Accessing and scripting CDK from Bioclipse

Ola Spjuthola.spjuth@farmbio.uu.seDept. Pharmaceutical BiosciencesUppsala University, Sweden

http://www.bioclipse.net

http://bioclipse.blogspot.com

Contents

•Introduction to Bioclipse

•The use of CDK in Bioclipse

•Scripting CDK in Bioclipse

•Calculating CDK properties

•Some ongoing Bioclipse projects

Before we start

Download latest Bioclipse now from Sourceforge

(see www.bioclipse.net for link)

Installation on lab computers does not work.

Please note:

We will be using a Beta in the workshop. Bioclipse 2.0 is scheduled for release in late May.

Bioclipse history

Prof. Wikberg’s group performed Proteochemometrics analyses:

•Heterogeneous data, many different software, incompatible file formats

•At the CDK workshop 2005 in Cologne, teamed up with Steinbeck et. al. to form the Bioclipse project.

•Internationally awarded 3 times

Introduction to Bioclipse

•Bioclipse is a Rich Client• Standalone app, not run in a browser• Today’s desktop computers and laptops

are powerful• Also take advantage of online resources

(e.g. data, services, HPC)

> Intuitive, native, responsive GUI

> Full integration with operating system

Introduction to Bioclipse

•Bioclipse is a built on Eclipse Rich Client Platform• Previously an IBM project, now an Open Source project

managed by the Eclipse Foundation (www.eclipse.org)

•Every application is a set of plugins• Even core modules

•Can be extended by adding more plugins

Component based architecture

Bioclipse

Proteochemometrics

2D

3DData analysis

Spectra

Molecular dynamics

Getting Bioclipse

•Download latest from Sourceforge (see www.bioclipse.net for link)

•Unzip

•Start

Bioclipse welcome page contains tutorials and links

Software updates

After installation and restart we have new functionality and more options!

Install Sample Data

Menu:

File > New…

Use name:

Sample Data

The Workspace

• Place on the local hard disk managed by Bioclipse• Track changes• Drag and drop or cut and paste into it

ProjectProject

FolderFolder

File(s)File(s)

Toolbar Perspective bar

Stacked views

Welcome

Jmol Editor Outline

Navigator

Properties

Javascript Console

The Bioclipse Workbench

Bioclipse basics

• Open files in editors• Double-click the file• Chose editor: Right-click file > Open with…

• Show views• Menu: Window -> Show View > Other..

• Customize workbench• Change size and drag views and editors

around• Edit preferences in menu: Window >

Preferences

• Help system• Menu: Help > Help contents

Cheat Sheets

Step by step tutorials inside the Workbench

Interactive with actions to perform

Menu:

Help > Cheat Sheets

Bioclipse domain objects

IBioObject All domain objects in Bioclipse (UID)

IMolecule All molecules implementations (must

provide SMILES and/or CML)

ICDKMolecule CDK implementation of IMolecule

ISequence

IBioJavaSequence

Enter commands in the Javascript Console

Scripting Bioclipse

Manager

Method

Parameter(s)

Scripting Bioclipse

List available managers:

help (or press Tab key)

Scripting Bioclipse

List methods in a manager:

help <manager name>

Scripting Bioclipse

Get help for a method:

help <manager name>.<method name>

Example: help cdk.loadMolecule

Some basic CDK commands in Bioclipse

Don’t forget tab-completion!Don’t forget tab-completion!

I/O and GUI interaction

1) Type

2) Drag and drop

Cheminformatics I/O

Ways to load molecules:

cdk.loadMolecule(“/Project/file.mol”)

cdk.loadMolecule(“/full/path/to/file.mol”)

Load several molecules:

cdk.loadMolecules(“/Project/file.sdf”)

cdk.loadMolecules(“/full/path/to/file.sdf”)

Javascript Editor

Edit and launch scripts with .js extension

Execute script

Script: /Sample Data/Javascripts/extractsmilesAndMass.js

Gists

Gist = versioned script [http://gist.github.com]

– Ideal for sharing scripts online– Find gists for Bioclipse:

• http://delicious.com/tag/bioclipse+gist

– Find gists for the workshop:• http://delicious.com/tag/bioclipse+gist+cdkws2009

Bioclipse has Gist support built-in:gist.download(95755)

gist.download(84188,”/Virtual/glu.js”)

Example script:

Download and visualize proteins

Script: /Sample Data/Javascripts/dnaiso.js

Gist: 95779

Multiple molecules

Script: /Sample Data/Javascripts/multimol.js

Gist: 95790

Scripting Jmol

Jmol manager:jmol.spinOn()

Run general Jmol script:

jmol.run(“spin on”)

2D coordinates

3D coordinates

2D/3D complete script

Script: /Sample Data/Javascripts/gencoords.js

Gist: 95755

Script JCP editing

Script: /Sample Data/Javascripts/buildmol.js

Gist: 96594

Balloon: Conformer generation

Generate 3D coordinatesres=balloon.generate3Dcoordinates("/Sample Data/2D

structures/ATP.mol")

Generate 10 conformationsres=balloon.generate3Dconformations("/Sample Data/2D

structures/ATP.mol", 10)

ui.open(res)

ui.open(res, "jmol")

ui.open(res)

[http://web.abo.fi/~mivainio/balloon]

Javascript in Javascript Console

Use Javascript mixed with Manager code!

var mols = cdk.loadMolecules("/Sample Data/SDF/Fragments2.sdf");

for (var i = 0; i < mols.size(); i++) {

js.print(mols.get(i).getSMILES() + "\n");

}

Plugins add new managers and new commands

Calculating CDK properties (descriptors)

List descriptors:qsar.getDescriptorIDs()

Calculate a descriptor:qsar.calculate(IMolecule, descriptorID)

Descriptor IDs are from the Blue Obelisk Descriptor Ontologyhttp://blueobelisk.sourceforge.net

Calculating CDK properties

Command:qsar.calculate(

molecule, descriptor)

Script: /Sample Data/Javascripts/qsar.js

Gist: 95194

Calculating CDK properties:Multiple molecules, multiple descriptors

Command:qsar.calculateNoParams(

molecules, descriptors)

Script: /Sample Data/Javascripts/qsar-multi.js

Gist: 95189

Bridging JS to R

• Bioclipse has an R-console• Menu: Window > Show View > Other > R-Console

• Access JS variables with `myJSvariable`

Calculating CDK properties:QSAR project

Create New QSAR project

Menu: File > New… > QSAR Project

QSAR Editor

Cheat Sheet:

QSAR Project

Use R on QSAR dataset

To sum up: What is Bioclipse?

Bioclipse is an intuitive workbench for end users in life science

Bioclipse is an advanced scriptable framework for power users

Bioclipse is a platform for rapid development and provisioning

Some ongoing Bioclipse projects

Speclipse:Spectrum analysis in Bioclipse

More information: Stefan Kuhn and Dr. Christoph Steinbeck, EBI, UK

MetaPrint2D:Site-of-metabolism prediction

Collaboration with Dr. Lars Carlsson, AstraZeneca, SE and Prof. Robert Glenn, Cambridge University, UK

Pharmacophores

Collaboration with Dr. John Van Drie (Van Drie Research LLC) and Dr . Rajarshi Guha (Indiana University)

Brunn: High Throughput Screening

Collaboration with Prof. Rolf Larsson, Dept Clinical Pharmacology, Uppsala University, Sweden

www.brunn.sf.net More information: Jonathan Alvarsson, Uppsala University, Sweden

Data analysis

Collaboration with Genetta Soft AB, Sweden. www.genettasoft.com

Bioclipse Licensing

Bioclipse: EPL - Eclipse public license– Flexible open source license

Plugins: Any license, even commercial– All plugins packaged with Bioclipse are

free and open source

AcknowledgementsDept. Pharmaceutical Biosciences, Uppsala University, Sweden

Prof. Jarl E. S. Wikberg

Dr. Egon Willighagen

Martin Eklund

Jonathan Alvarsson

Carl Mäsak

Eskil Anderssen

Annsofi Andersson

Arvid Berg

Bjarni Juliusson

Unilever Centre for Molecular Informatics, Univ. Cambridge, UK

Prof. Peter Murray-Rust

Prof. Robert Glen

Samuel Adams

Linnaeus Centre for Bioinformatics, Uppsala, Sweden

Dr. Erik Bongcam-Rudloff

Sofia Burvall

European Bioinformatics Institute, Hinxton, UK

Dr. Christoph Steinbeck

Stefan Kuhn

Dr. Gilleain Torrence

Cologne University Bioinformatics Centre (CUBIC), Germany

Dr. Tobias Helmus

Miguel Rojas

Thomas Kuhn

Dept Clinical Pharmacology, Uppsala University, Sweden

Prof. Rolf Larsson

Dr. Claes Andersson

Hanna Göransson

Ludwig-Maximilians-Universität, Munich, Germany

Dr. Johannes Wagener

Dept. Pharmaceutical Biosciences, Uppsala University, Sweden

Prof. Johan Åqvist

Dr. Martin Nervall

Göran Wallin

Global Safety Assessment, AstraZeneca, Mölndal Sweden

Dr. Scott Boyer

Dr. Lars Carlsson

Van Drie Research LLC, MA, US

Dr. John Van Drie

Indiana University, IN, USA

Dr. Rajarshi Guha

Others

Dr. Jerome Pansanel

… and all others for contributing code, feature requests, bug reports, proposals, and comments!

Thank you!Ola Spjuth

ola.spjuth@farmbio.uu.se

www.bioclipse.net