Cyni The Cytoscape Network Inference (Cyni) toolbox for gene regulatory

network inference

Oriol Guitart Pla Systems Biology Lab

Institut Pasteur Paris

Paris, September 18, 2014

Cytoscape!

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• Open source platform for biological network data integration, analysis, and visualization !

– Free! (Open source, LPGL) – Developed and maintained by universities,

companies, and research institutions – Expandable by Apps/Plugins

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Paris, September 18, 2014

Show  the  results

Cytoscape Workflow

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VizMapper Layouts

!Cytoscape  

Apps

Visualiza(on

Computa(onal  Analysis

Human analysis

Filtering  Selec8on

Data  import

Data  export

Paris, September 18, 2014

Why Cyni

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Paris, September 18, 2014

Why Cyni

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Users

Network Inference!Method

Network Inference!Method

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Paris, September 18, 2014

Why Cyni

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Why Cyni

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Network Inference!Method

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Network Inference!Method

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Paris, September 18, 2014

Cyni Toolbox App• To biologists:

– Cyni is a collection of tools for network inference • To bioinformaticians and inference researchers:

– Cyni is a framework that supports and simplifies implementation of new network inference algorithms

• First 3.x app that exports functionality • Cyni provides

– Several commonly used network inference techniques – Data imputation and discretization techniques – Several known metrics (correlation, bayesian,...) – Documented API – Tutorials and sample code

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Paris, September 18, 2014

Cytoscape 3.x

Cyni ToolboxGUI

Cyni API- Cyni Interfaces - Cyni Data Structure - Utility Methods

Data Imputation

Network Inference

Data Discretization

Metrics

Cyni Apps

User 2: Method Developer

New Network Inference Method

User 1: Biologists

User 3: Cy3 App Developer

Another app willing to use some of the

tools in Cyni

Paris, September 18, 2014

How to get Cyni• http://apps.cytoscape.org/cynitoolbox

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Paris, September 18, 2014

How to get Cyni• http://apps.cytoscape.org/cynitoolbox

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Paris, September 18, 2014

How to use Cyni

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How to use Cyni

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How to use Cyni

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Paris, September 18, 2014

How to use Cyni

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Paris, September 18, 2014

How to use Cyni

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How to use Cyni

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How to use Cyni

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Cyni Use case

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Infer a network from gene expression data

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Load Data

Cyni Use case

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Load Data

Cyni Use case

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Load Data

Cyni Use case

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Estimate Data

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Load Data

Cyni Use case

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Estimate Data

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Load Data

Cyni Use case

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Estimate Data Discretize Data

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Load Data

Cyni Use case

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Estimate Data Discretize Data

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Load Data

Cyni Use case

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Estimate Data Discretize Data Infer Network

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First “Cyni Apps”• ARACNE !

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• DREAM 8 Breast Cancer SubChallenge 1 winners – Stuart’s Lab (UCSC): LASSO regression along with the use of

prior biological knowledge by using a heat diffusion technique !

– Song’s Lab (NMSU): Discretization Gaussian mixture model along with a new non-constant functional chi-square metrics

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Paris, September 18, 2014

Cyni Framework

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Access and support

· Configurable GUI· Cyni API· Central fast data access

Cytoscape 3.1+

Cyni

Metrics apps

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Pearson correlation

Spearman rank

Data discretization apps

Manual

Equal frequencies

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Data imputation apps

Row Average

BCPA

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ARACNE (Califano et al.)

Hill climbing

K2

Network inference apps

DC-TDC (Stuart et al.)

Funchisq (Song et al.)

CytoscapeApps

User interface

Cont. Mutual Information

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Funchisq

Paris, September 18, 2014

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• Friendly user interface • Direct Cytoscape output visualization • Access to a larger number of users through

Cytoscape App Store • Benchmarking system

Why your algorithm in Cyni?

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Paris, September 18, 2014

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• Friendly user interface • Direct Cytoscape output visualization • Access to a larger number of users through

Cytoscape App Store • Benchmarking system

Why your algorithm in Cyni?

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Paris, September 18, 2014

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• Friendly user interface • Direct Cytoscape output visualization • Access to a larger number of users through

Cytoscape App Store • Benchmarking system

Why your algorithm in Cyni?

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Paris, September 18, 2014

!

• Friendly user interface • Direct Cytoscape output visualization • Access to a larger number of users through

Cytoscape App Store • Benchmarking system

Why your algorithm in Cyni?

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Paris, September 18, 2014

!

• Friendly user interface • Direct Cytoscape output visualization • Access to a larger number of users through

Cytoscape App Store • Benchmarking system

Why your algorithm in Cyni?

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Paris, September 18, 2014

!

• Friendly user interface • Direct Cytoscape output visualization • Access to a larger number of users through

Cytoscape App Store • Benchmarking system

Why your algorithm in Cyni?

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Paris, September 18, 2014

!

• Friendly user interface • Direct Cytoscape output visualization • Access to a larger number of users through

Cytoscape App Store • Benchmarking system

Why your algorithm in Cyni?

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Paris, September 18, 2014

!

• Friendly user interface • Direct Cytoscape output visualization • Access to a larger number of users through

Cytoscape App Store • Benchmarking system

Why your algorithm in Cyni?

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Paris, September 18, 2014

!

• Friendly user interface • Direct Cytoscape output visualization • Access to a larger number of users through

Cytoscape App Store • Benchmarking system

Why your algorithm in Cyni?

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Paris, September 18, 2014

!

• Friendly user interface • Direct Cytoscape output visualization • Access to a larger number of users through

Cytoscape App Store • Benchmarking system

Why your algorithm in Cyni?

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Paris, September 18, 2014

!

• Friendly user interface • Direct Cytoscape output visualization • Access to a larger number of users through

Cytoscape App Store • Benchmarking system

Why your algorithm in Cyni?

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Paris, September 18, 2014

!

• Friendly user interface • Direct Cytoscape output visualization • Access to a larger number of users through

Cytoscape App Store • Benchmarking system

Why your algorithm in Cyni?

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Paris, September 18, 2014

Cyni Current Status• Robust release available with first non beta API • More than 2000 downloads • ARACNE app already available in the App store and

two more apps on the way • Cyni paper submitted • Cyni Apps need to be implemented in Java

– Currently exploring options to support algorithms implemented in other programming languages like R or Python

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Paris, September 18, 2014

Thank you!

• If it does not work for you, do not give up. Tell us why !

• Please cite Cyni Algorithms and/or Cyni itself

• Questions: Welcome!

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