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Exploitation opportunities

Pasquale Pagano (CNR)
iMarine Technical Director
pasquale.pagano@isti.cnr.it
Outline
The Infrastructure
• Heterogeneous resources as a service
• Data Bonanza
• Virtual Research Environment
• Software platform
iMarine Catalogue
• StatsCube
• GeosCube
• BiolCube
• ConnectCube
I-MARINE EXTENDED BOARD

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Distinguishing capabilities of the iMarine e-infrastructure and its
enabling software

THE INFRASTRUCTURE

I-MARINE EXTENDED BOARD

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Concepts
The initiative
(the visionary leadership)

The e-infrastructure
(the operational platform)

The system
(the enabling sw system)
I-MARINE EXTENDED BOARD

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e-Infrastructure

Geographically
Distributed
Computing
Infrastructure

Service
Allocations,
Deployment,
Monitoring, and
Operation

Across
administrative
boundaries
Across private and
commercial
providers

Uniform resource
and data access

I-MARINE EXTENDED BOARD

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Infrastructure: key characteristics
• Efficient and tailored storage technologies
• Computational environments dealing with the volume
of the data
• Elastic management of the resources, monitoring,
alerting, recovery
• Collaborative environment to support scientific
communities
• Rich portfolio of applications to perform access,
validation, enriching, processing, sharing, and mash-up
of data
I-MARINE EXTENDED BOARD

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Infrastructure: Storage as Service
• Secure
• Fault-tolerant
• Replication

• Open source
RDBMS
• Up to 1 TB data

Virtual
Workspace

Relational
Databases

45 TB Currently Used
Spatial
Database

Large and
Active data
storage

• ISO
19115/10139
Metadata
• Catalogue

• Scalability and
high availability
• Across sites

I-MARINE EXTENDED BOARD

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330 Cores Currently Allocated

Infrastructure: Computing as Service

Hadoop

• MapReduce

Statistical
Manager

• Analysis/clustering/modeling

R clusters

• Windows and Linux

I-MARINE EXTENDED BOARD

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Infrastructure: Management as Service
Operation Machine readable SLAs
Machine readable monitoring, auditing, billing,
reporting, and notification
Machine readable resource/performance capabilities
description

Trust

Privacy, governance, and attribution

Security, trusted network

I-MARINE EXTENDED BOARD

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Infrastructure: Collaborative Environment
The Social Portal offers a familiar view of what is
happening on their VREs
A single place to
• Get status and updates from applications and other users they are interested in;
• Get notifications about messages, jobs completion, new generated products, etc.

I-MARINE EXTENDED BOARD

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Infrastructure: Collaborative Environment
The Social Portal offers a familiar view of what is
happening on their VREs
A single place to
• Manage all the portal extension.

W rk p Ms ags o atio sP e
o s ac es eNtific n ag
e

Se hiny u W rk p e
arc o r o s ac

H m So ial
oe c

I-MARINE EXTENDED BOARD

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Infrastructure: Collaborative Environment
The Social Portal offers a familiar view of what is
happening on their VREs
A single place to
• Manage data, store and preserve them
• Share data

I-MARINE EXTENDED BOARD

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Google Analytics iMarine portal

I-MARINE EXTENDED BOARD

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Data Bonanza
OBIS
WoR
MS

…

Data.
FAO

Validation

WoR
DS
Private
Cloud

EuroS
tat
Sharing

iMarine
iMarine
Registries

GBIF
Enriching

Commercial
Cloud

WOA

MyOc
ean

CoL

Processing
ITIS
NCBI

IRMN
G

I-MARINE EXTENDED BOARD

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Data Bonanza
SDMX *
- FAO CodeLists
- IRD CodeLists
- FAO Global
Aquaculture
Production
- FAO Global Capture
Production
- FAO Global
Production
- Eurostat
- …

Statistical

Biodiversity

Geospatial

DarwinCore / ISO19139
>35 M Observations (OBIS)
≈ 120 K Observed Species
(OBIS)
≈ 500 K Taxa (WoRMS)
>600 K Scientific Names
(ITIS)
>12 K Species Distribution
Maps (AquaMaps)
≈ 600 Species Extent (FAO)
… FishBase, SeaLifeBase
… CoL, GBIF

> 300
variables

ISO19139 (OGC W*S)
10 years Chemical and Physical variables in 2D space
Ice concentration and velocity, Chlorophyll, Oxygen, Nitrate, Phosphate,
Phytoplankton as carbon, Salinity, Temperature, …
On-demand Chemical and Physical variables in 3D space
Apparent Oxygen Utilization, Dissolved Oxygen, Salinity, Temperature, …
I-MARINE EXTENDED BOARD

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Not Only Access
• Access
– Retrieval of geospatial data as
space/time-varying phenomena
– Direct fine-grained access to feature
and feature property level.
• Validation
– User-defined quality and dissemination level

• Enriching
– Generation metadata, exploitation of reference data, linking to
environmental dataset

• Processing
– Analysis and mining exploiting e.g. R, Weka and RapidMiner
statistical frameworks

• Sharing
– User-driven process to decide how other agents (human / machine)
can access information
I-MARINE EXTENDED BOARD

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Features Clustering with StatsCube
Presence
Points
(FishBase
+
Obis)

Density Based Clustering
DBSCAN
(with outliers)

Other methods are also
available …

K-Means
X-Means
I-MARINE EXTENDED BOARD

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Ecological Modeling with BiolCube

I-MARINE EXTENDED BOARD

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Maps Comparison with GeosCube

MEAN=0.81
VARIANCE=0.02
NUMBER_OF_ERRORS=6691
NUMBER_OF_COMPARISONS=259200
ACCURACY=97.42
MAXIMUM_ERROR=1.0
MAXIMUM_ERROR_POINT=3005:363:1
COHENS_KAPPA=0.218
COHENS_KAPPA_CLASSIFICATION_LANDIS_KOCH=Fair
COHENS_KAPPA_CLASSIFICATION_FLEISS=Marginal
TREND=EXPANSION
RESOLUTION=0.5

FAO Eleutheronema tetradactylum
VS
AquaMaps Eleutheronema tetradactylum

I-MARINE EXTENDED BOARD

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Not Only Access, Validation, Enriching,
Processing, Sharing
• It is always possible to save the discovered
data in various Standard formats
• It is always possible to collaborate with coworkers through a dedicated workspace.
• Mash-up data across diversity
– Accessing statistical datasets in SDMX, geo-referencing
them, describing them in ISO19139, and making them
available via OGC W*S standard protocols
– Accessing species observation datasets in DwC, analysing
their distribution trend via R, and projecting them in
geographical space
– Accessing species taxonomies in DwCA and publishing
them as reference data in SDMX
I-MARINE EXTENDED BOARD

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Data Bonanza: a common vision
Integrate and harmonize crossdisciplinary data and information
across information systems and
workflows to support evidence-based
decision making
iMarine is implementing this vision through the
adoption of Standards, the identification of
common Methods and the implementation of
Tools which enable integration and
harmonization.
I-MARINE EXTENDED BOARD

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Is this enough?
• An ecosystem of
participatory data eInfrastructures
• Regulated by policies
• Enabled by standards
• Promoting not only
access but mash-up of
heterogeneous data

User centric
I-MARINE EXTENDED BOARD

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User-Centric View
User-centric view of an ecosystem of
participatory data e-Infrastructures to
• Cope with the overwhelming amount of data
and capacities
• Promote re-use of data
• Encourage sharing of resulting products
User-centric and workflow-oriented

I-MARINE EXTENDED BOARD

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Virtual Research Environment
iMarine is user-centric and workflow-oriented thanks to
the gCube VRE technology
Virtual Research Environment (VRE) is
• a distributed and dynamically created environment
• where subset of data, services, computational, and
storage resources
• regulated by tailored policies
• are assigned to a subset of users via interfaces
• for a limited timeframe
• at little or no cost for the providers of
the participatory data e-infrastructures
L. Candela, D. Castelli, P. Pagano (2013) Virtual Research Environments: An Overview and a
Research Agenda. Data Science Journal, Vol. 12
I-MARINE EXTENDED BOARD

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Flexible

Software Platform

Software platform to
abstract over differences
in location, protocols,
and models by

keeping failures partial and
temporary,

Storage, Discovery, Indexing,
Search, Execution, …

reacting to and recovering from
a large number of potential
issues.

I-MARINE EXTENDED BOARD

Feature-rich
Feature-rich

scaling no less than the
interfaced resources,

It turns resources and
technologies into a utility
by offering a single
registration, monitoring,
and access facilities

25
Software Platform

I-MARINE EXTENDED BOARD

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iMarine Exploitation models
Service

Data hosting

Infrastructure

Unlimited users, Infrastructure support, helpdesk, back-up, security
Validation (records)

Workspace

Hardware

Default Processing (<1MB)

Social Tool

Community Management

Storage 1TB

Cloud Resources

Validation (Datasets)

Custom Data Resources

Custom Processing (> 1MB)

Spatial Data integration

User Management

Large and Active Storage

Unlimited VRE’s

Hour/Day

Month

Year

27
Concept map of the products

I-MARINE OFFER

I-MARINE EXTENDED BOARD

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Application Bundles
Management and interpretation of biological and
ecological data in the environment
Complete full life-cycle data framework, from
observational data to aggregated data repositories
enriched with validation and analytical tools
Storage and interpretation of geospatial explicit
information, including WPS processing

Flexible sharing, storage, reporting, search and
retrieval, aggregation and projection facilities

I-MARINE EXTENDED BOARD

A BUNDLE is
a set of
services and
technologie
s grouped
according to
a family of
related
tasks for ac
hieving a
common
objective

29
Discussion time
Thank you
for your attention

www.i-marine.eu
I-MARINE EXTENDED BOARD

30

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iMarine exploitation opportunities

  • 1. Exploitation opportunities Pasquale Pagano (CNR) iMarine Technical Director pasquale.pagano@isti.cnr.it
  • 2. Outline The Infrastructure • Heterogeneous resources as a service • Data Bonanza • Virtual Research Environment • Software platform iMarine Catalogue • StatsCube • GeosCube • BiolCube • ConnectCube I-MARINE EXTENDED BOARD 2
  • 3. Distinguishing capabilities of the iMarine e-infrastructure and its enabling software THE INFRASTRUCTURE I-MARINE EXTENDED BOARD 3
  • 4. Concepts The initiative (the visionary leadership) The e-infrastructure (the operational platform) The system (the enabling sw system) I-MARINE EXTENDED BOARD 4
  • 6. Infrastructure: key characteristics • Efficient and tailored storage technologies • Computational environments dealing with the volume of the data • Elastic management of the resources, monitoring, alerting, recovery • Collaborative environment to support scientific communities • Rich portfolio of applications to perform access, validation, enriching, processing, sharing, and mash-up of data I-MARINE EXTENDED BOARD 6
  • 7. Infrastructure: Storage as Service • Secure • Fault-tolerant • Replication • Open source RDBMS • Up to 1 TB data Virtual Workspace Relational Databases 45 TB Currently Used Spatial Database Large and Active data storage • ISO 19115/10139 Metadata • Catalogue • Scalability and high availability • Across sites I-MARINE EXTENDED BOARD 7
  • 8. 330 Cores Currently Allocated Infrastructure: Computing as Service Hadoop • MapReduce Statistical Manager • Analysis/clustering/modeling R clusters • Windows and Linux I-MARINE EXTENDED BOARD 8
  • 9. Infrastructure: Management as Service Operation Machine readable SLAs Machine readable monitoring, auditing, billing, reporting, and notification Machine readable resource/performance capabilities description Trust Privacy, governance, and attribution Security, trusted network I-MARINE EXTENDED BOARD 9
  • 10. Infrastructure: Collaborative Environment The Social Portal offers a familiar view of what is happening on their VREs A single place to • Get status and updates from applications and other users they are interested in; • Get notifications about messages, jobs completion, new generated products, etc. I-MARINE EXTENDED BOARD 10
  • 11. Infrastructure: Collaborative Environment The Social Portal offers a familiar view of what is happening on their VREs A single place to • Manage all the portal extension. W rk p Ms ags o atio sP e o s ac es eNtific n ag e Se hiny u W rk p e arc o r o s ac H m So ial oe c I-MARINE EXTENDED BOARD 11
  • 12. Infrastructure: Collaborative Environment The Social Portal offers a familiar view of what is happening on their VREs A single place to • Manage data, store and preserve them • Share data I-MARINE EXTENDED BOARD 12
  • 13. Google Analytics iMarine portal I-MARINE EXTENDED BOARD 13
  • 15. Data Bonanza SDMX * - FAO CodeLists - IRD CodeLists - FAO Global Aquaculture Production - FAO Global Capture Production - FAO Global Production - Eurostat - … Statistical Biodiversity Geospatial DarwinCore / ISO19139 >35 M Observations (OBIS) ≈ 120 K Observed Species (OBIS) ≈ 500 K Taxa (WoRMS) >600 K Scientific Names (ITIS) >12 K Species Distribution Maps (AquaMaps) ≈ 600 Species Extent (FAO) … FishBase, SeaLifeBase … CoL, GBIF > 300 variables ISO19139 (OGC W*S) 10 years Chemical and Physical variables in 2D space Ice concentration and velocity, Chlorophyll, Oxygen, Nitrate, Phosphate, Phytoplankton as carbon, Salinity, Temperature, … On-demand Chemical and Physical variables in 3D space Apparent Oxygen Utilization, Dissolved Oxygen, Salinity, Temperature, … I-MARINE EXTENDED BOARD 15
  • 16. Not Only Access • Access – Retrieval of geospatial data as space/time-varying phenomena – Direct fine-grained access to feature and feature property level. • Validation – User-defined quality and dissemination level • Enriching – Generation metadata, exploitation of reference data, linking to environmental dataset • Processing – Analysis and mining exploiting e.g. R, Weka and RapidMiner statistical frameworks • Sharing – User-driven process to decide how other agents (human / machine) can access information I-MARINE EXTENDED BOARD 16
  • 17. Features Clustering with StatsCube Presence Points (FishBase + Obis) Density Based Clustering DBSCAN (with outliers) Other methods are also available … K-Means X-Means I-MARINE EXTENDED BOARD 17
  • 18. Ecological Modeling with BiolCube I-MARINE EXTENDED BOARD 18
  • 19. Maps Comparison with GeosCube MEAN=0.81 VARIANCE=0.02 NUMBER_OF_ERRORS=6691 NUMBER_OF_COMPARISONS=259200 ACCURACY=97.42 MAXIMUM_ERROR=1.0 MAXIMUM_ERROR_POINT=3005:363:1 COHENS_KAPPA=0.218 COHENS_KAPPA_CLASSIFICATION_LANDIS_KOCH=Fair COHENS_KAPPA_CLASSIFICATION_FLEISS=Marginal TREND=EXPANSION RESOLUTION=0.5 FAO Eleutheronema tetradactylum VS AquaMaps Eleutheronema tetradactylum I-MARINE EXTENDED BOARD 19
  • 20. Not Only Access, Validation, Enriching, Processing, Sharing • It is always possible to save the discovered data in various Standard formats • It is always possible to collaborate with coworkers through a dedicated workspace. • Mash-up data across diversity – Accessing statistical datasets in SDMX, geo-referencing them, describing them in ISO19139, and making them available via OGC W*S standard protocols – Accessing species observation datasets in DwC, analysing their distribution trend via R, and projecting them in geographical space – Accessing species taxonomies in DwCA and publishing them as reference data in SDMX I-MARINE EXTENDED BOARD 20
  • 21. Data Bonanza: a common vision Integrate and harmonize crossdisciplinary data and information across information systems and workflows to support evidence-based decision making iMarine is implementing this vision through the adoption of Standards, the identification of common Methods and the implementation of Tools which enable integration and harmonization. I-MARINE EXTENDED BOARD 21
  • 22. Is this enough? • An ecosystem of participatory data eInfrastructures • Regulated by policies • Enabled by standards • Promoting not only access but mash-up of heterogeneous data User centric I-MARINE EXTENDED BOARD 22
  • 23. User-Centric View User-centric view of an ecosystem of participatory data e-Infrastructures to • Cope with the overwhelming amount of data and capacities • Promote re-use of data • Encourage sharing of resulting products User-centric and workflow-oriented I-MARINE EXTENDED BOARD 23
  • 24. Virtual Research Environment iMarine is user-centric and workflow-oriented thanks to the gCube VRE technology Virtual Research Environment (VRE) is • a distributed and dynamically created environment • where subset of data, services, computational, and storage resources • regulated by tailored policies • are assigned to a subset of users via interfaces • for a limited timeframe • at little or no cost for the providers of the participatory data e-infrastructures L. Candela, D. Castelli, P. Pagano (2013) Virtual Research Environments: An Overview and a Research Agenda. Data Science Journal, Vol. 12 I-MARINE EXTENDED BOARD 24
  • 25. Flexible Software Platform Software platform to abstract over differences in location, protocols, and models by keeping failures partial and temporary, Storage, Discovery, Indexing, Search, Execution, … reacting to and recovering from a large number of potential issues. I-MARINE EXTENDED BOARD Feature-rich Feature-rich scaling no less than the interfaced resources, It turns resources and technologies into a utility by offering a single registration, monitoring, and access facilities 25
  • 27. iMarine Exploitation models Service Data hosting Infrastructure Unlimited users, Infrastructure support, helpdesk, back-up, security Validation (records) Workspace Hardware Default Processing (<1MB) Social Tool Community Management Storage 1TB Cloud Resources Validation (Datasets) Custom Data Resources Custom Processing (> 1MB) Spatial Data integration User Management Large and Active Storage Unlimited VRE’s Hour/Day Month Year 27
  • 28. Concept map of the products I-MARINE OFFER I-MARINE EXTENDED BOARD 28
  • 29. Application Bundles Management and interpretation of biological and ecological data in the environment Complete full life-cycle data framework, from observational data to aggregated data repositories enriched with validation and analytical tools Storage and interpretation of geospatial explicit information, including WPS processing Flexible sharing, storage, reporting, search and retrieval, aggregation and projection facilities I-MARINE EXTENDED BOARD A BUNDLE is a set of services and technologie s grouped according to a family of related tasks for ac hieving a common objective 29
  • 30. Discussion time Thank you for your attention www.i-marine.eu I-MARINE EXTENDED BOARD 30