EMBO Practical Course on Plant Bioinformatics: Going -OMICs, co-funded by the ESF-ENSS research networking programme (RNP)
This practical course will provide a comprehensive overview of data resources and tools for plant bioinformatics, from with an emphasis on dealing with large-scale dataset production and challenges in high-throughput data handling and analysis.
This course specifically addresses the challenges, uses and needs of bioinformatics resources and tool for plant researchers. It will bring together lead researchers in the field of plant bioinformatics, experts in biological data resources, and a highly motivated group of experimental researchers through a common theme centred on plant-based research. The course will combine lectures and led discussions to identify the key challenges, opportunities and bottlenecks. There will be computer-based practical sessions on genomics, transcriptomics, proteomics, interactomics and metabolomics, using plant-based use cases and public-domain data resources.
Target Audience:
Owing to the practical nature of the course, and to optimise interactions, group activities and tutorials, we will accept a maximum of 25 students. The course will be aimed at early-stage researchers, and participants will be selected by a scientific committee in consultation with EMBO.
| Time | Topic |
|---|---|
| Sunday 10 June | |
| After 13:30 | Delegates arrive and check in at Arundel House Hotel, Cambridge |
| Day 1 - 11 June (Plant Genome Sequencing -NGS) | |
| 08:45 | Transport to EBI from Hotel |
| 09:00 | Registration with coffee |
| 10:00 | Welcome and Introduction (Vicky Schneider, John Walshaw and Paul Kersey) |
| 11:00 | Plant Genome data and NGS technologies (Paul Kersey) |
| 12:30 | Lunch |
| 14:00 | Genetic Linkage Mapping: an introduction to the problem and its computational solutions (Jo Dicks) |
| 15:30 | Tea/Coffee break |
| 16:00 | Getting to know you: Participants Flash (2minute) presentations, all |
| 17:00 | Poster session*, all |
| 17:30 | The DNA sequence archiving: data repositories, compression and collaboration (Marc Rossello) |
| 18:30 | Panel discussion, all |
| 19:00 | Transport from EBI to Hotel |
| Day 2 - 12 June (Plant Genome Data: dealing with polyploidy) | |
| 08:45 | Transport to EBI from Hotel |
| 09:30 | Browsing Genomic Information with Ensembl Plants (Bert Overduin) |
| 10:00 | Hands on Browsing Genomic Information with Ensembl Plants (Bert Overduin) |
| 10:30 | Tea/Coffee break |
| 11:00 | Hands on Browsing Genomic Information with Ensembl Plants continues (Bert Overduin) |
| 12:30 | Lunch plus ENA/SRA Interaction table (Rajesh Radhakrishnan, Marc Rosello and Arnaud Oisel) |
| 13:30 | Quick round discussion, all |
| 14:00 | Comparative Genomics (Alessandro Cestaro) |
| 14:45 | Hands on Comparing genomes (Alessandro Cestaro) |
| 15:30 | Tea/Coffee break |
| 16:00 | Genomic approaches for discovering genes controlling complex traits (Michela Troggio) |
| 17:00 | Poster session*, all |
| 18:00 | Transport from EBI to Hotel |
| Day 3 - 13 June (Plant Sequence Searching and Alignments) | |
| 08:15 | Transport to EBI from Hotel |
| 09:00 | Exploiting plant genomes in term of polyploidy: how and why? (Alessandra Vigilante) |
| 10:30 | Tea/Coffee break |
| 11:00 | Plant sequence databases (John Walshaw) |
| 12:30 | Lunch |
| 13:30 | Quick round discussion |
| 14:00 | Understanding Alignments (Fran Lewitter) |
| 15:30 | Tea/Coffee break |
| 16:00 | Hands on alignments (Fran Lewitter) |
| 18:00 | Transport from EBI to Hotel |
| Day 4 - 14 June (Plant RNAs and Plant Expression Data-Functional Genomics) | |
| 08:45 | Transport to EBI from Hotel |
| 09:30 | RNA in Plants (Krys Kelly) |
| 10:30 | Tea/Coffee break |
| 11:00 | Hands on RNA in Plant (Krys Kelly) |
| 12:30 | Lunch |
| 13:30 | Expression Analysis of RNA-seq data (Manuel Corpas) |
| 14:15 | Getting to the 'root' of gene expression- A hands-on introduction to ArrayExpress and Atlas (Emma Hastings) |
| 15:45 | Tea/Coffee break |
| 16:00 | From transcriptome (SNP/EST/cDNA/NGS) to genome (BACs/WGS): how to get a reliable functional annotation (Alessandra Traini) |
| 18:00 | Transport from EBI to Hotel |
| Day 5 - 15 June (Phylogenomics of Plant Genomes) | |
| 08:45 | Transport to EBI from Hotel |
| 09:30 | Molecular Phylogenetics: basic concepts and methods (Julie Hawkins) |
| 10:30 | Tea/Coffee break |
| 11:00 | Optimising de novo assembly of plant transcriptomes from short sequencing reads (Steve Kelly) |
| 12:30 | Lunch |
| 14:00 | Genome composition analysis: from structure to evolution (Miriam di Filippo) |
| 15:30 | Tea/Coffee break |
| 16:00 | Genome composition analysis: from structure to evolution (Miriam di Filippo) |
| 18:00 | Transport from EBI to Hotel |
| Day 6 - 16 June (Plant Proteomics Data Analysis) | |
| 08:30 | Transport to EBI from Hotel |
| 09:30 | Plant proteomics: where are we now? (John Walshaw) |
| 10:00 | General principles of proteomics (Joe Foster) |
| 11:00 | Tea/Coffee break |
| 11:30 | Retreiving and validating plant data from PRIDE - practical (Joe Foster) |
| 13:00 | Transport to Arundel House Hotel, Cambridge. Collect packed lunch from hotel and 'free afternoon taking in the sites of Cambridge City' |
| 19:00 | Course Dinner in Queens College, Cambridge |
| Day 7 - 17 June (Plant Metabolomics & Plant Microbiome Metagenomics) | |
| 08:45 | Transport to EBI from Hotel |
| 09:30 | Plant Microbiomes: revealed by metagenomics, metatranscriptomics and next-generation sequencing (John Walshaw) |
| 10:30 | Tea/Coffee break |
| 11:00 | Resources and Tools (John Walshaw) |
| 12:30 | Lunch |
| 14:00 | Quick round discussion |
| 14:30 | Plant Metabolomics (Manfred Beckmann) |
| 15:30 | Tea/Coffee break |
| 16:00 | Plant Metabolomics continued (Manfred Beckmann) |
| 17:00 | Transport from EBI to Hotel |
| Day 8 - 18 June (Plant Interactomes and Networks) | |
| 08:45 | Transport to EBI from Hotel |
| 09:30 | Lecture: Data Integration for Gene Discovery in Plant Genetics and Genomics (Chris Rawlings) |
| 10:30 | Tea/Coffee break |
| 11:00 | Molecular Interactions (Jyoti Khadake) |
| 12:30 | Lunch |
| 13:30 | Quick round discussion |
| 14:30 | Molecular networks and what do they mean (Nadezhda T. Doncheva) |
| 15:30 | Tea/Coffee break |
| 16:00 | Build, visualise and analyse your own network in Cytoscape (Nadezhda T. Doncheva) |
| 17:45 | Transport from EBI to Hotel |
| Day 9 - 19 June (Plant Reactions and Pathways, Systems Biology) | |
| 08:15 | Transport to EBI from Hotel |
| 09:00 | Computational Morphodynamics: when Systems Biology meets plant tissue modelling (Henrik Jönsson) |
| 10:30 | Tea/Coffee break |
| 11:00 | How Ondex can be used to support plant systems biology (Jan Taubert, Artem Lysenko & Keywan Hassani-Pak) |
| 12:30 | Lunch |
| 13:30 | How Ondex can be used to support plant systems biology (Jan Taubert, Artem Lysenko & Keywan Hassani-Pak) |
| 15:00 | Tea/Coffee break |
| 15:30 | Hands on Computational Morphodynamics: when Systems Biology meets plant tissue modelling (Henrik Jönsson) |
| 17:00 | Wrap up and Feedback (survey) |
| 17:15 | Delegates to make their own travel arrangements |
* Posters will be exhibiting throughout the course and speakers will select the best three posters.
Registration will be via a selection process therefore applicants should be aware that, in order to be considered for place on this course, they MUST complete the application page as well as submit a short CV, research interests and a letter of support from their supervisor or another senior co-worker. Incomplete applications will NOT be considered. Details of how to submit these extra documents will be provided on your application confirmation email.
Information on how to submit this additional information is contained in your completed application for registration. Application registration closes 11 April 2012 (12:00 midday GMT). There will be a maximum of 25 participants on this course. Successful applicants will be notified by 20 April 2012 and will then be asked to confirm their place on the course by re-registering.
Registration Fees:
This course is free of charge as it is jointly funded by EMBO Practical Courses and ESF-ENSS research networking programme (RNP).
Please note that the course includes:
- All meals (breakfast, lunch, dinner and refreshment breaks)
- Accommodation for 9 nights (check in 10 June 2012, check out 19 June 2012), in the Arundel House Hotel, Cambridge (http://www.arundelhousehotels.co.uk/)
- Transport to/from the accommodation to/from the EBI during the 9 days
- Course materials
- Use of EBI IT Training Room computer during the 9 day course.
NOTE: All delegates will need to arrange their own travel to and from the course. There will be some travel grant funding available for the successful delegates, more information will be provided.
Registration/application:
Please complete the application form through the link below. Items marked * are mandatory. Incomplete registrations will not be processed:
APPLICATION IS NOW CLOSED