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Mobyle 1.5 - Mobyle Workshop - September 28, 2012

Herv辿 M辿nager
Herv辿 M辿nager

Mobyle is a bioinformatics workflow and data management platform. Version 1.5 includes new features such as advanced workspace management that allows users to easily rename and organize jobs and data, support for multiple data inputs to programs, customizable tutorials, and visualization/editing widgets. It is available in two flavors - with or without the BMID programs editor and BMPS graphical workflows editor. The release provides improved usability and flexibility over previous versions.

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Mobyle 1.5 28 septembre 2012, Institut Pasteur
What is Mobyle
What's new in Mobyle 1.5 Workspace management Multiple data Tutorials BMID BMPS Availability
Advanced workspace management it becomes hard to navigate and manage user data and jobs: jobs have generic names: service name + date data sometimes have generic names: parameter name or file name regular users can have large numbers of jobs and data stored in their workspace solution: provide a way for users to easily rename their important jobs/data or remove the ones which are useless
Advanced workspace management Bookmark as "x" Generic job/ bookmark names
Advanced workspace management Rename jobs Remove or sort jobs / data (click on the pen icon) bookmarks in the overview panel
Advanced workspace management Rename jobs
Advanced workspace management Job is renamed
Advanced workspace management jobs/data bookmarks can also be renamed in the Overview panels
"Multiple" data Sometimes a program accepts a list of n files as input In Mobyle 1.0.x, it is not possible to specify this behaviour The workaround is to create web interfaces with a fixed but limited number of parameters which will be translated into files not flexible enough!
"Multiple" data Three databoxes let you specify three files at most as program input
"Multiple" data You can add new databoxes "on the fly" with the [+] button You can remove them with the "remove" button
"Multiple" data The order of the inputs is preserved through Two files have been used as input the order on the command line for the same parameter
"Multiple" data You specify a "multiple" type by merely Process the value using the separator and the adding the "Multiple" prefix to the datatype command line formatting code in <format>
Tutorials Tutorials in Mobyle 1.0.x are hard-coded: a limited list of HTML pages Depending on the context of each server, one might want to add/remove such pages: to provide help pages about a given service to explain a given use-case This requires the modification of Mobyle code (portal templates) which is overwritten on each update and may even break it altogether. not flexible enough!
Tutorials Tutorials are HTML web pages Tutorials can be added, classified and which can now be deployed the same way searched the same way as the other as others "services"
Tutorials Locally stored dependencies can be stored in a local directory that has the same name as the XML file, minus its extension (just like viewers/widgets) A tutorial is a service XML consisting mostly of an <interface> tag that contains the displayed HTML
Visualization/Edition Widgets
Edition and chaining
Export snapshots
Roadmap Edition widgets: Mobyle 1.0.5+, May 2012 BMID BMPS Mobyle 1.5, September 2012 Availability http://bit.ly/NyVaUl $apt-get install mobyle http://bit.ly/PTG0N7
Mobyle distribution from 1.5 version Mobyle exists in two flavors: Mobyle+BCBB-1.xx.tar.gz . With BMID (programs editor) and BMPS (user graphical workflows) Mobyle-1.xx.tar.gz . Without BMID (programs editor) and BMPS (user graphical workflows)
Acknowledgements NIAID: BMID and BMPS development Nick Weber Ramandeep Kaur Janet He Jennifer Dommer GenOuest: packaging effort and more... Olivier Sallou

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Mobyle 1.5 - Mobyle Workshop - September 28, 2012

  • 1. Mobyle 1.5 28 septembre 2012, Institut Pasteur
  • 3. What's new in Mobyle 1.5 Workspace management Multiple data Tutorials BMID BMPS Availability
  • 4. Advanced workspace management it becomes hard to navigate and manage user data and jobs: jobs have generic names: service name + date data sometimes have generic names: parameter name or file name regular users can have large numbers of jobs and data stored in their workspace solution: provide a way for users to easily rename their important jobs/data or remove the ones which are useless
  • 5. Advanced workspace management Bookmark as "x" Generic job/ bookmark names
  • 6. Advanced workspace management Rename jobs Remove or sort jobs / data (click on the pen icon) bookmarks in the overview panel
  • 9. Advanced workspace management jobs/data bookmarks can also be renamed in the Overview panels
  • 10. "Multiple" data Sometimes a program accepts a list of n files as input In Mobyle 1.0.x, it is not possible to specify this behaviour The workaround is to create web interfaces with a fixed but limited number of parameters which will be translated into files not flexible enough!
  • 11. "Multiple" data Three databoxes let you specify three files at most as program input
  • 12. "Multiple" data You can add new databoxes "on the fly" with the [+] button You can remove them with the "remove" button
  • 13. "Multiple" data The order of the inputs is preserved through Two files have been used as input the order on the command line for the same parameter
  • 14. "Multiple" data You specify a "multiple" type by merely Process the value using the separator and the adding the "Multiple" prefix to the datatype command line formatting code in <format>
  • 15. Tutorials Tutorials in Mobyle 1.0.x are hard-coded: a limited list of HTML pages Depending on the context of each server, one might want to add/remove such pages: to provide help pages about a given service to explain a given use-case This requires the modification of Mobyle code (portal templates) which is overwritten on each update and may even break it altogether. not flexible enough!
  • 16. Tutorials Tutorials are HTML web pages Tutorials can be added, classified and which can now be deployed the same way searched the same way as the other as others "services"
  • 17. Tutorials Locally stored dependencies can be stored in a local directory that has the same name as the XML file, minus its extension (just like viewers/widgets) A tutorial is a service XML consisting mostly of an <interface> tag that contains the displayed HTML
  • 21. Roadmap Edition widgets: Mobyle 1.0.5+, May 2012 BMID BMPS Mobyle 1.5, September 2012 Availability http://bit.ly/NyVaUl $apt-get install mobyle http://bit.ly/PTG0N7
  • 22. Mobyle distribution from 1.5 version Mobyle exists in two flavors: Mobyle+BCBB-1.xx.tar.gz . With BMID (programs editor) and BMPS (user graphical workflows) Mobyle-1.xx.tar.gz . Without BMID (programs editor) and BMPS (user graphical workflows)
  • 23. Acknowledgements NIAID: BMID and BMPS development Nick Weber Ramandeep Kaur Janet He Jennifer Dommer GenOuest: packaging effort and more... Olivier Sallou