Building research data handling systems with open source tools - Open Source Software in Life Science Research - page 24

LSP4All is Postgresql [47], an open source database being used by many
big corporations in many different industries [48] and therefore likely to
support our database needs. Another, perhaps more natural, option
would be MySQL [49]; however, following the acquisition of MySQL by
Oracle there seems to be a tendency in the open source community to
move to Postgresql.
The chemical structure needs of LSP4All will be handled by something
like Ketcher [50], a pure open source Javascript-based editor, for structure
depiction and like RDKit [51] for the structure searches. RDKit supports
Postgrsql and therefore fi ts with the choice of open source database.
Several new well-functioning open source chemistry packages and
cartridges have appeared lately, so in the future there will be more options
from which to choose.
The LSP4All project is hosted at Github and we expect to open the
repository to the public during 2012. Then all university labs, small
biotechs and other relevant organisations will have the opportunity to
download and run a full data management package with chemistry
support for free. It will be a big step towards more open source
collaboration in the biopharmaceutical informatics space.
We hope you will all join in!

1.12 References

[1] Wikipedia Data warehouse. http://en.wikipedia.org/wiki/Data_warehouse .
Updated 16 August 2011. Accessed 18 August 2011.
[2] Homepage of H. Lundbeck A/S. http://www.lundbeck.com . Accessed
18 August 2011.
[3] Agrafi otis, DK, et al. Advanced Biological and Chemical Discovery (ABCD):
centralizing discovery knowledge in an inherently decentralized world.
Journal of Chemical Information and Modeling 2007;47:1999-2014.
[4] Pfi zer Rgate - http://www.slideshare.net/bengardner135/stratergies-for-the-
intergration-of-information-ipiconfex . Accessed 28 September 2011.
[5] Homepage of FDA - GLP Regulations. http://www.fda.gov/ICECI/
EnforcementActions/BioresearchMonitoring/NonclinicalLaboratories
InspectedunderGoodLaboratoryPractices/ucm072706.htm . Updated 8 May
2009. Accessed 28 September 2011.
[6] Homepage of SAP. http://www.sap.com/uk/index.epx# . Accessed 18 August
2011.
[7] Wikipedia MDL Information Systems. http://en.wikipedia.org/wiki/MDL_
Information_Systems . Updated 3 December 2010. Accessed 18 August 2011.
[8] Wikipedia Symyx Technologies. http://en.wikipedia.org/wiki/Symyx_
Technologies . Updated 2 December 2010. Accessed 18 August 2011.

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