Computational Biology Applications

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Computational Biology Applications

• Bartosz Nowierski
• Poznan Univeristy of Technology

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Laboratory of Bioinformatics (1)

• Institute of Bioorganical Chemistry (Polish
  Academy of Sciences)
• Founded 1.11.1999
• Members
• Prof. Dr. Habil. Jacek Blazewicz - director
• Ph.D. Piotr Formanowicz
• Ph.D. Marta Kasprzak
• M.Sc. Marcin Jaroszewski
• M.Sc. Piotr Lukasiak
• M.Sc. Piotr Wierzejewski

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Laboratory of Bioinformatics (2)

• Basic research area
• algorithms for sequencing by hybridisation
• analysis of DNA graphs
• analysis of NMR spectra for RNA chains
• restriction map constraction
• constracting phylogenetic trees
• constructing bio-server for selected problems of
  computional biology
• prediction of protein secondary structures
• DNA sequence assembly

• Basic research area
• algorithms for sequencing by hybridisation
• analysis of DNA graphs
• analysis of NMR spectra for RNA chains
• restriction map constraction
• constracting phylogenetic trees
• constructing bio-server for selected problems of
  computional biology
• prediction of protein secondary structures
• DNA sequence assembly

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Laboratory of Bioinformatics (3)

• International cooperation
• Universite LeHavre, France
• Max Planck Institutes, Germany
• TmBioscience, Canada
• Rutgers University, USA
• TU Clausthal, Germany
• RIKEN, Japan

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Applications

• DNA sequence assembly
• Prediction of protein secondary structures
• Constracting phylogenetic trees
• Motivation
• popular subject
• great demend
• faster gt distributed

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DNA Sequence AssemblyProblem specification

• Alphabet A, C, G, T
• Problem

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DNA Sequence AssemblyOverlap graph

• input sequence ? vertex
• overlap of sequences ? arc
• shift
• weight
• ACTGCCTA
• CTAGGATC
• TCAAGA

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DNA Sequence AssemblyRedundant arcs

• Arc deletion

ATGACTACT GACTACTGA ACTGAATCA
24 6
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DNA Sequence AssemblyHamiltionan path with max.
weight

• NP-hard problem gt heuristic
• Selection of first element
• unatractive successor of any vertex
• Selection of next elements
• atractive succesor, but not attractive to others

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DNA Sequence AssemblyParallelization

• Overlaps distrbute set of sequences
• Arc reduction distrib. set of vertices
• First vertex distribute set of vertices
• Next vertices ?

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Protein Secondary StructuresProblem specification

• aminoacid ? secondary structure
• A,C,D,E,F,G,H,I,K,.... ? H,E,X

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Protein Secondary StructuresRule usage

• Logical Analysis of Data approach

VASYDYLVIGGGSGG
VASYDYLVIGGGSGG
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Protein Secondary StructuresRule generation

• Good rule properties
• rule says e.g. H ? it must be right
• rule says e.g. not H ? it should be right
• The best rules
• if 1 variable is out, its not good anymore

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Protein Secondary StructuresRule generation -
algorithm

• Algorithm
• generate all reasonable 0-1 arrays
• Clasifier generation
• set of rules (logical OR)
• mathematical formula
• Parallelization
• division of array space

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Phylogenetic TreesProblem specification
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Phylogenetic TreesAlgorithm

• Branch Bound

• Parallelization
• distribution of subtrees
• exchange of information about solutions

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Usage of GridLab (1)

• Resource management (GRMS)
• assignment of resources
• application structure (master-slave)
• checkpointing migration
• dynamic assignment of new resources
• frameworks
• distributed shared memory (?)

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Usage of GridLab (2)

• Monitoring
• dynamic link/processor states (tuning)
• estimation of end time (GRMS, end user)
• Others
• visualisation
• security
• mobile users

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Contact

• Director
• Prof. Dr. Habil. Jacek Blazewicz
• Jacek.Blazewicz_at_cs.put.poznan.pl
• DNA Sequence Assembly
• B.Sc. Bartosz Nowierski
• Bartosz.Nowierski_at_cs.put.poznan.pl
• Protein Secondary Structures
• M.Sc. Piotr Lukasiak
• Piotr.Lukasiak_at_cs.put.poznan.pl
• Phylogenetic Trees
• Ph.D. Piotr Formanowicz
• Piotr.Formanowicz_at_cs.put.poznan.pl