17-18 May 2010
EMBL-EBI IT Training Room, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
The R programming environment has emerged as a powerful platform for a variety of bioinformatics and chemometric analysis. However, for chemometric and cheminformatics problems, the environment does not natively support manipulation of molecular representations. This session will describe how the integration of the CDK with R provides the ability to load, manipulate and analyse chemical structure and associated data seamlessly within the R environment. The session will start with a brief R tutorial and then explore the capabilities of the R-CDK package using examples from QSAR modelling and similarity searching. We will also learn about the R-Pubchem package that allows one to directly access PubChem structure and bioassay data from within R. The session will end with a discussion on how the packages can be extended by writing R or Java code.
Dr Rajarshi Guha is a research scientist at the NIH Chemical Genomics Center and has been using R for QSAR modelling and chemical data mining for the last 7 years.
In Metabolomics research, many experiments are comprised of hundreds to thousands of samples. This amount of data requires automated processing. Several packages in the Bioconductor project are able to analyse mass spectrometry data, combining powerful statistics and visualisation. The session will focus on the processing of LC/MS profilling data, and identification of compounds with the Metlin spectral library.
Dr Steffen Neumann is the head of the Bioinformatics and Mass spectrometry group at the Institute for Plant Biochemistry in Halle, where several tools and databases for MS profilling and identification are developed, including several Bioconductor packages.
Rajarshi Guha, NIH Chemical Genomics Center (R-CDK and R-Pubchem)
Steffen Neumann, AG Massenspektrometrie & Bioinformatik ( XCMS, Rdisop, CAMERA)
H. Paul Benton, Imperial College London.
David Broadhurst, Cork University Maternity Hospital.
There is a charge of £25 per day (£50 for both days) for this course to cover the cost of refreshments and course materials.
Registration for this workshop closes Monday 3 May 2010, 12 noon GMT