BioVeL (Biodiversity Virtual e-Laboratory) is an e-laboratory that supports research on biodiversity using large amounts of data from cross-disciplinary sources.
Near and mid-infrared spectroscopic determination of algal compositionzhenhua82
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Near and mid-infrared spectroscopic determination of algal compositionzhenhua82
The objective of this study was to evaluate whether near-infrared reflectance spectroscopy (NIRS) or mid-infrared reflectance spectroscopy (MIRS) could be used to determine the composition of algal turf scrubber samples. We assayed a set of algal turf scrubber (ATS) samples (n = 117) by NIRS, MIRS, and conventional means for ash, total sugar, mono-sugar, total N, and P content. A subset of these samples (n = 64) were assayed by conventional means, MIRS, and NIRS for total lipid and total fatty acid content. We developed calibrations using all the samples and a one-out cross-validation procedure under partial least-squares regression. This process was repeated using 75% of randomly selected samples to develop the calibration and the remaining samples as an independent test set. Results using the entire sample set demonstrated that NIRS and MIRS can accurately determine ash (r (2) = 0.994 and 0.995, respectively) and total N (r (2) = 0.787 and 0.820, respectively) content, but not phosphorus, total sugar, or mono-sugar content in ATS samples. Results using the 64 sample subset indicated that neither NIRS nor MIRS can accurately determine lipid or total fatty acid content in ATS samples.
Is Marcellus Shale Frack Wastewater More Radioactive Than Previously Thought?Marcellus Drilling News
A study by the University of Iowa researchers, titled "Understanding the Radioactive Ingrowth and Decay of Naturally Occurring Radioactive Materials in the Environment: An Analysis of Produced Fluids from the Marcellus Shale" and published in the peer reviewed journal Environmental Health Perspectives in April 2015. The research reportedly shows a new method for testing the total potential radioactivity of shale wastewater not previously considered. The chief shortcoming of the research is that it is based on a single sample from a single Marcellus Shale well.
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The cost of sequencing a genome has been dramatically reduced by several orders of magnitude in the last decade, and the natural consequence is that more and more researchers are sequencing more and more new genomes, both within populations and across species. Because individual researchers can now readily sequence many genomes of interest, the need for a universally accessible genomic curation tool logically follows. Each new exome or genome sequenced requires visualization and curation to obtain biologically accurate genomic features sets, even for limited set of genes, because computational genome analysis remains an imperfect art. Additionally, unlike earlier genome projects, which had the advantage of more highly polished genomes, recent projects usually have lower coverage. Therefore researchers now face additional work correcting for more frequent assembly errors and annotating genes split across multiple contigs.
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Perspectives on Collaborative Research Environments offered by D4ScienceFAO
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More information at: http://d4science.eu/node/173
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Biodiversity Virtual e-Laboratory (BioVeL)
1. Biodiversity Virtual
e-Laboratory
Project Overview
BioVeL is an e-laboratory that supports research
on biodiversity using large amounts of data from
cross-disciplinary sources.
Alex Hardisty
Project Coordinator
Cardiff University 1
2. Biodiversity Virtual e-Laboratory
An international network of experts connecting 2
scientific communities: ICT and biodiversity
Offers access to a variety of data processing
services, linked as ‘workflows’ for assisting
studies in biodiversity science
• You will hear about these during this
workshop
• You will be able to influence their design
Aims to foster cooperation in the community by:
• Discussing use cases
• Identifying important Web Services
• Training scientists 2
3. Biodiversity Virtual e-Laboratory
BioVeL is a powerful data processing tool
• Import data from your own research and/or from existing libraries
• Use workflows (series of data analysis steps) for data processing
• Build your own workflow by selecting and applying successive Web
services (data processing techniques)
• Access a library of workflows and re-use existing workflows
• Cut down research time and overhead expenses
Workflow for population modelling (stage-based matrix projection models)
based on Stubben and Milligan. Journal of Statistical Software, 22(11), Sept 2007
3
4. Biodiversity Virtual e-Laboratory
Showcase study 1: create a workflow*
Study on the ecological niche of the south east Asian horseshoe crab,
an endangered species:
• Import south east Asian data from external library
• Apply succession of “services” = workflow
• Result: ecological niche map
4
* courtesy Matthias Obst, University of Gothenburg, Sweden
5. Biodiversity Virtual e-Laboratory
Showcase study 2: re-use a workflow
Study on the ecological niche of the American horseshoe crab
• Import American data
• Re-use south east Asia crab study workflow
• Result: ecological niche map for American horseshoe crab
Compare the ecological niches of the south east Asian and American crabs.
Potential study of the ecological niche of an African animal
• Import African data
• Re-use horseshoe crab study workflow
• Result: ecological niche map for African animal
5
6. What does BioVeL consist of? (1)
Biodiversity Data Data Services Catalogues /
User
Repositories
xls, csv BioVeLData
REST
Manager
documents
GenBank REST
Collections
Genomic data Catalogue
REST
Taxonomic data of Life CSW
Observations GBIF REST
Spatial (Web) OGC
raster sensor nodes
data data
BioVeL REST
Collaboration GeoServer OGC
Annotations
Workflows
6
7. What does BioVeL consist of? (2)
Catalogues / Execution
Biodiversity Services
Repositories environment
Phylogenetic
BLAST,Hmmer,
Provenance
WebDaV Data
MrBayes, Management
Blast, PAML,
EMBOSS,… Taverna
Taxonomic Workbench
OpenSearch
Synonyms
Visualization
BioSTIF
Taverna
Google Refine CSW Workflow Engine
Modelling /
Authentication /
Authorisation
GeoProcessing
R Grid, Cloud, etc.
openModeller
WPS / WCPS
7
8. Service sets driven by science
• Phylogeny and metagenomics services
– Measures of genetic diversity and
adaptation to changing conditions
• Taxonomy services
– Checklists, identification, data cleaning, ...
• Niche and population modelling services
– Processes of conservation and invasive
species management
• Ecosystem functionality and valuation
services
– Modelling of ecosystem services and CO2
sequestration
8
• Visualization and geospatial
9. Biospheric CO2 sequestration (1)
SCIENCE & POLICY CONTEXT
Emission is continuously increasing – 10 GtC in 2010
Sequestration is the only sustainable
process to mitigate
Terrestrial Sequestration highly depends
on land use & climate change
SCIENTIFIC CHALLENGES
Model improvement
Model & data downscaling
Model verification
>> data-model calibration
>> higher processing capacity
9
10. Biospheric CO2 sequestration (2)
REVIEW IN PROGRESS
Collected papers 39
Selected and annotated papers 35
MOST RELEVANT RESEARCH GROUPS/PROJECTS
The Global Carbon Project, Fluxnet – eddy covariance tower
measurements, GHG Europe, ICOS, NTSG (University Montana)
and Biome-BGC users & developers worldwide
Biome-BGC is a computer model that estimates fluxes and storage of energy,
water, carbon, and nitrogen for the vegetation and soil components of
terrestrial ecosystems.
TYPICAL „WORKFLOWS” around Biome-BGC
Weather to Biome-BGC; Biome-BGC CARBON; Biome-BGC
Sensitivity Analysis; Biome-BGC Data-Model Harmonization
WEB SERVICES
no such kind of services operating yet
new service sets identified and prioritised to develop:
4 data retrieval services 10
6 Biome-BGC modelling services
11. Ecosystem functioning / valuation (1)
SCIENCE & POLICY CONTEXT
„Over the past 50 years, humans have changed ecosystems more
rapidly and extensively than … this has resulted in a substantial and
largely irreversible loss in the diversity of life on Earth.”
„… degradation of many ecosystem services [causes] increased risks
of nonlinear changes …”
„… reversing the degradation of ecosystems while meeting
increasing demands for their services can be partially met under some
scenarios …, but these involve significant changes in policies, institutions,
and practices that are not currently under way.” MEA 2005
SCIENTIFIC CHALLENGES
Role of biodiversity and community ecology in ecosystem functioning
How productive and effective are various ecosystem services (ES)
- maintaining hydrologic cycles, regulating climate, cleansing air/water
Trade offs between ecosystem functions and management regimes
>> quantify ecosystem functioning
>> develop ecosystem service indicators
11
>> potential of metagenomics in ES valuation
12. Ecosystem functioning / valuation (2)
REVIEW IN PROGRESS
Collected papers 14 (will be completed)
Selected and annotated papers -
MOST RELEVANT RESEARCH GROUPS/PROJECTS
not evaluated yet
TYPICAL „WORKFLOWS”
calculating ecosystem service indicators based on model simulation
… will be completed
WEB SERVICES
no such kind of applicable services operating yet
new service sets identified and prioritised to develop:
2 services for Stand level Ecosystems Service Indicators (SESSI)
2 services for Landscape level ES Indicators (LESSI)
TAXO, NICHE, META & POP services also need to be considered
12
13. Invasive species management (1)
SCIENCE & POLICY CONTEXT
Invasions of alien species are a leading cause of biodiversity loss
and related economic damages. They degrade ecosystem services,
generate human health problems and impact outdoor recreation
...
SCIENTIFIC CHALLENGES
Risk assessment as climate change proceeds
and considering the effect of different human activities
Simulating pest control or mitigation strategy options
>> ecological niche modelling (ENM)
13
14. Invasive species management (2)
REVIEW IN PROGRESS
Collected papers 9 (will be completed)
Selected and annotated papers -
MOST RELEVANT RESEARCH GROUPS/PROJECTS
GISIN – Global Invasive Species Information Network
and … but not evaluated yet
TYPICAL „WORKFLOWS”
Ecological Niche Modelling of (potential) invasive alien
species
Ecological Niche Modelling of (forest) pest species
…
WEB SERVICES
openModeller service with environmental data layers
TAXO, NICHE, …
14
15. Biodiversity Virtual e-Laboratory
BioVeL is a consortium of 15 partners from 9 countries
1. Cardiff University, UK – Coordinator
2. Centro de Referência em Informação
Ambiental, Brazil
3. Foundation for Research on Biodiversity,
France
4. Fraunhofer-Gesellschaft, Institute IAIS,
Germany
5. Free University of Berlin – Botanical
Gardens and Botanical Museum, Germany
6. Hungarian Academy of Sciences Institute of
Ecology and Botany, Hungary
7. Max Planck Society, MPI for Marine
Microbiology, Germany
8. National Institute of Nuclear Physics, Italy
9. National Research Council: Institute for
Biomedical Technologies and Institute of
Biomembrane and Bioenergetics, Italy
10. Netherlands Centre for Biodiversity (NCB 13. University of Eastern Finland, Finland
Naturalis), The Netherlands 14. University of Gothenburg, Sweden
11. Stichting European Grid Initiative, 15. University of Manchester, UK
The Netherlands
12. University of Amsterdam, Institute of
Biodiversity and Ecosystem Dynamics,
The Netherlands
15
16. Supported by many friends
• Become a ‘Friend of BioVeL’
– Deploy robust (Web) services for
biodiversity analysis and workflow
– Encourage adoption of the workflow
approach towards processing and
analysis of biodiversity data 16
17. Fits in a portfolio of initiatives
NoE: ALTER-Net, EDIT/PESI, LTER-Europe, EuroMarine, etc.
Projects: agINFRA, Aquamaps, ArtDataBanken, BioFresh, Envri,
EU BON, EUBrazilOpenBio, Fauna Iberica, iMarine, MicroB3,
OpenPlantBio, ViBRANT
Global: Catalogue of Life, COOPEUS, CReATIVE-B, EoL, GBIF, GSC
Biodiversity WG, TreeBase, and many more
Recognised as providing an
important contribution of
infrastructure
17
18. • Exploring patterns of biodiversity and
processes of biodiversity across time and
space and scales
Genetic <-> Species <-> Ecosystem<-> Landscape
A Systems approach
• A European Research Infrastructure
– Distributed observatories / sensors
– Databases, processing and analytical tools
– Computational capability and capacity
– Collaborative environments
– Support, training, partnering, fellowship
– Open access, single portal
1995 2005 2008 2011 2016
Operation &
Earlier projects Conceive Preparations Construction
19 5+2 Evolution
€5m ~ €234m
19. LifeWatch as a distributed
research infrastructure
Independent
entities contributing to
LifeWatch operations
Distributed core
operations
owned by
LifeWatch
20. LifeWatch as a distributed
research infrastructure
Independent
entities contributing to
LifeWatch operations
National contributions
• Belgium
Distributed core
operations
• Hungary
owned by
LifeWatch
• Italy
• Netherlands
Core operations • Romania
• BioVeL • Spain
• European Taxonomic Backbone • Sweden
• Other ICT Core elements
Thematic contributions
• Population biology of migrating birds
• Understanding the role of marine wetlands on biodiversity migration patterns
• Impacts of invading alien species
• Assessment of regional biodiversity
• Preservation of ecosystem services (curing habitat destruction)
• Human observations of biodiversity
21. Finally ... ...
• White Paper initiative
– Our community vision for biodiversity
informatics, to inform Horizon 2020
– http://is.gd/WhitePaperChapters
• Now,
– Listen, enjoy the presentations
– Network and socialise
– Express your opinions and influence
our work for the next months 22
22. Biodiversity Virtual e-Laboratory
BioVeL is funded by the European Commission
7th Framework Programme (FP7).
It is part of its e-Infrastructures activity.
Under FP7, the e-Infrastructures activity is part of the Research Infrastructures programme,
funded under the FP7 'Capacities' Specific Programme. It focuses on the further development
and evolution of the high-capacity and high-performance communication network (GÉANT),
distributed computing infrastructures (grids and clouds), supercomputer infrastructures,
simulation software, scientific data infrastructures, e-Science services as well as on the
adoption of e-Infrastructures by user communities.
BioVeL is free and available via internet.
www.biovel.eu, contact Alex Hardisty: HardistyAR@cardiff.ac.uk
23
Editor's Notes
BioVeLfocusses on:DNA sequence-based phylogeny and metagenomics services that help link knowledge of model organisms to a broad range of species, that provide a measure of genetic diversity used in conservation planning and that help to understand adaptation in relation to climate change;Taxonomy services to provide the underpinning checklist of diversity in Europe, identification aids to native, invasive and economic species; Niche and population modelling for species, to better understand the processes of conservation and invasive species management; and, Ecosystem functionality and valuation services, to improve modelling capabilities to ecosystem services and CO2 sequestration.
Terrestrial sequestration is also increasing, but only 26% of the total emission, oceans can eliminate about 24%About 50% of the total emission remains and accumulates in the atmosphere --- In 2010REF: Global Carbon Project 2010; Updated from Le Quéré et al. 2009, Nature Geoscience; Canadell et al. 2007, PNAS
Fluxnet –coordinates regional and global analysis of observations from micrometeorological tower sites. The flux tower sites use eddy covariance methods to measure the exchanges of carbon dioxide (CO2), water vapor, and energy between terrestrial ecosystems and the atmosphere. NTSG : Numerical Terradynamic Simulation GroupGHG-Europe : Greenhouse Gas management in European land use systems
„Over the past 50 years, humans have changed ecosystemsmore rapidly and extensively than in any comparable period oftime in human history, largely to meet rapidly growing demands forfood, fresh water, timber, fiber, and fuel. This has resulted in a substantialand largely irreversible loss in the diversity of life on Earth.”Millenium Ecosystem Assessment 2005Challenges:Role of biodiversity and community ecology in ecosystem functioning2. "How much are the productivity and other services of the ecosystems in given ecological circumstances and management regimes? - maybe it would be better (provoking) to say "How much (and what measure) are the other ecosystem services than productivity?" - Because we know a lot about productivity of different type of ecosystems (easy to measure in agroecosystems, not so easy to measure/estimate in natural ecosystems), but what about other ecosystem services such as maintaining hydrologic cycles, regulating climate, cleansing air and water, maintaining atmospheric composition, pollination, soil genesis, storing and cycling of nutrients ...3. "What is the trade off among different ecosystem functions and management regimes in various ecosystems at landscape levels?" - mostly if we consider extensive and/or sustainable agriculture and/or various mosaic of landuse patterns, not massive uniform large croplands ...