1. Bioinformatics (and Systems Biology?) in Biomedical Research Donald Dunbar Systems Biology Club 30th November 2005

2. November 30th 2005Donald Dunbar: Systems Biology Club Introduction Bioinformatics at QMRI Who we work with What we do Our focus Systems Biology at QMRI? Where we’d like to apply systems biology Can we do it? what data do we have and what do we need? can we build useful models for these data? can we find collaborators?

3. November 30th 2005Donald Dunbar: Systems Biology Club Bioinformatics at QMRI Queen’s Medical Research Institute Centre for Cardiovascular Science Hypertension, atherosclerosis, thrombosis, diabetes, obesity, heart failure Centre for Inflammation Research Lung, kidney, vascular, and other diseases associated with inflammation Centre for Reproductive Biology Female and male reproductive health and disease We work with cardiovascular and inflammation scientists Providing bioinformatics support in several areas Gene expression experiment analysis Genome mining Text mining Databasing and data-mining Bioinformatics workflows

4. November 30th 2005Donald Dunbar: Systems Biology Club Bioinformatics at QMRI Gene expression

5. November 30th 2005Donald Dunbar: Systems Biology Club Bioinformatics at QMRI Gene expression Genome mining

6. November 30th 2005Donald Dunbar: Systems Biology Club Bioinformatics at QMRI Gene expression Genome mining Text mining

7. November 30th 2005Donald Dunbar: Systems Biology Club Bioinformatics at QMRI Gene expression Genome mining Text mining Databasing & Data- mining

8. November 30th 2005Donald Dunbar: Systems Biology Club Bioinformatics at QMRI Gene expression Genome mining Text mining Databasing & Data- mining Bioinformatics workflows

9. November 30th 2005Donald Dunbar: Systems Biology Club Bioinformatics at QMRI Focus on data integration and access Across levels Molecule, cell, organism Across disciplines Genomics, proteomics, genetics, physiology, pathology, biochemistry Use the literature as well as in-house data Knowledge capture

10. November 30th 2005Donald Dunbar: Systems Biology Club Systems Biology at QMRI? Where we’d like to apply it We have systems like this ALDO GC renin AGTANGII ACTH Physiology & Measurements Blood pressure Renal clearance, GFR Urine electrolytes Plasma electrolytes Plasma steroids Plasma AGT, renin Plasma Aldosterone Body weight, fat mass Drinking, eating quantities Multiple tissue pathology q-RTPCR Microarrays, proteomics Mouse models Ren1 KO/TG 11b KO/TG AS KO/TG HSD1 KO/Liver TG/Adipose TG/Brain TG HSD2 KO/Kidney TG Treatments & Conditions Aldo, - Na, Kidney mass ACTH + Na C57Bl6 controls, 12-20weeks Pharmaceuticals, siRNA

11. November 30th 2005Donald Dunbar: Systems Biology Club Systems Biology at QMRI? Why? The biology is very complex More information available from system Reduced systems lose meaning & context Don’t want to study components separately Want to identify missing links (indirect interactions) Use models to help us understand the biology Use models to help us predict (eg new experiments) Utilise multidisciplinary research

12. November 30th 2005Donald Dunbar: Systems Biology Club Systems Biology at QMRI? Can we do it? What data do we need? Genes (sequence and level), proteins, metabolites Interactions Physiology, pathology Time courses (short, long), end points In vivo, cell culture, in vitro Does “classical” SB scale to tissues, organs etc…? Are these “systems” too complex? What would models look like?

13. November 30th 2005Donald Dunbar: Systems Biology Club Systems Biology at QMRI? Who can we work with Biologists (genetics, physiology…) Bioinformaticians Statisticians Mathematicians Computer scientists Doctoral training centre Can the Edinburgh SB community create a network of collaborating scientists?

14. November 30th 2005Donald Dunbar: Systems Biology Club Summary Bioinformatics at QMRI being established Working with two large research centres Want to apply systems biology approach Can we do it?

15. November 30th 2005Donald Dunbar: Systems Biology Club Visit our Web Pages http://www.bioinf.mvm.ed.ac.uk