Galaxy: resource for bioinformatic analyses

CIRAD computer centerfor the South green platform

Bioinformatics without Galaxy

Bioinformatics in biologist teams

?Problem including bioinformatic questions

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.

Sometimes the analyses are "simple" and consists into employing classical tools

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

Use softwares, command line tools, online servers...

...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, role and usage ?

Galaxy

Communication

Galaxy deals with somes difficulties of "do it yourself"

Communication

Galaxy

Galaxy deals with somes difficulties of "do it yourself"

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 - Main window

Toolbox

Data

Galaxy - Main window

Tool configuration

Each software can be configured precisely

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 - Data access

Data can be loaded from shared librairies

Public data

Librairies access

Galaxy - Historic

Histories are powerful tools to manage and share data

Current history

Personnal and published histories

Galaxy - Historic

History managment

History selection

Temporary or permanent deletion

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 in South green platform

Computer center, platform, research team

Galaxy, role in the platform

Analysed and explorable dataData to analyse

Reproductibility

Standard user

Expert user

Galaxy in live