Presentation at Digital Infrastructures for Research Conference, Oct. 9, 2019 by Sorina Pop from CNRS.

1. @openaire_eu
Open Science for the
Neuroinformatics community
Sorina Pop, Axel Bonnet, Camille Maumet, Michael Kain,
Christian Barillot, Tristan Glatard
DI4R | Lisbon| 9 - 11 October 2018

2. •Context
• Growing number of platforms and tools to store and process data
• Technological fragmentation and lack of interoperability
•Aims
• Cross-platform interoperability for scientific app, data sharing and processing
• Open and reproducible science
•Proposed solutions
• CARMIN API for platform interoperability (e.g., VIP and Shanoir)
• Boutiques tools to describe, publish, integrate and execute command-line
applications across platforms
• Open Science publishing and OpenAire Connect tools as-a-Service
Interoperability and Open Science

3. SHAring NeurOImaging Resources
An open source web platform for neuro-imagingDownload
stored data
Support for
processed
(derived) data
Online
Visualization of
stored data
Data de-identification
and patient privacy
Download
Processed data
Support for multi-
centric research
studies
User access
control
Support for clinical and
neuropsychological scores
Web
Portal
Collect neuroimaging data from several
sources :
• Dicom CD / DVD
• PACS (via Dicom Q& R)
• Nifti / Analyze image files
a model build on an formal
ontology to
• Enhance data integrity
• Structure the data
• Manage data provenance
• Facilitate collaborative research
• Pool resources

4. Web portal
Users
1000+ registered users in October 2018
44 publications since 2011
Neuro-image analysisCancer therapy simulation
Prostate radiotherapy plan simulated
with GATE(L. Grevillot and D. Sarrut)
Image simulation
Echocardiography simulated with
FIELD-II (O. Bernard et al)
Modeling and optimization of
distributed computing systems
Acceleration yielded by non-clairvoyant
task replication (R. Ferreira da Silva et al)
Brain tissue segmentation
with Freesurfer
Scientific applications
Infrastructure
Supported by EGI Infrastructure
Uses biomed VO (~65 sites in Europe and beyond)
230 cumulated CPU years utilized by VIP applications in 1 year
DIRAC
France-Grilles
Application as a service
File transfer to/from grid
Virtual Imaging Platform (VIP)
https://vip.creatis.insa-lyon.fr

5. @openaire_eu
What about interoperability?
Could these platforms work
together?

6. CARMIN
● CARMIN is an API that enables
communication between services
● Interoperability among data (Shanoir)
and computing platforms (VIP)
● Example: get all VIP functionalities
from the Shanoir interface
● Launch and monitor executions
● Consult the results
Medical database
Neuro.nii
Launch Freesurfer
segmentation on VIP
Usage example

7. • Describe, publish, integrate and
execute command-line applications
across platforms
– facilitate application porting
– import and exchange of applications
– open and reproducible science
• Versatile JSON format to describe the
command-line, inputs and outputs
• Use of Linux containers to facilitate
application installation and sharing
• https://github.com/boutiques
Example of a simple Boutiques descriptor
Boutiques

8. Web
portal
Users
Application
importer
Give Boutiques application
descriptor
Launch application
Vip admin
CARMIN
API
External Tool
Launch application
from an other tool
Send CARMIN
requests
Storage tools
CARMIN
API
CARMIN
API
Fetch external
data
Application
Runner
EGI
VIP
Icons by Paomedia / CC BY
Local
resources

9. @openaire_eu
How does all this link to
OpenAIRE-Connect?

10. Dashboard for Research Communities
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fund
Harvest Harmonize
Deduplicate Inference
Repositories of publications, datasets, projects, methods, packages
Research Community Service
Research
Community
Operator
Researchers
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• Deposit (DOI)
• Claim
• Stats: research impact & OA
• Manage users
• Configure stats
• Configure inference
fund
Crédits: OpenAire Connect

11. • Become providers/repositories from which OpenAire
Connect can harvest software (Boutiques pipelines,
Dockers, etc) and data
• Upload such products to Zenodo (and get a DOI)
• Boutiques implements “bosh publish” to Zenodo
with support for tags
• Enable interoperability and reproducibility
VIP and Shanoir CAN

12. Neuro pipelines in Zenodo

13. Thank you!
Sorina POP
sorina.pop@creatis.insa-lyon.fr

14. • Represented by members of the France Life Imaging (FLI)
collaboration
• Focus on e-infrastructure services to enable
interoperability between in-vivo image acquisition
platforms at National and international level (EGI)
• Use OpenAIRE-Connect services and promote their
adoption across neuroinformatics scientists
• Generate and share packages of research artefacts
Neuroinformatics community