Bioinformatics in biologist teams
?Problem including bioinformatic questions
I have a bioinformatician in my team
Bioinformatics in biologist teams
?Problem including bioinformatic questions
I have a bioinformatician in my team
● He isn't omniscient.● He isn't omnipotent.● His time is limited.● He relies on a computer center.
Bioinformatic in biologist teams
?Problem including bioinformatic questions
I have a bioinformatician in my team
● He isn't omniscient.● He isn't omnipotent.● His time is limited.● He relies on a computer center.
A platform is available
Bioinformatics in biologist teams
?Problem including bioinformatic questions
I have a bioinformatician in my team
● He isn't omniscient.● He isn't omnipotent.● His time is limited.● He relies on a computer center.
A platform is available
● Hard to find the right interlocutor.● Reaction times are variable.
The "Do it yourself" procedure
Sometimes the analyses are "simple" and consists into employing classical tools
DIY: Do it yourself !
The "Do it yourself" procedure
Sometimes the analysis are "simple" and consists into employing classical tools
DIY: Do it yourself !
Command line prompt
Computing cluster
The "Do it yourself" procedure
Communication
● Learning basic Linux commands● Learning cluster specific commands
...The "Do it yourself" procedure
Build a complete analyse
Interoperability Interoperability
● Assume the technical and scientific survey.● Deal with formats.● Deal with data transfers.● Scripting.
Galaxy
Direct access to cluster
Usable from any computer
User accounts
Data sharing
Workflow sharing
Galaxy deals with somes difficulties of "do it yourself"
Galaxy - Data access
Data can be uploaded from your computer
Import data from your hard drive
Import data using copy/past
Explanations about file formats
Galaxy - Historic
Histories are powerful tools to manage and share data
Current history
Personnal and published histories
Galaxy - Historic
Current history
Multiple histories are central in the Galaxy data managment
Never use any accents in any metadata of Galaxy
Content display
Attributes modification
Suppression
Galaxy - Toolbox
Numerous tools, classified into categories
Tested and maintained tools
Default tools
● Original Galaxy is distributed with numerous tools● Southgreen platform added dozens of tools● Tools can be explored by keywords
Galaxy - Workflows
Workflows are a flow of customized tools, that can be saved and shared
Edition canevasParameters
Galaxy - Workflows
You can decide which data you want to keep and display as a result for a workflow
This file will be hidden, but could be display afterwards
This file will be displayed as soon as available
If nothing is checked, everything is considered
checked
Galaxy, role in the platform
Analysed and explorable dataData to analyse
Reproductibility
Standard user
Expert user