A series of hands-on informatics workshops have been organised that are linked to iEOS2013 and targeted at Environmental ‘Omics users of different levels of experience. As spaces are restricted, you are requested to select the workshops you wish to attend when you register. There will be minimal additional costs associated with catering (teas/coffees/lunches) during the workshops which will be added to your registration cost. Draft outlines of these workshops can be found under the tabs above.
INTERNATIONAL ENVIRONMENTAL OMICS SYNTHESIS CONFERENCE (IEOS) DAY 1 –9TH SEPTEMBER
TECHNOLOGY TRAINING WORKSHOP (IEOS-TTW) – NERC BIOMOLECULAR ANALYSIS FACILITY
13.30 – 14.30 INTRODUCTION TO ‘OMICS IN THE ENVIRONMENTAL SCIENCES
Prof Steve Paterson, Prof Mark Viant, Dr Karim Gharbi
Sir Martin Evans Building C/0.13
14.30 – 16.30 Training sessions (Four parallel sessions)
SESSION 1. HANDS-ON WORKSHOP ON RNASEQ GENE EXPRESSION ANALYSIS USING R-BIOCONDUCTOR – Sir Martin Evans Building E/PC1
Prof Steve Paterson (Director of the NBAF Liverpool node) and Dr Gareth Weedall will run this workshop, including analysis of a model organism in response to environmental stress as an example of how this technology can be applied in the environmental arena. No prior knowledge of high throughput sequencing data analysis is required but experience with the R statistical package would be advantageous.
SESSION 2. HANDS-ON WORKSHOP ON RESTRICTION-SITE ASSOCIATED DNA (RAD) DATA ANALYSIS – Sir Martin Evans Building, TLRC Computer room.
Dr Karim Gharbi (manager of the NBAF Edinburgh node) and other NBAF staff will run this workshop, including an introduction to RAD sequencing in the environmental genomics context and hands-on analyses of a representative RAD dataset using popular software (e.g. STACKS). No prior knowledge of high throughput sequencing data analysis is required but experience with the Linux environment and basic command line tools would be advantageous.
SESSION 3. CASE STUDIES IN METABOLOMICS - Sir Martin Evans Building C/0.13.
Drs. Ulf Sommer, Jaspreet Sihra and Rob Davidson (the staff scientists at the NBAF Birmingham node) will each present a case study to highlight the capabilities of metabolomics as well as the analytical and computational approaches used. Q&As will be strongly encouraged throughout this training session. No prior knowledge is required.
SESSION 4. BIO-LINUX, A TASTER SESSION - Main Building, Science Library IT Room 2.
Tim Booth (CEH Wallingford) and Dan Pass (Cardiff University) will present a small group introduction to the Bio-Linux system highlighting some important tools and techniques in the software environment. Due to the short time period over which this course will be run, we require people coming to this course have familiarized themselves with the basics of the Linux system and the rudiments of the command line by reading up to page 22 of the introductory tutorial and preferably trying the practical exercises. There are various ways to get access to Bio-Linux for this purpose. For assistance, and to receive a USB stick of the software, please contact Tim directly via firstname.lastname@example.org.
TECHNOLOGY TRAINING WORKSHOP (IEOS-TTW) – WORKSHOP. MODELING AND ANALYSIS OF BIOLOGICAL NETWORKS – 11TH SEPTEMBER
Sir Martin Evans Building Physiology A /C0.07
Chairs. F. Falciani and L. Gasieniec
Centre for Computational Biology and Modeling (CCBM), University of Liverpool
15.30 – 15.45 Coffee and cake – Foyer Sir Martin Evans building
15.45 – 16.00 Introduction to the Workshop
SESSION 1:SYSTEMS BIOLOGY: A TOOL FOR UNDERSTANDING COMPLEX SYSTEMS
16.00 – 16.30 Reverse engineering and systems biology modelling of endocrine disruption in fish. Ed Perkins (USA Army Corps of Engineers, USA)
16.30 – 17.00 Elucidating adverse outcome pathways in ecotoxicology. Natalia G. Reyero Vinas (Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, USA)
17.00 – 17.30 Knowledge Management in Systems Biology, lessons for Environmental Research? Dieter Mayer (BioMax, Germany)
17.30 – 18.00 Integrated Analysis of Blood Gene Expression and Biomarker Data to Define Asthma Endotypes in Children. Stephen Edwards (Environmental Protection Agency, USA)
TECHNOLOGY TRAINING WORKSHOP (IEOS-TTW) – WORKSHOP. MODELING AND ANALYSIS OF BIOLOGICAL NETWORKS – 12TH SEPT. 2013
Sir Martin Evans Building Glass Box C/0.12
SESSION 2:INFERENCE, ANALYSIS AND VALIDATION OF BIOLOGICAL NETWORKS
09.00 – 09.30 Visual Analytics for Biological Network Data. Karsten Klein (The University of Sydney, Australia).
09.30 – 10.00 Algorithmics of Complex Networks. Leszek Gasieniec (Computer Science, University of Liverpool, Liverpool, UK).
10.00 – 10.30 Coalitional games applied to large biological data sets. Stefano Moretti (Laboratoire d’Analyse et Modélisation de Systèmes pour l’Aide à la decision, Université Paris-Dauphine, Paris, France).
10.30 – 11.00 Coffee W/0.12 Available all day for food
SESSION 3: HANDS ON TRAINING SESSION
11.00 – 12.30 Introductory Material
• Large scale datasets and their analysis
• Network reconstruction using knowledge databases and experimental data
• Integration of multi-level data in a modeling framework
• Predicting biological outcome
12.30 – 13.30 Lunch W/0.12
13.30 – 15.00 Practical
• Network reconstruction using knowledge databases
• Network reconstruction from experimental data
• Integration of multi-level data in a modeling framework
15.00 – 15.30 Coffee W/0.12
15.30 – 17.00 Practical Cont.
• Analysis of complex networks
• Predicting biological outcome from network models
17.00 -17.30 Conclusion
There will be some satellite meetings during the day Sir Martin Evans Building C/1.24 & Computer is booked and skype available.
- NERC Environmental: Omics A Community Vision
- STFC/NERC Environmental Synthesis Sandpit
- Newton Fund / British Council / FAPESP Researcher Links Workshop
- EON (Environmental Omics) Network
- Omics Synthesis Centre
- Mathematics and Informatics for Environmental ‘Omic Data Synthesis (‘Omics) programme
- Discipline Hopping Scheme
- STFC/NERC Bioinformatics & Environmental ‘Omics Network
- International Environmental Omics Conference