Embedding Scilab within Galaxy

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Jean-Claude BOULET
INRA - FRANCE

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About chemometrics…
INFORMATIONS
ABOUT THE
SAMPLE
A SPECTRUM (e.g. NIR)

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About chemometrics…
REGRESSIONS DISCRIMINANT ANALYSIS

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CheMoocs:
a MOOC
about chemometrics
2016-2017-2018

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Several partners

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1- A MOOC :
« KNOWLEDGE »
2- A TOOL :
« PRACTICE »
?

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Previous work : an Atoms module
in chemometrics, named FACT

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Large possibilities... but issues
1- not all functions
in Scilab
(or other languages)
2- need to learn line
commands

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ChemFlow:
a web application
for chemometrics
https://galaxyproject.org/
https://vm-chemflow-
francegrille.eu/
A solution with Galaxy

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ChemFlow:
More detailed fields
with help

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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 !

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Example
of a wrapper
- requirements
- Scilab command
- inputs
- Scilab script
- outputs
- help

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Which languages can be
wrapped in Galaxy?
- EVERY LANGUAGE !
+ Python / C-C++ / Pearl / Java ...

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Many advantages
- RECYCLING CODE
- SYNERGY BETWEEN LANGUAGES
- NO LINE COMMANDS
- EXCHANGE DATA
- WORKFLOWS

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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