Summer School on Bioinformatics








The core research objectives of Mr. SymBioMath are:


  • Research on the Big-Data problems and computational intensive applications in high-performance computing:
    • New software libraries for out-of-core management of Big-Data, specially for I/O
    • Reduction of the computational space and runtime for all-all sequences
    • New data structures for in-core data management to reduce memory demand

  • New data processing applications in comparative genomics, especially those related to Big-Data sets, to allow genome-wide association studies, such as:
    • Modelling evolutionary events (SNP, mutations, translocations, deletions, duplications, inversions, etc.) aimed to understand evolution and extrapolate from them the divergence between sequences for phylogenetic tree construction
    • Comparison and synthesis of inter-genome distances
    • Gene-Gene interactions studies correlated with phenotype data

  • Implementing and packing commercial application prototypes to evaluate the potential for their exploitation in biomedical cases, in concrete in the study of
    • Adverse reactions to treatment in allergic patients
    • Interfacing, visualisation, and integration of external data sources as well as functional annotations

Agenda:
Tuesday, 10th of September: Bioinformatics
Time
Presenter
Content
8:30 - 9:00

Registration
9:00 - 9:15
Oswaldo Trelles (UMA, Spain)
Welcome to the summer school
9:15 - 11:15
Alois Regl (JKU Linz, Austria)
- Introduction to bioinformatics
- Sequence analysis basics

Coffee break

11:45 - 13:30
Oswaldo Trelles (UMA, Spain)
Comparative genomics scenarios in Mr. SymBioMath

Lunch

14:30 - 16:30
Jose Ramon Valverde (Centro National de Biotechnologia, Spain)
Metagenome analysis

Wednesday, 11th of September: Biomedicine and Systems Biology
Time
Presenter
Content
8:45 - 9:00
James Perkins (SAS, Spain)
Introduction and overview of the day's presentations
9:00 - 9:45
Miguel Blanca, M.D. (Hospital Carlos Haya, Malaga)
Introduction to allergies
9:45 - 10:30
Jose Antonio Cornejo (Hospital Carlos Haya, Malaga)
Using high-troughput studies (e.g. GWAS)
to find genes involved in disease and patology
10:30 - 11:15
Ulrich Bodenhofer (JKU Linz, Austria) (TBC)
Overview of GWAS Data analysis

Coffee break

11:30 - 12:30
Miguel Angel Medina (Biochemistry Dep., UMA, Spain)
An overview of systems biology
12:30 - 13:00
Juan Antonio Ranea (UMA, Spain)
Graphical models of networks and their analysis

Lunch

14:00 - 14:35
Armando Reyes Palomares (Biochemistry Dep., UMA, Spain)
Tools to investigate the genetic basis of disease
14:35 - 15:10
Aurelio Moya (Biochemistry Dep., UMA, Spain)
Systems pharmacology -
using biological networks for drug repositioning
15:10 - 16:30
Patrick Aloy (Institute for Research and Biomedicine, Barcelona, Spain)
Systems biology:
Combining wet lab and dry lab experiments
16:30 - 16:50
Marc Streit (ICG, Johannes Kepler University Linz, Austria)
Visualizing bio-molecular data

Thursday, 12th of September: Cloud computing
Time
Presenter
Content
8:45 - 9:00
Michael Krieger (RISC Software, Austria)
Introduction and overview of the day's presentations
9:00 - 10:00
Paul Heinzlreiter (RISC Software, Austria)
Overview on Cloud Computing
10:00 - 11:00
Michael Krieger (RISC Software, Austria)
Hadoop, HBase, And MapReduce (Theory)

Coffee break

11:30 - 13:00
Paul Heinzlreiter (RISC Software, Austria)
Cloud Computing (Practice)

Lunch

14:00 - 16:30
Michael Krieger (RISC Software, Austria)
Hadoop, HBase, and MapReduce practice