TSL Funding Source Gatsby Core Other (BBSRC, EU etc)
TSL Research “The Sainsbury Laboratory is dedicated to making fundamental discoveries about plants and how they interact with microbes and viruses and favours daring, long-‐ term research over work that could be equally well carried out elsewhere”. Basic and translational research into Plant/Pathogen interactions
genomics HTGS eﬀector ﬁnding R gene cloning assembly de novo resequencing SNP detection annotation pipelines transcriptomics RNA seq ChIP seq arrays proteomics high throughput image analysis pipeline development image segmentation statistical methods for object detection spectrum analysis algorithm development
TSL Tech Illumina GA II Opera HCA Imaging Orbitrap LC-‐MS 5 groups, ~ 80 scientists => 2 bioinformaticians understand, manage, analyze
Training Workshops: Perl, Ruby, CMD Line, MySQL, R + Stats, Excel VB Browsers and Desktop tools… Resource provision: Workshop notes, Workshop Podcasts, Quick ‘How do I’ podcasts Library Integration of best practice: Lab meetings, Journal Clubs, An open dialogue – most important is to have someone approachable, who wants to do it
Systems Development (SOP for common tasks – keeping the house in order) Shared Data Common data storage – results and raw data Don’t inconvenience Make access easy Make messing it up hard Need to get PLs on-‐side…
Systems Development Shared Data Local validation rules for features and sequence • Annotation (GFF3) consistent with local specs • Dbxref, IDs, sl_id, species_id, Sequence and feature databases • version and update tracking – central store
Systems Development galaxy Workﬂows – great for sharing ‘vanilla’ analysis protocols Customisable – great for running in-‐house scripts
Supplementary Research Reference-‐free SNP detection De Bruijn graph representations of polymorphisms in sequence reads New method – reduces steps in SNP ﬁnding, makes possible where no reference available Collaboration with Mario Caccamo at TGAC
Advantage Time • Get analysis know-‐how into heads with biology • Reduce workload • Improve reproducibility • These things propagate…
Summary • There is a lot a ‘biologist’ can do themselves • Start a dialogue • Get tough, get your house in order • Lower the barriers to access and capability
Acknowledgements • Dr Graham Etherington • Michael Burrell • Sophien Kamoun • Jonathan Jones • Silke Robatzek • Eric Ward • Richard Leggett • Mario Caccamo
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