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INRA @ Scilab Conference 2018

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Embedding Scilab within Galaxy

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INRA @ Scilab Conference 2018

  1. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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. 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

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