SlideShare a Scribd company logo
1www.esi-group.com
Copyright © ESI Group, 2018. All rights reserved.Copyright © ESI Group, 2018. All rights reserved.
www.esi-group.com
Jean-Claude BOULET
INRA - FRANCE
2www.esi-group.com
Copyright © ESI Group, 2018. All rights reserved.Copyright © ESI Group, 2018. All rights reserved.
www.esi-group.com
About chemometrics…
INFORMATIONS
ABOUT THE
SAMPLE
A SPECTRUM (e.g. NIR)
3www.esi-group.com
Copyright © ESI Group, 2018. All rights reserved.Copyright © ESI Group, 2018. All rights reserved.
www.esi-group.com
About chemometrics…
REGRESSIONS DISCRIMINANT ANALYSIS
4www.esi-group.com
Copyright © ESI Group, 2018. All rights reserved.Copyright © ESI Group, 2018. All rights reserved.
www.esi-group.com
CheMoocs:
a MOOC
about chemometrics
2016-2017-2018
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Copyright © ESI Group, 2018. All rights reserved.Copyright © ESI Group, 2018. All rights reserved.
www.esi-group.com
Several partners
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Copyright © ESI Group, 2018. All rights reserved.Copyright © ESI Group, 2018. All rights reserved.
www.esi-group.com
1- A MOOC :
« KNOWLEDGE »
2- A TOOL :
« PRACTICE »
?
7www.esi-group.com
Copyright © ESI Group, 2018. All rights reserved.Copyright © ESI Group, 2018. All rights reserved.
www.esi-group.com
Previous work : an Atoms module
in chemometrics, named FACT
8www.esi-group.com
Copyright © ESI Group, 2018. All rights reserved.Copyright © ESI Group, 2018. All rights reserved.
www.esi-group.com
Large possibilities... but issues
1- not all functions
in Scilab
(or other languages)
2- need to learn line
commands
9www.esi-group.com
Copyright © ESI Group, 2018. All rights reserved.Copyright © ESI Group, 2018. All rights reserved.
www.esi-group.com
ChemFlow:
a web application
for chemometrics
https://galaxyproject.org/
https://vm-chemflow-
francegrille.eu/
A solution with Galaxy
10www.esi-group.com
Copyright © ESI Group, 2018. All rights reserved.Copyright © ESI Group, 2018. All rights reserved.
www.esi-group.com
ChemFlow:
More detailed fields
with help
11www.esi-group.com
Copyright © ESI Group, 2018. All rights reserved.Copyright © ESI Group, 2018. All rights reserved.
www.esi-group.com
What do you need to configure
Galaxy?
- INSTALLING GALAXY
AND REMOVING THE EXISTING TOOLS
- CONFIGURING 2 OR 3 CONFIG FILES (XML)
- CREATING XML WRAPPERS
- HAVING SCILAB (OR OTHERS) TOOLS TO RUN !
12www.esi-group.com
Copyright © ESI Group, 2018. All rights reserved.Copyright © ESI Group, 2018. All rights reserved.
www.esi-group.com
Example
of a wrapper
- requirements
- Scilab command
- inputs
- Scilab script
- outputs
- help
13www.esi-group.com
Copyright © ESI Group, 2018. All rights reserved.Copyright © ESI Group, 2018. All rights reserved.
www.esi-group.com
Which languages can be
wrapped in Galaxy?
- EVERY LANGUAGE !
+ Python / C-C++ / Pearl / Java ...
14www.esi-group.com
Copyright © ESI Group, 2018. All rights reserved.Copyright © ESI Group, 2018. All rights reserved.
www.esi-group.com
Many advantages
- RECYCLING CODE
- SYNERGY BETWEEN LANGUAGES
- NO LINE COMMANDS
- EXCHANGE DATA
- WORKFLOWS
15www.esi-group.com
Copyright © ESI Group, 2018. All rights reserved.Copyright © ESI Group, 2018. All rights reserved.
www.esi-group.com
Looking forward
- NEED TO BETTER DEFINE A DATASET FORMAT
FOR LARGE DATASETS
CSV, XML, MAT HAVE LIMITATIONS
NEED FOR AN INTERACTIVE EDITOR
- MORE METHODS
- SUSTAINABLE FUNDING...
BENCHMARK
SPONSORSHIP
GIFTS
AND SCILAB IS HDF5-BASED

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INRA @ Scilab Conference 2018

  • 1. 1www.esi-group.com Copyright © ESI Group, 2018. All rights reserved.Copyright © ESI Group, 2018. All rights reserved. www.esi-group.com Jean-Claude BOULET INRA - FRANCE
  • 2. 2www.esi-group.com Copyright © ESI Group, 2018. All rights reserved.Copyright © ESI Group, 2018. All rights reserved. www.esi-group.com About chemometrics… INFORMATIONS ABOUT THE SAMPLE A SPECTRUM (e.g. NIR)
  • 3. 3www.esi-group.com Copyright © ESI Group, 2018. All rights reserved.Copyright © ESI Group, 2018. All rights reserved. www.esi-group.com About chemometrics… REGRESSIONS DISCRIMINANT ANALYSIS
  • 4. 4www.esi-group.com Copyright © ESI Group, 2018. All rights reserved.Copyright © ESI Group, 2018. All rights reserved. www.esi-group.com CheMoocs: a MOOC about chemometrics 2016-2017-2018
  • 5. 5www.esi-group.com Copyright © ESI Group, 2018. All rights reserved.Copyright © ESI Group, 2018. All rights reserved. www.esi-group.com Several partners
  • 6. 6www.esi-group.com Copyright © ESI Group, 2018. All rights reserved.Copyright © ESI Group, 2018. All rights reserved. www.esi-group.com 1- A MOOC : « KNOWLEDGE » 2- A TOOL : « PRACTICE » ?
  • 7. 7www.esi-group.com Copyright © ESI Group, 2018. All rights reserved.Copyright © ESI Group, 2018. All rights reserved. www.esi-group.com Previous work : an Atoms module in chemometrics, named FACT
  • 8. 8www.esi-group.com Copyright © ESI Group, 2018. All rights reserved.Copyright © ESI Group, 2018. All rights reserved. www.esi-group.com Large possibilities... but issues 1- not all functions in Scilab (or other languages) 2- need to learn line commands
  • 9. 9www.esi-group.com Copyright © ESI Group, 2018. All rights reserved.Copyright © ESI Group, 2018. All rights reserved. www.esi-group.com ChemFlow: a web application for chemometrics https://galaxyproject.org/ https://vm-chemflow- francegrille.eu/ A solution with Galaxy
  • 10. 10www.esi-group.com Copyright © ESI Group, 2018. All rights reserved.Copyright © ESI Group, 2018. All rights reserved. www.esi-group.com ChemFlow: More detailed fields with help
  • 11. 11www.esi-group.com Copyright © ESI Group, 2018. All rights reserved.Copyright © ESI Group, 2018. All rights reserved. www.esi-group.com What do you need to configure Galaxy? - INSTALLING GALAXY AND REMOVING THE EXISTING TOOLS - CONFIGURING 2 OR 3 CONFIG FILES (XML) - CREATING XML WRAPPERS - HAVING SCILAB (OR OTHERS) TOOLS TO RUN !
  • 12. 12www.esi-group.com Copyright © ESI Group, 2018. All rights reserved.Copyright © ESI Group, 2018. All rights reserved. www.esi-group.com Example of a wrapper - requirements - Scilab command - inputs - Scilab script - outputs - help
  • 13. 13www.esi-group.com Copyright © ESI Group, 2018. All rights reserved.Copyright © ESI Group, 2018. All rights reserved. www.esi-group.com Which languages can be wrapped in Galaxy? - EVERY LANGUAGE ! + Python / C-C++ / Pearl / Java ...
  • 14. 14www.esi-group.com Copyright © ESI Group, 2018. All rights reserved.Copyright © ESI Group, 2018. All rights reserved. www.esi-group.com Many advantages - RECYCLING CODE - SYNERGY BETWEEN LANGUAGES - NO LINE COMMANDS - EXCHANGE DATA - WORKFLOWS
  • 15. 15www.esi-group.com Copyright © ESI Group, 2018. All rights reserved.Copyright © ESI Group, 2018. All rights reserved. www.esi-group.com Looking forward - NEED TO BETTER DEFINE A DATASET FORMAT FOR LARGE DATASETS CSV, XML, MAT HAVE LIMITATIONS NEED FOR AN INTERACTIVE EDITOR - MORE METHODS - SUSTAINABLE FUNDING... BENCHMARK SPONSORSHIP GIFTS AND SCILAB IS HDF5-BASED