Tasks that are commonly approached include:
  
• Pre- and post processing of data and analysis files,
  
• Batch processing of bioinformatics tasks such as blast jobs and results parsing, and automation of mundane computing tasks such as file format conversions,
• Creation of bioinformatics pipelines and workflows
• Statistical analyses
• Database and web interface design and implementation
• Data visualisation through DAS, GBrowse or GenQuery
  
• Bioinformatics computing infrastructure installation and advice for use, including installation and advice about the Bio-Linux platform and access to clusters such as those based at CEH or the National Grid Service for computationally demanding analyses,
• Sample management solutions such as barcoding using the NEBC Handlebar system, which includes an online database of sample information,
• Activities towards submission of data to public databases, including annotation, annotation advice, and support for standards compliance can be included when you are applying for NBAF-O involvement in bioinformatics through a NERC grant.
  
  
  
  

Scientific remit of projects

Bioinformatics tasks conducted by this facility must lie within the NERC scientific remit. Applicants must fulfil standard NERC eligibility requirements for research funding.

How to apply for NBAF-Wallingford Services

Please see the NBAF webpage on applying for NBAF services, and the NERC web page about applying to facilities, in addition to the information here. 

NBAF services can be requested directly using the NBAF application form or as part of a NERC grant application. The details below are for NBAF-Wallingford but the general principles apply to all the nodes. Please feel free to discuss aspects of your proposal with us. You will need time estimates or costings from us for either type of application.

If you apply directly to NBAF, the request you make will be considered in light of the scientific case you lay out in the NBAF application form and the services you are requesting. You can apply for up to 10% of an NBAF-Wallingford member's time for a given period in this manner. This route is expected to cover defined tasks that would benefit from bioinformatician time, and especially tasks that perhaps could not have been envisioned when the research was originally planned due to the fast moving changes in technology and computing methods.  

Requests for more extensive involvement by NBAF-Wallingford staff should be made by including costed time in your NERC grant application. We request that you contact us in good time before the grant deadline for cost estimates, preferably at least six weeks prior to a deadline and before the full application has been written. This is to give us enough time to engage with you about your project. This ensures that we are costing for what you need and that we commit to providing appropriate data manipulations and/or analyses to make it possible to address your scientific questions. Our costings would be included in the Other Directly Incurred Costs section. You will need to include information about what we will provide in your Justifications of Resources. 

If you receive a grant from the NERC in which you have costed NBAF support, you will still need to fill in an NBAF application form requesting services. This is so that the NBAF Steering Commitee can look at the technical information specific to the work to be done at the facility in detail.  They can then confirm any details with you that aren't clear from prior discussions or from the grant proposal itself.

Contacts

General Enquiries:  helpdesk"at"nebc.nerc.ac.uk
Facility Director: Dr Dawn Field     email  dfield"at"ceh.ac.uk