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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

ComputationalBiology and Approaches

Raquell M. Holmes, Ph.D.

Computational Biology Workshop

Howard University and Boston University

August 15, 2005

this morning
This morning

Computational Biology

  • Snapshots of existing models
  • Transition in biological views

Computing and computational science

computational biology
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
Computational Biology: Dynamics

Jacquet et al 2003, JCB

slide6

Actin polymers: models

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

ways of studying properties
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

gallery
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

neuromuscular junction
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

classical view of mapk pathways
Classical View of MAPK Pathways

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

the protein network view
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
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

Submitted by: Hirotada MORI

Organism: E.coli

Raw data

slide17

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
views from the center for cell dynamics
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)
views from the center for cell dynamics19
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

views from the center for cell dynamics20
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

views from the center for cell dynamics21
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

what do we discover
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
computational science interdisciplinary research and education

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

elements of computational science
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
what is supercomputing leading edge to consumer electronics
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)

ci vision
CI Vision

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

computational science interdisciplinary research and education27

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