Department of Bioinformatics - BiGCaT 1

Very brief overview of

Open Science in *

Egon WillighagenBiGCaT - Maastricht University

OpenScreen workshop 2012/09, EBI

Department of Bioinformatics - BiGCaT 2

Message to EU-OPENSCREEN

1. Many solutions (fact: we all have different deadlines and different objectives)

2. Standardize solutions or interoperability?1. Where is the API?2. Where is the communication standard? (e.g. ontology)

3. Focus on practical problems and not on our scientific problems1. Can we upgrade them to speed up discovery rather than

being an (advanced) hard disk?

Department of Bioinformatics - BiGCaT 3

Open *

• Methods–CDK–Bioclipse–Blue Obelisk–Linked Data

• EU projects–ToxBank /

OpenTox–Open PHACTS

*: drug discovery, toxicology, metabolomics, data warehouses, molecular modeling, ...

Department of Bioinformatics - BiGCaT 4

Open Source Cheminformatics

• Metabolomics• Drug discovery• Toxicology

Department of Bioinformatics - BiGCaT 5

CDK applications

• OrChem • KNIME workflows

Department of Bioinformatics - BiGCaT 6

Bioclipse / Brunn (J. Alvarsson, 2011)

Department of Bioinformatics - BiGCaT 7

O'Boyle et al., JChemInf, 2011

Blue Obelisk: Open Data, Open Source, Open Standards (or: interoperability)

Department of Bioinformatics - BiGCaT 8

Linked Open Data (W3C HCLS ig)

Samwald et al., JChemInf, 2010

Department of Bioinformatics - BiGCaT 9

Open PHACTS

Department of Bioinformatics - BiGCaT 10

WikiPathways / PathVisio

Department of Bioinformatics - BiGCaT 11

SEURAT-1 “...replacing animal testing”

Department of Bioinformatics - BiGCaT 12

OpenTox / ToxBank

Department of Bioinformatics - BiGCaT 13

More info?

• egon.willighagen@gmail.com

• http://www.blueobelisk.org/

• http://wiki.bioclipse.net/index.php?title=Brunn

• http://cdk.sf.net/

• http://opentox.org/

• http://openphacts.org/

or @egonwillighagenor http://chem-bla-ics.blogspot.com/