Massimiliano Assante from CNR on The AGINFRA+ Virtual Research Environment (VRE). Joint Workshop on Food Risk Assessment Research & Practice 24th November 2017, Wageningen University & Research, Netherlands

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AGINFRA PLUS - Accelerating user-driven e-infrastructure innovation
in Food & Agriculture has received funding from the European Union’s
Horizon 2020 research and innovation programme under grant
agreement No 731001.
The AGINFRA+ Virtual Research
Environment (VRE)
Food Risk Assessment Research & Practice
Wageningen, Netherland | 22 NOV 2017
D4Science Operations Manager | CNR
Massimiliano Assante, PhD

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The D4Science infrastructure
Data Infrastructure
combining over 500 software components into a
coherent and centrally managed system of
hardware, software, and data resources
Data Analytics & Processing Layer (WP3)
Progress and current status

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D4Science Identity
D4Science is
• connecting +3900 scientists in 44 countries
• integrating data from +50 heterogeneous providers
• executing +50,000 models & algorithms/month
• providing access to over a billion quality records in
repositories worldwide
• operating with 99,7% service availability
D4Science hosts 100+ Virtual Research Environments to serve
the biological, ecological, environmental, social mining,
culture heritage, and statistical communities world-wide.
Data Analytics & Processing Layer (WP3)
Progress and current status

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D4Science for Geeks
• uses cloud-computing technologies to manage
+300 servers (more than 5 TB Ram, +1700 CPUs,
400 TB storage)
• is monitored via Nagios and Ganglia
• is maintained via Ansible (Application
Deployment + Configuration Management +
Continuous Delivery)
• is governed by deployment and operation policies
• has established SLA
• is operated according to defined Terms of Use
Data Analytics & Processing Layer (WP3)
Progress and current status

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Storage as Service
01/02/2018
Intr
odu
ctio
n to
Exis
ting
Tec
hno
logi
es
and
Ena
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to host and maintain data
Database
High-availability
Standard
Ready-to-use
Cloud Storage
Scalable
Reliable
Secure
Geographical DB
Scalable
OGC Standard
Privacy and Attribution

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Applications as a Service
01/02/2018
Intr
odu
ctio
n to
Exis
ting
Tec
hno
logi
es
and
Ena
6
to curate and manage data
Metadata Generation
Geospatial Data
Biodiversity Data
Statistical Data
Textual Data
Harmonization
Disambiguate
Validate
Integrate and Consistency Check
Data Exchange
OGC protocols
DarwinCore
SDMX
DublinCore

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Computing as Service
01/02/2018
Intr
odu
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n to
Exis
ting
Tec
hno
logi
es
and
Ena
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to process and extract knowledge
Scalable
Easy to Manage
Across Boundaries
Tailored
Elastic
Assignment of Computing
Assignment of Processors
Virtual Research Environment
Rich and Heterogeneous
High Throughput
Map-Reduce
Parallel R

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Born from the user needs
01/02/2018
Intr
odu
ctio
n to
Exis
ting
Tec
hno
logi
es
and
Ena
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to analyze datasets
to manage the full data life-cycle from import to validation,
curation, harmonization and publication
to reduce the costs of data maintenance
to host applications in a secure and scalable environment
to maintain and preserve data
to securely delivery data to known users
to access authoritative datasets
to mash-up data
to analyse big datasets
to validate datasets and provide a standard access to them

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Virtual Research Environment
Dat
a
Ana
lyti
cs
&
Pro
ces
sing
Lay
er
(W
to access, share and collaborate
Share
Database Tables
Workflow
Files
Communicate
Post
Comments
Likes
Organize
Dynamic VRE Creation
Secure
Policy Control

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https://aginfra.d4science.org/home
Project communication & data exchanging tools 10
SocialNetworking
Applications
Private Cloud
Storage
Activity Tracker &
WIKI
Data analytics and
processing platform

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AGINFRA VRE Page structure and Apps
Project communication & data exchanging tools 11
Posting to other VRE users
News Feed
About area
Managers &
Groups
Recent
documents
added to
VRE folder
Available
apps
VREPageandApplications

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Posting messages to other VRE users
• Paste links, attach files, use #hashtags,
mention people
Project communication & data exchanging tools 12
Attach file from Desktop
Notify VRE users (via email by default)
VREPageandApplications

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Post replies via email
• It is possible to reply to post via email
Project communication & data exchanging tools 13
Start typing your reply …
VREPageandApplications

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Top topics
Project communication & data exchanging tools 14
Top
Topics
VREPageandApplications

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VRE Members
Project communication & data exchanging tools 15
VREPageandApplications

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The Dockbar
Always on top: Home, Workspace (WS), Messages, Notifications, Search WS or
#Topic, User Profile.
Project communication & data exchanging tools 16
Workspace
HomeSocial

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Workspace
Exploring the workspace
Project communication & data exchanging tools 17

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Folders
• Private, Shared
and VRE Folders
• Managing
permissions
Links
• Sharable Link
• Public Link
• Public folder
links
File Uploads
• Multiple File
Uploads
• Drag & Drop
Worth a note
• History
• Notifications
• Versioning
Exploiting the Workspace, main features
Project communication & data exchanging tools 18
ExploitingtheWorkspace

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Messages
Project communication & data exchanging tools 19

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Notifications
Project communication & data exchanging tools 20
NotificationsPage

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User Profile
Project communication & data exchanging tools 21

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Activity Tracker integrated
Project communication & data exchanging tools 22
Fully-fledged and
customizable Redmine
instance avaibalbe by SSO
VREPageandApplications

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Integrated Wiki
Project communication & data exchanging tools 23
VREPageandApplications

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Help scientists in computational statistics experiments
Supply precooked state-of-the-art algorithms as-a-Service
Perform calculations by using Map-Reduce in a seamless
way to the users
Share input, results, parameters and comments with
colleagues by means of Virtual Research Environment
Data Analytics & Processing Layer (WP3) -
Progress and current status - M. Assante
Data Miner & Rstudio Cluster
Data
Miner
D4Science
Computational
Facilities
Sharing
Setup and execution

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CONSORTIUM
WWW.PLUS.AGINFRA.EU
Thank you! @maxassante
linkedin.com/in/maxassante