Providing bioinformatics collaborations and support to UK researchers in the the NERC Biomolecular Analysis Facility - Wallingford.
NBAF-Wallingford democratizes bioinformatics analysis for the community by providing systems, tools and documentation, training and expert consultation. The purpose of the NBAF-W node is to empower the community to undertake its own analyses independent of the four data generating nodes of NBAF, as well as to work with these nodes to ensure that all the bioinformatics needs of the community are covered.
The primary strength of NBAF-Wallingford is the Bio-Linux computing platform, an open source and freely available Ubuntu Linux distribution that caters to bioinformaticians and biologists alike - from desktop to cluster to cloud - containing over 500 software packages, including NBAF-developed software. Maintaining this distribution to a high standard over nearly a decade has earned Bio-Linux an unrivaled reputation in the world of bioinformatics and thousands of enthusiastic users around the world. The more recent sister project, CloudBioLinux, which puts Bio-Linux onto the Cloud, has gained rapid traction and has its own user community, while depending strongly on the core packages provided by Bio-Linux.
A major focus of NBAF-Wallingford is training the community and sharing the expertise. For this purpose, NBAF-Wallingford started organizing NBAF Bio-Linux Courses to maximize training and outreach into the community. To date, a total of 13 courses were taught where all courses have been significantly oversubscribed receiving excellent feedback from the community and demand for future places on courses is substantial.
- All course material is publicly available and can be found here.
- The list of past and future courses can be found here.
NBAF-Wallingford has strong connections to development groups
(Debian-Med, Galaxy, myGRID, QIIME, MG-RAST) and an open community of users
and contributors. Furthermore, NBAF-Wallingford actively engages with global initiatives such as the Earth Microbiome Project (EMP), Genomic Standards Consortium (GSC) and Genomic Observatories (GOs) to name a few.
NBAF-Wallingford aims to support the Analysis Cycle, depicted in the diagram above. In providing such support, examples of the expertise NBAF-Wallingford can offer are listed below.
- Bio-Linux Training, NERC-funded researchers of all levels are encouraged to sign up for our popular NBAF Bio-Linux courses, which is taught in terms of 1 or 2-day courses, introducing participants to Linux and bioinformatics on Bio-Linux (List of upcoming courses here, course material here).
- Sequence Analysis e.g. sequence assembly, homology searching, genomic and metagenomic annotation, quality control, clustering, creation of analysis pipelines and workflows, statistical analyses
- Modelling e.g. behavioral modelling (agent-based, mathematical, hybrid modelling), modelling of metagenomic datasets (predicted relative metabolic turnover (PRMT) and microbial assembledge prediction (MAP))
- 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
- Database and web interface design and implementation
- Data visualisation through 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
- 3-day projects: The three-day projects are particularly useful to those requiring assistance relatively quickly and to facilitate immediate sharing of expertise, i.e. assistance with manipulating tabulated BLAST reports to tabulate statistics, where 3 days is sufficient to establish user requirements,create and document scripts, hand the results back to the user including minor additions and fixes, and place generated scripts on Code Catalogue. No application form is required for this service.
- NBAF-W standard application: These projects are costed for up to 44 days per year, where any of the solutions listed above can be requested. NBAF-Wallingford Application Form is required to be filled. Please consult NBAF-Wallingford staff prior to filling the form.
- Recurring projects: These are long-term projects that can be costed for up to 44 days per year. They recur periodically, i.e. annual maintenance of the Galaxy package on Bio-Linux, which involves updating dependency packages of Galaxy periodically.
- NERC grant application: Requests for more extensive involvement of 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".
- Mesude Bicak
- Tim Booth
- Hyun Soon Gweon
- Katja Lehmann
All of the above can be included when you are applying for NBAF-W involvement in bioinformatics through a NERC grant. We work in collaboration with other nodes of the NERC Biomolecular Analysis Facility to co-ordinate bioinformatics processing where relevant.
Scientific remit of projects
Bioinformatics tasks conducted by this facility must lie within the
NERC scientific remit. Applicants must fulfill standard NERC eligibility
requirements for research funding.
How to apply for NBAF-Wallingford Services
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.
NBAF-Wallingford has four different mechanisms for application:
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 Committee 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.
Who are we
General Enquiries: helpdesk"at"nebc.nerc.ac.uk
Facility Director: Professor Dawn Field