The BGRS'2008 International Summer School for Young Scientists "Evolution, Systems Biology and High Performance Computing Bioinformatics"

Saturday, 28 June

11.00 – 14.00 Registration at the Institute of Cytology and Genetics

14.00 Opening Ceremony

14.10 – 15.45 Lecture 1.

Prof. Falk Schreiber, IPK Gatersleben, Germany.

Analysis of biological networks and related data.

16.00 -17.45 Lecture 2.

Prof. Ralf Hofestädt, Bielefeld University, Germany.

Metabolic network analysis

18-00 – 19.35 Seminar 1.

Mr. Yury Vyatkin, Institute of Cytology and Genetics, Novosibirsk, Russia.

Introduction to HPC.

 

Sunday, 29 June

9.30 – 11.05 Lecture 3.

Prof. Dmitry Scherbakov, Limnological Institute SB RAS, Irkutsk, Russia.

Discrete models for molecular evolution simulation at the population level.

11.25-13.00 Lecture 4.

Dr. Luciano Milanesi, CNR-Institute for Biomedical Technologies, Milan, Italy

Bioinformatics applications by using the GRID computing technology.

Lunch

15.00 – 16.35 Lecture 5.

Dr. Srinivasan Ramachandran, Institute of Genomics and Integrative Biology, Delhi, India

Application Bioinformatics for infectious diseases

17-00 – 18.35 Seminar 2.

Dr. Daniil Naumoff, GosNIIgenetika, Moscow, Russia.

Practical course on the protein sequence analysis: searching for homologues and their hierarchical classification

20-00 – 24-00 Cultural Program. Evening Novosibirsk excursion. Fireworks festival dedicated to Novosibirsk 115^th annivesary.

 

Monday, 30 June

9.30 – 11.05 Lecture 6.

Prof. Alexis Ivanov, V.N. Orechovich Institute of Biomedical Chemistry RAMS, Moscow, Russia.

Platform «From Gene to Lead Compound»: integration in silico and in vitro technologies

11.25-13.00 Lecture 7.

Dr. Olga Krebs, EML Research gGmbH, Heidelberg, Germany.

Integration of reaction kinetics data: and modeling of metabolic networks: SABIO RK and SYCAMORE.

Lunch

15.00 – 16.35 Lecture 8.

Dr. Stefan Heinrich, EML Research gGmbH, Heidelberg, Germany.

PIPSA: Comparison of protein interaction properties.

17-00 – 18.35 Seminar 3.

Dr. Olga Krebs, Dr. Stefan Heinrich, EML Research gGmbH, Heidelberg, Germany.

Practical course on SABIO RK and SYCAMORE.

19-00 Cultural Program. Foolball match between ICG and non-ICG participants dedicated to EURO-2008.

 

Thursday, 1 July

9.30 – 11.05 Lecture 9.

Prof. Thomas Ludwig, Ruprecht-Karls-Universitat, Heidelberg, Germany.

Introduction to high-performance computing. (1) Architecture of high performance computers

11.25-13.00 Lecture 10.

Prof. Thomas Ludwig, Ruprecht-Karls-Universitat, Heidelberg, Germany.

Introduction to high-performance computing. (2) Parallel programming principles

Lunch

15.00 Young scientists presentations.

 

Wednesday, 2 July

9.30 – 11.05 Lecture 11.

Prof. Thomas Ludwig, Ruprecht-Karls-Universitat, Heidelberg, Germany.

Introduction to high-performance computing. (3) Message passing with MPI

11.25-13.00 Lecture 12.

Prof. Thomas Ludwig, Ruprecht-Karls-Universitat, Heidelberg, Germany.

Introduction to high-performance computing. (4) Advanced issues with message passing

Lunch

15.00 – 16.35 Lecture 13.

Dr. Alexandros Stamatakis, Ludwig-Maximilians-University, Munich, Germany

Models, Algorithms, and Parallel Computing for Large-Scale Phylogenetic Inference

17-00 Closing Ceremony

 

Young Scientists presentation program.

Oral presentations. (Time for presentation: 15 min + 5 min for questions)

I. Anischenko, Belarusian State University, Minsk, Belarus. HIV-1 gp120 v3-loop comparative structure analysis: search for the structurally conserved regions.

E. Chaplygina, Institute of Applied and Fundamental Medicine, Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia. Phylogenetic classification  of the HECT-domain ubiquitin-protein ligase family

N. Eltsov, Institute of cytology and genetics SB RAS, Novosibirsk, Russia. The new algorithm for phylogenetic reconstruction of non-recombining DNA sequences.

V. Fazalova, Limnological Institute SB RAS, Irkutsk, Russia. To be announced.

Yu. Grushetsky, United Institute of Informatics Problems of NASB, Minsk, Belarus. Prediction of protein interactions using homologous interfaces.

I. Kulakovskiy, Engelhardt Institute of Molecular Biology RAS, Mocsow, Russia. Incorporating different types of experimental data on DNA-protein binding into the single in silico model.

Yu. Medvedeva, GosNIIgenetika, Moscow, Russia. Reduced level of synonymous substitution in CpG containing codons suggests functional role of intragenic and 3’ CpG islands in human genes.

A. Nyporko, Institute of Cell Biology and Genetic Engineering of NAS of Ukraine, Kiev, Ukraine. Influence of amino acid replacements associated with multidrug resistance on beta-tubulin molecular dynamics.

 

Poster presentations

V. Kovalyov, Institute of Applied and Fundamental Medicine, Nizhny Novgorod State Medical Academy, Nizhny Novgorod, Russia. UBIQUITOMIX database: a new resource on ubiquitin system.

N. Prakhov, University of Nizhni Novgorod, Nizhni Novgorod, Russia. Validation of viral EBNA1 protein as the perspective target for drug discovery.