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 |
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