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.

1. Mobyle 1.5
28 septembre 2012, Institut Pasteur

2. What is Mobyle

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

7. Advanced workspace management
Rename jobs

8. Advanced workspace management
Job is renamed

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

18. Visualization/Edition Widgets

19. Edition and chaining

20. Export snapshots

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