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Computational Biology and Approaches. Raquell M. Holmes, Ph.D. Computational Biology Workshop Howard University and Boston University. August 15, 2005. This morning. Computational Biology Snapshots of existing models Transition in biological views Computing and computational science.

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Computational biology and approaches l.jpg

ComputationalBiology and Approaches

Raquell M. Holmes, Ph.D.

Computational Biology Workshop

Howard University and Boston University

August 15, 2005


This morning l.jpg

This morning

Computational Biology

  • Snapshots of existing models

  • Transition in biological views

    Computing and computational science


Computational biology l.jpg

Computational Biology

  • Bioinformatics, Genomics, Proteomics, Metabolome

    • Sequences analysis and comparison

    • Database searches

    • Statistics, Graph theory, Strings, Markov Models

    • High throughput data generation

  • Protein structure, folding, energy

    • Molecular dynamics, Monte Carlo


  • Computational biology dynamics l.jpg

    Computational Biology: Dynamics

    Jacquet et al 2003, JCB


    What exists l.jpg

    What exists…


    Slide6 l.jpg

    Actin polymers: models

    http://www.cytochemistry.net/Cell-biology/actin_filaments.htm


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    Ways of studying properties

    • Microscope:

      • Watch growth and shrinkage

      • Use fluorescent probes for growth, shrinkage, orientation

      • Rates of monomer addition

    Myosin, actin, ATP

    In_vitro_motility_assay


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    Gallery

    Heart muscle fibers

    http://www.psc.edu/research/graphics/gallery/heart.html

    Daniel Mocanu, Joachim Kettenbach, Michael O. Sweeney, Bruce H. KenKnight, Ron Kikinis and Solomon R. Eisenberg –Boston University


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    Neuromuscular junction …

    All images were produced by Joel Stiles using DReAMM (www.mcell.psc.edu/DReAMM) software. Citation:  Stiles, JR, Ford, WC, Pattillo, JM, Deerinck, TE, Ellisman, MH, Bartol, TM, and Sejnowski, TJ. (2004) Spatially realistic computational physiology: past, present, and future. In: Parallel Computing: Software Technology, Algorithms, Architectures & Applications, ed. Joubert, G, et al. Elsevier, Amsterdam


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    Posterior patterns determination


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    Network for Wing Formation


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    Conceptual models are changing


    Classical view of mapk pathways l.jpg

    Classical View of MAPK Pathways

    adapted from C.Roberts, et al., Science, 287, 873 (2000)


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    The Protein Network View

    • Highly interconnected, not just a linear pathway!

    • Some proteins are missing from the protein interaction data sets (Cdc42, Ste20).

    • Includes several additional proteins (especially Akr1, Kss1).

    adapted from C.Roberts, et al., Science, 287, 873 (2000)


    Expression data l.jpg

    Expression data

    • KEGG:

      • retrievable expression data sets

    • EcoCyc:

      • input expression data to view in relation to metabolic data.

    • Expression data is one way of viewing the behavior of a system.


    Slide16 l.jpg

    Submitted by: Hirotada MORI

    Organism: E.coli

    Raw data


    Slide17 l.jpg

    MicroArray Data: fold changes in expression

    Hypothetical data

    • Changes in gene expression:

      • Single time point,Various conditions

      • Multiple time points, One condition

    • GenMapp tools highlight changes


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    Views from the Center for Cell Dynamics

    • Experimentalist use of confocal microscope

      • Static 3D image: microtubules and cytokinesis (Garry Odell)

      • Live label: GFP-EB1 in S. droebachiensis. (Mike Danilchik & George von Dassow)

    • Model Animation

      • Aster microtubules (George von Dassow)


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    Views from the Center for Cell Dynamics

    Static 3D image: microtubules and cytokinesis (Garry Odell)

    • Experimentalist use of confocal microscope

    • ImageJ, maximum projection

    • Digital capture- single processor

    Movie source http://raven.zoology.washington.edu/celldynamics/gallery


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    Views from the Center for Cell Dynamics

    Live label:

    GFP-EB1 in S. droebachiensis.

    (Mike Danilchik & George von Dassow)

    • Experimentalist use of confocal microscope

    • Spinning confocal, multiple frame captures, a single plane

    • Digital capture- single processor Simulation

    Movie source http://raven.zoology.washington.edu/celldynamics/gallery


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    Views from the Center for Cell Dynamics

    Model Animation

    Aster microtubules (George von Dassow)

    • assigned color values,

    • numerical simulation results.

    • multiple processors

    Movie source http://raven.zoology.washington.edu/celldynamics/gallery


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    What do we discover?

    • New questions:

      • Hysteresis in cell cycle

  • New understandings and conceptual models:

    • Metabolic control analysis

  • Missing pieces:

    • Calcium dynamics in neuroblastoma cells


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    Science Discipline

    Physics, Chemistry, Biology, etc.

    Computer Science

    Hardware/Software

    Applied Mathematics

    Numerical Analysis, Modeling,

    Simulation

    Computational Science:Interdisciplinary Research and Education

    Slide by Kris Stewart, EdCenter, San Diego State University


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    Elements of Computational Science

    Landau and Yasar, SIAM Review 2003

    EPIC-Virtual Institute, 2005

    • Computational tools

    • High performance computing*

    • Applied mathematics and computational methods*

    • Application in science and engineering*

    • Simulation and modeling

    • Visualization tools

    • Large scaledata sets: statistical and visual analysis


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    What is Supercomputing?Leading Edge to Consumer Electronics

    1985

    Cray X-MP: 1.2 Gflop

    Cost:$8,000,000

    60,000 watts of power

    No Built in Graphics

    56 kbps NSFnet Backbone

    2005 X-Box: ~5 Gflop peak

    Cost: $140

    ~100 watts of power

    3D Graphics (125M P/S)

    (100 Mbps etherNet)


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    CI Vision

    http://www.nsf.gov/news/special_reports/cyber/index.jsp


    Computational science interdisciplinary research and education27 l.jpg

    Science Discipline

    Physics, Chemistry, Biology, etc.

    Computer Science

    Hardware/Software

    Applied Mathematics

    Numerical Analysis, Modeling,

    Simulation

    Computational Science:Interdisciplinary Research and Education

    In the Room

    Slide by Kris Stewart, EdCenter, San Diego State University


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