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eBiodiversity
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Biodiversity informatics deals with the application of information technology to biodiversity information, with particular focus on data storage, capture, provision, retrieval and analysis of individual organisms, populations and taxa; it is therefore distinct from bio-informatics, which focuses largely on genomics and proteomics. The two-day workshop is aimed at the biodiversity informatics community, both researchers and practitioners. The domain is characterised by disparate fields of enquiry, ranging from the compilation of a catalogue of life to collation and analysis of ad hoc species observations records. Within the biodiversity informatics community there is only limited awareness of the potential of grid computing to manipulate the disparate heterogeneous data characteristic of biodiversity informatics.
The Course organiser is John Lee from Oxford Brookes University.
The morning of the first day will comprise a brief introduction to the aims of the workshop followed by an introduction to biodiversity informatics by way of a summary presentation and descriptions of case studies. The afternoon of the first day will focus on the fundamentals of eScience and grid computing, ranging from a general introduction to a more technical exploration. The morning of the second day will comprise more technical sessions focusing on grid middleware, running grid applications and the Access Grid. The afternoon will comprise break-out sessions aimed at identifying the major issues facing biodiversity informatics and the grid.
The workshop will allow the participants to explore and identify the current issues facing biodiversity informatics and the extent to which escience and grid computing are being used in biodiversity informatics.
| 10.30 | Coffee and registration |
| Session 1: Introduction | |
| 11.00 | Introduction. John Lee (Oxford Brookes) |
| 11.15 | Intoduction to eScience. Stuart Ballard (NIEeS) |
| Session 2: Grid applications | |
| 12.00 | Designing and building a Biodiversity GRID: experiences from the BiodiversityWorld project. [ppt] Andy Jones (Cardiff) |
| 12.30 | Scientific Environement for Ecological Knowledge. Jessie Kennedy (SEEK, Napier University) |
| 1.00 | Lunch |
| Session3: Tools for e-Biodiversity | |
| 2.00 | Data exchange within the National Biodiversity Network. Andy Brewer (National Biodiversity Network) |
| 2.30 | The NBN Species Dictionary Project - creating an electronic, flexible, species nomenclature for the UK. John Tweddle and Charles Hussey (Natural History Museum) |
| 3.00 | Automated extraction of biodiversity data from monographs using XML parsing. Gordon Curry (Glasgow) |
| 3.30 | Coffee/tea break |
| Session 4: Breakout sessions | |
| 4.00 | e-Biodiversity concepts and themes discussion. Suggested discussion topics: (1) taxonomy and classification, (2) data storage and access, (3) data analysis, methods and models and (4) data input (5) data output/visualisation and how to inform policy (6) data standrds |
| 5.00 | Reporting back |
| 5.30 | Close and book in to accommodation |
| 7.00 | Drink reception |
| 7.30 | Workshop dinner |
| Session 5: Alternative views of e-Biodiversity | |
| 9.30 | Recording - the politics and policy" by Sarah Whild, and The Nature of the Data by Alex Lockton (BSBI) |
| 9.50 | Phylogeographical Information Science. David Kidd (St Andrew's) |
| 10.10 | Cataloguing our Complete Genome Collection.[ppt] Dawn Fields (CEH) |
| 10.30 | Palaeontological collection curation databases - a source for biodiversity studies? Mike Howe (BGS) |
| 10.50 | Biodiversity Informatics for species recording. Stewart Thompson and Ian Ruddy |
| 11.10 | Coffee/tea break |
| Session 6: Breakout session: A roadmap for e-Biodiversity | |
| 11.40 | Breakout discussion |
| 12.40 | Lunch |
| 1.40 | General discussion and closing remarks |
| 2.30 | Close |
The main meetings of the workshop, and lunches, will be held in Pavillion A of the Centre for Mathematical Sciences Cambridge (main entrance shown in photograph below).
Details of the location of the meeting, including travel plans, can be obtained here.
Overnight accommodation is being provided in Queens' College Cambridge, including the conference dinner on the evening of 11 January and breakfast will also be held in Queens' College. Accommodation, meals and registration for members of the UK academic/research community will be provided free of cost.
It is anticipated that the workshop may generate interest in some follow-on activities. We will discuss the sort of follow-on activities that can be arranged, such as visits to NIEeS to demonstrate some of the escience/grid technologies and to provide help with installation and usage.
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There is no registration charge. Accommodation in College and meals (including the conference dinner) for UK academic participants will be provided with no charge. Registration is essential and must be done using our on-line form. The NIEeS will refund travel expenses. Please book early to ensure that you are able to obtain a place. In the event of any difficulty in booking, including not receiving an email confirmation within 24 hours, please email the NIEeS office. |
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For information about registration, and all other types of queries, please contact the NIEeS office in the first instance.
