Biomedicine and Big Data Analyzing spatio-temporal patterns in biomedical data Normal Stif f Wavy
Biomedicine and Big Data
Feb 24, 2016
Biomedicine and Big Data. Normal. Analyzing spatio -temporal patterns in biomedical data. Stiff. Wavy. My Research Group. Dr. Chakra Chennubhotla Ph.D. Computer Science University of Toronto. Shannon Quinn B.S. Computer Science Georgia Tech. Andrej Savol B.S. Applied Mathematics - PowerPoint PPT Presentation
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Biomedicine and Big DataAnalyzing spatio-temporal patterns in biomedical data
Normal
Stiff
Wavy
My Research GroupDr. Chakra ChennubhotlaPh.D. Computer ScienceUniversity of Toronto
Andrej SavolB.S. Applied MathematicsUniversity of Pittsburgh
Virginia BurgerM.S. MathematicsUniversity of Vienna
Shannon QuinnB.S. Computer ScienceGeorgia Tech
Our MissionHigh-throughput biomedical data
analysis
Problem and SolutionBiomedical and biological data
are BIGMapReduce! C0 C1 C2 C3
M0
M1
M2
M3
IO0 IO1 IO2 IO3
R0 R1
FO0
FO1
chunks
mappers
Reducers
Map
Pha
seR
educ
e Ph
ase Shuffling Data
Specifically…
Clustering!
RequirementsJavaApache Hadoop or Amazon EC2Apache MahoutComfortable with linear algebra
◦Ax = b◦X = UΣUT
Hive, HBase, Giraph, GraphLab, etc optional but awesome
Final ThoughtsDistributed computing
◦Open source development◦Programming at scale
Large project management◦Software engineering principles,
toolsBiomedical context
◦Biological data is huge◦Diagnostics: helping people
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