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Computational Biology: 1. Beyond the spherical cow 2. Segmentation in silico Part 1 Computational Biology Beyond the spherical cow John Doyle Nature, 411, 151-152 (2001) For what? make sense of the huge amounts of data produced unravel how complex biochemical systems really work

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Computational biology 1 beyond the spherical cow 2 segmentation in silico l.jpg

Computational Biology:1. Beyond the spherical cow2. Segmentation in silico


Part 1 computational biology l.jpg
Part 1 Computational Biology

Beyond the spherical cow

John Doyle

Nature, 411, 151-152 (2001)


For what l.jpg
For what?

  • make sense of the huge amounts of data produced

  • unravel how complex biochemical systems really work

http://www.biology.arizona.edu/cell_bio/tutorials/cell_cycle/cells3.html


Enablers l.jpg
Enablers

  • Discovery science

  • Acceptance that biology is now a cross-disciplinary science

  • Maturation of the internet as a forum for collaborations


Enablers5 l.jpg
Enablers

  • Notion: Biology is an information-based rather than qualitative science

  • High-throughput platforms capable of capturing global sets of information quickly and affordably

  • Medical imaging systems


Slide6 l.jpg
Goal

“… the computational approaches discussed… were firmly focused on the dynamics and control of the networks of genes and proteins at work in cells.”


Developments l.jpg
Developments

  • Gaining more access to technology

  • Mathematical modeling and computation

  • Design and implementation of synthetic gene networks


Considerations l.jpg
Considerations

  • Interaction between experiment and simulation

  • Fluctuations

  • Chemical dynamics

  • Mechanical dynamics

  • Interaction of chemical and mechanical dynamics


Applications l.jpg
Applications

  • Cell division cycle

  • Virtual vs. Real mutated genes

  • Developmental principles

http://www.biology.arizona.edu/cell_bio/tutorials/cell_cycle/cells2.html


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Applications

  • More efficient route to drug discovery and development

  • integrated biological circuits

    • “wet” nano-robots

    • engineered oncolytic adenovirus


Example l.jpg
Example

  • Computer modeling of individual ion channels in cardiac cells

    • Pacemaker activity

    • Genetic defects underlying arrythmic heartbeats

    • Mechanical-electrical feedbacks

    • Regional patterns of expression


Example12 l.jpg
Example

  • Model for cell motility

http://expmed.bwh.harvard.edu/projects/motility/motility.html


Example13 l.jpg
Example

  • Reaction-diffusion model

http://www.math.vanderbilt.edu/~morton/cs395/roth/fig2.gif


Example14 l.jpg
Example

  • Dynamics of calcium ions

http://www.compbiophysics.uni-hd.de/Signal_Transduction.html


Limitations l.jpg
Limitations

  • Biology needs more theory

  • Theory has a rather bad reputation among biologists


Slide16 l.jpg

“It took Humpty Dumpty apart but left the challenge of putting him back together again”

- John Doyle


References l.jpg
References putting him back together again”

  • Doyle, J. 2001. “Computational Biology: Beyond the spherical cow.” In Nature, 411:151-152.

  • Hasty, J., McMillen, D., and Collins, J. J. 2002. “Engineered gene circuits. “ In Nature, 420:224-230.

  • http://www.the-scientist.com/yr2003/feb/feature_030224.html

  • http://www.the-scientist.com/yr2003/feb/prof4_030224.html

  • http://www.the-scientist.com/yr2003/feb/feature2_030224.html

  • http://www.the-scientist.com/yr2003/feb/feature1_030224.html


Part 2 segmentation in silico l.jpg

Part 2: putting him back together again”Segmentation in silico

Peter Dearden and Michael Akam

Nature 406, 131-132 (2000)


Protocol von dassow et al l.jpg
Protocol (Von Dassow,et.al.) putting him back together again”

Collection of data

Key interactions

Simplification

Final model


Final model l.jpg
Final model putting him back together again”


Results l.jpg
Results putting him back together again”


Results22 l.jpg
Results putting him back together again”


Results23 l.jpg
Results putting him back together again”


Results24 l.jpg
Results putting him back together again”

frequency of ‘solutions’ allowed the model to generate correct pattern of segmentation


Conclusion l.jpg
Conclusion putting him back together again”

“ It is the organization of the gene networks that provides stability, not the fine tuning of molecular interactions.”


Drosophila segmentation wolpert l.jpg
Drosophila segmentation (Wolpert)] putting him back together again”


Box 1 von dassow et al l.jpg
Box 1 (von Dassow,et.al.) putting him back together again”


Implications l.jpg
Implications putting him back together again”

  • Allows possibility to explore effects of variations in parameter values

  • Allows possibility of studying the effect of varying initial conditions

  • Allows possibility of making complex gene networks more understandable


Implications29 l.jpg
Implications putting him back together again”

  • Emergence of a new breed of biologist-mathematicians


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