1. Bioinformatics Xin-Yi Chua Peter Ansell, Chris Bowles, Lawrence Buckingham, James M. Hogan, Scott Mann, Paul Roe, Jiro Sumitomo, Jan M. Weinert www.mquter.qut.edu.au/bio Oct-15 1

2. BioinformaticsOverview Another Genomic Revolution Bio 2.0: Navigate and Share the graph Bringing ‘GIS’ to Comparative Genomics Future Directions Oct-15 2

3. Bioinformatics Another Genomic Revolution An explosion in genomic data The rise of population genomics & proteomics Alignment does not scale to the new BioScience Comparative genomics Gene regulation Protein characterisation Oct-15 3

4. Bioinformatics Searching for similar genes Oct-15 4 BLAST 3e-56 5e-56 9e -45 9.9 … Results “Hits” Reference gene

5. Bioinformatics Oct-15 5

6. Bioinformatics Oct-15 6 Example ClustalW alignment mammalian sulfatases: first 110 residues of the catalytic domain

7. Bioinformatics Bio2.0: Navigate & Share the Graph We allow scientists to visualise the graph Make the topology fit the question Visualisation is navigation Let the graph answer the question Refine and test hypotheses And then make the answer available Peer communities & link-based publication Sharing the vision… Oct-15 7

8. Bioinformatics Bringing ‘GIS’ to Comparative Genomics The new ‘GIS’ – Genomic Information System All about distances and what works for the user Linking to data sources via Bio2RDF Combining a collection of data sources together Exploiting tags and ontologies Oct-15 8

9. Bioinformatics SilverMap Model Oct-15 9 SilverMap Blast component Bio2RDF BlastDB Tags TRN Protein-protein interactions User defined distance measures

10. BioinformaticsDemo Oct-15 10

11. Bioinformatics Future directions Future applications Support user defined distances Transcriptional Regulatory Network analyses Protein-Protein interactions Bringing our tools to the community Making SilverMap the lingua franca of genomic publication The lab wiki and public web site Integration, tagging and sharing of views Oct-15 11

12. BioinformaticsAcknowledgements Oct-15 12