eubrazilopenbio technologies

The Technologies behind EUBrazilOpenBio Services and Tools

Leonardo Candela

National Research Council of Italy

Science as an Open Enterprise: some key sentences

• “Rapid and pervasive technological change has created new ways of acquiring, storing, manipulating and transmitting vast data volumes, as well as stimulating new habits of communication and collaboration amongst scientists.”

• R1: “Scientists should communicate the data they collect and the models they create, to allow free and open access, and in ways that are intelligible, assessable and usable for other specialists in the same or linked fields wherever they are in the world.”

EUBrazilOpenBio Technologies 2Recife, 19th Sep. 2012

The Technological Challenges

• Nowadays science is posing “systems” engineers with challenging tasks:– highly-evolving requirements;

– large scale resources and players distribution;

– heterogeneity;

• This makes standard development approaches often too expensive and not sustainable– “from-scratch” development of ad-hoc solutions

– HW investment (even if intermittently needed)

… infrastructures …


Infrastructure vs e-Infrastructures

• Science has been traditionally based on infrastructures


• e-Infrastructures are becoming popular gathering (computer) resources and exposingthem to the scientific community throughuser-friendly interfaces

An Hybrid Data Infrastructure Approach

• A facility where research resources (HW, SW, Data) can be shared and exploited on-demand

• … built on existing systems, infrastructures and repositories

• … conceived to supplement but not supplant“systems” mandates and arrangements

• … supporting an innovative application-delivery-model


Hybrid Data Infrastructure

Application #1

Application #2

Application #N

Infrastructure /system A

Infrastructure /system B

Infrastructure /system Z

…

…

data

server

service

apps

Supporting Virtual Research Environments


A Virtual Research Environment is a complete “system” consisting of hardware, data, and applications deployed to support the needs of a community of

practice and promoting an effective collaboration

Supporting Virtual Research Environments [cont.]

User uploads/selects apps

User registers/selects data sets

User exploits most suitable resources

User invites co-workers


A Virtual Research Environment is a complete “system” consisting of hardware, data, and applications deployed to support the needs of a community of practice and

promoting an effective collaboration

EUBrazilOpenBio offers apps through a software repository

EUBrazilOpenBio offers a rich array of mediators interfacing with data sources

EUBrazilOpenBiodeploys, configures, executes and monitors services

EUBrazilOpenBio controls authentication and enforces policies

Supporting two models of provision

• For end-users– A GUI-centric approach focusing

on visual interfaces for accessing Data Infrastructure facilities via a Web Browser

• For service providers– An API-Centric approach focusing

on comprehensive set specifications and methods for accessing Data Infrastructure facilities in a programmatic way


EUBrazilOpenBio Infrastructure Current Constituents

• Rely on existing European and Brazilian resources and efforts– Data Providers

• CoL, speciesLink, Brazilian Flora, GBIF, PANGAEA, Biodiversity Heritage Library, Bioline International

– Service Providers• D4Science, VENUS-C, COMPSs

– Software Providers• gCube, openModeler, USTO.RE


…

* more will come from the community *

Data Discovery and Access Facilities

• Conceived to accommodate existing data repositories“integration” and exploitation– beyond “data import”– by relying on standards and protocols (e.g. TAPIR, OAI-PMH)– aiming at reducing the costs of developing ad-hoc mediators– aiming at improving data providers service (e.g. caching, query

expansion)

• Support for a rich array of data and metadata formats– from files to tabular data and complex objects– information objects can be annotated with multiple metadata

• Cater for efficient and scalable data storage• Offering unifying views over data coming from

heterogeneous and distributed systems


Data Processing Facilities

• A comprehensive offering of computational approaches and facilities

– different computational models and platforms

• Simplifying the realisation of advanced services having computation-intensive needs (e.g. ENM service)

• Hundreds of “computers” made available to the community


What OpenBio can do for the Biodiversity Community now

• Support for the deployment and operation of multiple VREs on demand

• Amplifying data providers “markets” – E.g. by enlarging the set of data presentation “formats”

• Support Taxonomies Integration by catering for– Effectively and easily comparing checklists – Extraction of checklists from multiple data sources– Enabling users to simply upload their checklists

• Support Ecological Niche Modeling by catering for– modeling, testing and projection “as-a-Service”, directly from

the web-browser. – retrieval of occurrence points from multiple data sources and

visualisation– enabling users to use their own data– massive modeling activities by relying on distributed

computing capabilities

* live demonstration after the break *


Clips & Pointers

• EUBrazilOpenBio Gateway

portal.eubrazilopenbio.d4science.org

*** Publicly available ***

• Project Website

www.eubrazilopenbio.eu


eubrazilopenbio technologies

Documents

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data sourceseubrazilopenbio

eubrazilopenbio services

vast data volumes

complete system

research resources hw

community of practice

systems engineers