Table 1 Blue Obelisk Open Source Software projects discussed in the text

CMLXOM

https://bitbucket.org/wwmm/cmlxom/

JUMBO

http://sourceforge.net/projects/cml/

Cheminformatics Toolkits

Chemistry Development Kit (CDK)

http://cdk.sf.net

Cinfony

http://cinfony.googlecode.com

Indigo

http://ggasoftware.com/opensource/indigo

JOELib

http://sf.net/projects/joelib

Open Babel

http://openbabel.org

RDKit

http://rdkit.org

Web Applications

ChemDoodle Web Components

http://web.chemdoodle.com

Jmol

http://jmol.org

Integration

Bioclipse

http://www.bioclipse.net

CDK-Taverna

http://cdktaverna.wordpress.com

Lensfield2

https://bitbucket.org/sea36/lensfield2/

Interconversion

CIFXOM [95]

https://bitbucket.org/wwmm/cifxom/

JUMBO-Converters

https://bitbucket.org/wwmm/jumbo-converters/

OPSIN

http://opsin.ch.cam.ac.uk

OSRA

http://osra.sf.net

Structure Databases

Bingo

http://ggasoftware.com/opensource/bingo

Chempound (Chem#)

https://bitbucket.org/chempound

Mychem

http://mychem.sf.net

OrChem

http://orchem.sf.net

pgchem

http://pgfoundry.org/projects/pgchem/

Text mining

ChemicalTagger [96]

http://chemicaltagger.ch.cam.ac.uk/

OSCAR4

https://bitbucket.org/wwmm/oscar4/

Computational Chemistry

Avogadro

http://avogadro.openmolecules.net

cclib

http://cclib.sf.net

GaussSum

http://gausssum.sf.net

QMForge

http://qmforge.sf.net

Computational Drug Design

Confab [97]

http://confab.googlecode.com

Pharao

http://silicos.be/download

Piramid

http://silicos.be/download

Sieve

http://silicos.be/download

Stripper

http://silicos.be/download

Other Applications

AMBIT2

http://ambit.sf.net

Brunn

http://brunn.sf.net

Toxtree

http://toxtree.sf.net

XtalOpt

http://xtalopt.openmolecules.net