Helping Biodiversity Researchers to do their Work

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Helping Biodiversity Researchers to do their Work

• Collaborative e-Science and Virtual Organisations
• Richard White
• Cardiff University
• r.j.white_at_cs.cardiff.ac.uk

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Biodiversity research

• Biologists are working to understand the
  adaptation of organisms to their environmental
  niche,
• eventually by combining knowledge at all the
  levels of biological organisation
• and to predict their interactions with their
  environment

• tissue
• organ
• individual whole organism
• population
• species
• evolutionary pathways

• genome
• transcription
• proteome
• metabolic pathways
• cell

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Examples of biodiversity resources

• Scientists working with biodiversity information
  employ a wide variety of resources which may be
  available on various local and remote computer
  platforms.
• Data sources
• Names Species 2000 ITIS Catalogue of Life
• Data GBIF, sequence databases
• Geography Gazetteers
• Collections and distributions BioCASE, MaNIS
• Analysis tools
• Statistical and multivariate analysis
• Modelling
• Presentation and visualisation

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Use of resources together

• Scientists frequently need to use several of
  these resources in sequence to carry out their
  research.
• When working with biodiversity data, much effort
  is currently expended in
• initially acquiring resources
• installing and sometimes adapting them to run on
  the users own machine
• converting and transporting data sets between
  stages of the analysis process

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Problem-Solving Environments

• A problem-solving environment (PSE) is a
  software workbench to help
• scientists build bigger analyses and models more
  easily, and thus
• make it easier to answer Big Questions,
  especially those with the complexity of
  biodiversity informatics
• A PSE allows the user to
• select appropriate local and remote resources
• arrange them into a workflow
• execute the workflow
• automatically manage access to the chosen
  resources
• save a workflow for modification and re-use

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The Biodiversity World (BDWorld) project

• A 3-year e-Science project funded by BBSRC (UK)
• To design, build and demonstrate a working proof
  of concept PSE with appropriate data and analysis
  resources to support biodiversity research
• 3 example applications showing how scientists can
  use it to assist biodiversity research
• Our goals are to develop and enhance this
  approach to collaborative computing and to
  encourage its wide adoption, by research in the
  areas described later

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Example Climate-space modelling

• Modelling and predicting changes in distribution
  in response to climate changes such as those
  brought about by global warming
• Steps involved
• Get current distribution of a species (e.g.
  specimen records)
• Get current or recent climate data for those
  localities
• Calculate a model for the climate space the
  species can occupy
• Predict the distribution the species would have
  in any specified climate (may be different to the
  climate used above)
• Project back on world map

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Example work-flow (Climate-space Modelling)
Submit scientific name retrieve accepted name
synonyms for species
Species 2000
Climate
Present or recent climate surfaces
Localities
ClimateSpace Model
Retrieve distribution data for species of interest
Model of climatic conditions where species is
currently found
Prediction of suitable regions for species of
interest
Prediction
Climate
Possibly different climate surfaces (e.g.
predicted climate)
Base Maps
World or regional maps
Projection
Projection of predicted distribution on to base
map
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BDWorld / Triana in operation1Workflow creation
(design, editing)
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Triana screen-shots
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Triana screen-shots
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Triana screen-shots
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Triana screen-shots
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Triana screen-shots
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Triana screen-shots
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Triana screen-shots
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BDWorld / Triana in operation 2Workflow
execution (enactment, run-time)
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Triana screen-shots
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Triana screen-shots
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Triana screen-shots
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Triana screen-shots
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Triana screen-shots
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Design of architecture

• to facilitate
• resource discovery
• semantic mediation
• workflow creation and enactment
• management of data generated by workflows, etc.

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Workflows

• Resources are called into use in an appropriate
  sequence from an interactive workflow.
• The facility for scientists to be able to create
  their own workflows, without the need for regular
  assistance from computer scientists, is an
  essential part of the BDWorld system. Accessible
  tools for resource discovery and for workflow
  design, enactment and re-use are therefore
  required.

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Difficulties with resources

• Finding the resources
• Knowing how to use these heterogeneous resources
• Originally constructed for various reasons, often
  with little attention to standards or
  interoperability
• Have to pass data sets from one to another
• Some involve user interaction

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User interface

• The drag-and-drop metaphor needs further research
  into the best ways to support
• resource discovery
• resource matching
• data management (e.g. temporary storage of
  intermediate results)
• Perhaps using a plug-in architecture, so that
  third parties can extend it as required

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Extensibility

• to allow scientific and technical users to add
  new resources to the environment, without the
  involvement of the system programmers wherever
  possible

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Flexibility

• software libraries that can be extended to
  provide interfaces to new resources, but which
  can also be configured for many common
  requirements without the need for programmed
  extensions

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Intelligent agents

• mediation or facilitation to manage the semantic
  heterogeneity encountered in all aspects of the
  PSE, including the names of organisms and their
  components, resolution of geographical data, etc.

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Virtual Organisations

• The facilities described so far can be used by a
  single scientist working on their research.
• By adding additional functionality to the PSE, it
  can be used to support collaboration between
  scientists in virtual organisations.

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Security and authentication

• the PSE and all the relevant resources and
  results will be
• accessible with a single log-on
• can be shared with other members of a virtual
  organisation

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Management

• Mechanisms for managing the experiments and
  analyses which the workflows represent, including
  
• maintenance of logs and provenance information,
• distributed storage of intermediate data sets,
  etc.,
• to reduce the burden on the scientists and
  increase their productivity. This
• (not only) helps individual scientists look after
  their own data and results
• (but also) imposes order and helps scientists
  collaborate in the same or linked analyses

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Role of metadata

• Metadata is needed to enable discovery of
  resources and to indicate how they are to be
  used.
• Properties to help locate appropriate resources
• Check interoperability, suggest transformations
• Provenance of data sets
• Log of work-flows executed

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Knowledge-base

• Metadata, thesaurus and knowledge management to
  support the facilities described above, in which
  provenance data and biodiversity-specific
  knowledge are recorded, maintained, and used by
  other components of the PSE.
• In addition, it can translate between different
  terminology as used by different scientists
  trying to collaborate
• For example, by providing concept-based
  cross-mapping between alternative taxonomies as
  described by Andrew Jones

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A dream

• A desktop environment in which scientists can
  drag and drop data sources, analysis and
  modelling tools, and visualisation interfaces
  into a desired sequence of operations which can
  be run automatically.
• BDWorld is just about at this stage at present.
• With the additional features described above,
  such an environment could be made richer, easier
  to use, more productive, and support research
  groups.
• Something like a component-based visual
  programming environment.
• Not just for biodiversity!

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Summary

• Problem-solving Environment
• Architecture
• User interface
• Extensibility
• Virtual organisations
• Managing use of workflows and results
• Knowledge-base

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Acknowledgements

• BBSRC (UK)
• Collaborators in the BDWorld project
  Universities of Reading and Southampton Natural
  History Museum (London)
• Organisations that have co-operated with these
  research projects, especially
• Species 2000
• ILDIS
• FishBase
• Hadley Centre for Climate Prediction and Research

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Merry Christmas

• And a Convergent New Year!