Scientific Program and abstracts of Young scientists school “Bioinformatics and systems biology” – .pdf
The Fourth Young scientist’s school “Bioinformatics and systems biology” will be held 30 June – 2 July 2012 within the framework of the BGRS/SB-2012 conference. Young scientists, PhD students and undergraduate students are invited to participate at the school. Particularly, we encourage those of you who are interested in modern theoretical approaches in biology and their application on different biological objects. The school program includes lecture session and practical works in modern approaches of biological data analysis and high-throughput methods of computer calculation in bioinformatics. The young scientist’s school includes also poster and oral presentation of young scientists. The best presentations will be awarded by certificates and prizes.
The working language is English.
From April 16 till May 10 you may send your abstract to kviki@bionet.nsc.ru
The program of youngs scientists school is available here.
The photos from young scientists school are available here
Lectures and lecturers:
Prof. Evgeny Rogaev (head of laboratory of brain molecular genetics in Mental Helth Research Center RAMS, Moscow; head of laboratory in University of Massachusetts Medical School)
Lecture: New trends in medical genomics
Prof. Robert Giegerich (Bielefeld University, Germany)
Lecture: Dynamic Programming in Bellman’s GAP
Applications of the dynamic programming paradigm are ubiquitous computer science, and especially so in bioinformatics. The discipline of algebraic dynamic programming liberates programmers from cumbersome coding and debugging, as algorithms can be described on a declarative level of abstraction. Teaching DP algorithms becomes more rewarding, as crucial ideas are better exhibited in a more abstract representation. The algebraic discipline underlies a good number of bioinformatics tools, such as RNAshapes, RNAlishapes, RNAhybrid, PknotsRG, KnotInFrame, Locomotif, and pKiss, (see bibiserv.cebitec.uni-bielefeld.de), some of which are used quite widely.
Quite in contrast to this success, the proliferation of algebraic dynamic programming as a method remains marginal. It has been hindered by the fact that its original implementation was based on a Haskell-derived syntax and provided only marginal compiler optimizations.
Prof. Eric Mjolsness (Department of Information and Computer Science; Department of Mathematics University of California, Irvine, USA)
Lecture: Quasi-equilibrium and non-equilibrium modeling of biochemical reaction networks
Basic tools of mathematical physics, including equilibrium and nonequilibrium statistical mechanics, seу new application in computational systems biology generally and biochemical reaction networks in particular. For example, transcriptional regulation networks and allosteric enzymes can often be modeled with quasi-equilibrium or simple nonequilibrium methods. General reaction networks can be decomposed into dynamics given by equilibrium free energies, thermodynamic forces on cycles, and transition state free energies. Relate technical tools will be introduced as well.
Dr. Maksim Zakhartsev (Institute of Biochemical Engineering, University of Stuttgart; Institute of Pharmacy and Molecular Biotechnlogy, University of Heidelberg, Germany)
Lecture: Fundamentals of flux analysis
Analysis of intracellular fluxes in microbial cells is one of the major research tools in modern Metabolic Engineering and Systems Biology. In this lecture we will review modern analytical techniques to perform experiments and measure metabolic fluxes as well as consider fundamentals of unstructured and structured metabolic models and methods for their mathematical analysis. We are going to use MATLAB and some specialized software (for example InSilico Discovery) to perform an analysis of experimental data.
Prof. Roman Efremov (head of laboratory of biomolecular modeling, Institute of bioorganic chemistry RAS, Moscow)
Lecture: Numerical experiment in molecular biophysics of proteins an membraines: tasks and solutions proteomics
Dr. Olga Krebs (Heidelberg Institute for Theoretical Studies, Germany)
Lecture: Data integration in systems biology: SySMO DB on the focus
Fernando Izquierdo (HITS gGmbH, Heidebelg, Germany)
Lecture: Parallel computations applied to phylogenetics
Due to the rapid pace of molecular data accumulation and the slower increase in CPU speeds, parallel computing has established as a demanded standard technique in Bioinformatics. We will introduce some of the main paradigms in parallel computer architectures and show how these can be applied to the field of computational phylogenetics to enable the analysis of large datasets
Practical Tutorials:
Practical exercises in flux analysis (Dr. Maksim Zakhartsev, Germany)
Enjoy Dynamic Programming in Bellman’s GAP (Prof. Robert Giegerich)
Introduction to bioinformatics: search and analysis of genomic sequences (Dr. Dmitry Afonnikov, Russia)
Computational proteomic for beginners
Parallel computations applied to phylogenetics (Fernando Izquierdo, Germany)
Data Integration in systems biology: SEEK, JERM and RightFiled tools (Dr. Olga Krebs, Germany)
For all questions related to Young Scientist School “Bioinformatics and System Biology”, please contact the Chairperson of the Young Scientist School Organizing committee:
Victoria Mironova, kviki@bionet.nsc.ru, Теl. +7 (383) 363-4922 (*3408)