Bridging the gap between modellers and biologists: Systems Biology Graphical Notation &
Download
1 / 21

Bridging the gap between modellers and biologists: Systems Biology Graphical Notation & - PowerPoint PPT Presentation


  • 62 Views
  • Uploaded on

Bridging the gap between modellers and biologists: Systems Biology Graphical Notation & CellDesigner. April 24th, 2012 Richard Adams [email protected] The challenge of reconstructing complex systems.

loader
I am the owner, or an agent authorized to act on behalf of the owner, of the copyrighted work described.
capcha
Download Presentation

PowerPoint Slideshow about ' Bridging the gap between modellers and biologists: Systems Biology Graphical Notation & ' - fausto


An Image/Link below is provided (as is) to download presentation

Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author.While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server.


- - - - - - - - - - - - - - - - - - - - - - - - - - E N D - - - - - - - - - - - - - - - - - - - - - - - - - -
Presentation Transcript

Bridging the gap between modellers and biologists: Systems Biology Graphical Notation &

CellDesigner

April 24th, 2012

Richard Adams

[email protected]


The challenge of reconstructing complex systems
The challenge of reconstructing complex systems Biology Graphical Notation &

"The greatest challenge today, not just in cell biology and ecology but in all of science, is the accurate and complete description of complex systems.

Scientists have broken down many kinds of systems. They think they know most of the elements and forces.

The next task is to reassemble them, at least in mathematical models that capture the key properties of the entire ensembles.”

E.O. Wilson –’Consilience’ 1998

the synthesis of knowledge from different specialized fields of human endeavor


There s a lot of information
There’s a lot of information… Biology Graphical Notation &

  • PubMed has > 20 million citations dating 1860-2012.

  • Growing at 2 per minute

  • How to organise information suitable for modelling?


Diagrams can help
Diagrams can help…. Biology Graphical Notation &


But diagrams are of uncertain utility
..but diagrams are of uncertain utility Biology Graphical Notation &


  • Plk1 activity regulates APC/C in multiple ways to promote mitotic progression. In early mitosis, Plk1 activity triggers the degradation of Emi1 via SCFß-TRCP, a prerequisite for the generation of an active APC/CCdc20 complex. However, in case of an activated spindle assembly checkpoint, Mad2 and/or BubR1 bind to Cdc20, thereby inhibiting the APC/C. Plk1 acts antagonistically to the spindle checkpoint and regulates the kinetochore localization of Mad2. Silencing of the spindle checkpoint enables the formation of active APC/CCdc20 and the degradation of cyclin B1. When Cdc20 is replaced by Cdh1, additional substrates, like Cdc20 itself and Plk1, are degraded. Finally, active APC/CCdh1 allows mitotic exit and entry into the subsequent G1 phase


What s wrong with drawing my diagrams in powerpoint
What’s wrong with drawing my diagrams in Powerpoint? mitotic progression. In early mitosis, Plk1 activity triggers the degradation of Emi1 via SCFß-TRCP, a prerequisite for the generation of an active APC/CCdc20 complex. However, in case of an activated spindle assembly checkpoint, Mad2

  • Most pathway diagrams are :

    • Ambiguous

    • Not amenable to computational analysis

    • Not interpretable without figure legend.

    • Use ‘one-off’ graphical symbols that must be learned

    • Hard to disseminate (colour, line-width, dashes).


What we really need is
What we really need is … mitotic progression. In early mitosis, Plk1 activity triggers the degradation of Emi1 via SCFß-TRCP, a prerequisite for the generation of an active APC/CCdc20 complex. However, in case of an activated spindle assembly checkpoint, Mad2


Cancer Cell - 2002, mitotic progression. In early mitosis, Plk1 activity triggers the degradation of Emi1 via SCFß-TRCP, a prerequisite for the generation of an active APC/CCdc20 complex. However, in case of an activated spindle assembly checkpoint, Mad2 2, 179-182


Sbgn goals
SBGN goals mitotic progression. In early mitosis, Plk1 activity triggers the degradation of Emi1 via SCFß-TRCP, a prerequisite for the generation of an active APC/CCdc20 complex. However, in case of an activated spindle assembly checkpoint, Mad2

  • A single diagram has a single meaning.

  • Self-explanatory.

  • Allow connectivity/ network analysis.

  • To cope with missing/incomplete information.

  • Processes to be drawn at different levels of granularity.

  • Unrestricted in use.

  • Not dependent on single software product.

  • Can be drawn by hand or printed without loss of information.


Three types of diagram
Three types of diagram mitotic progression. In early mitosis, Plk1 activity triggers the degradation of Emi1 via SCFß-TRCP, a prerequisite for the generation of an active APC/CCdc20 complex. However, in case of an activated spindle assembly checkpoint, Mad2

  • Process Description

  • Entity Relationship

  • Activity Flow


Mitotic exit in SBGN-PD mitotic progression. In early mitosis, Plk1 activity triggers the degradation of Emi1 via SCFß-TRCP, a prerequisite for the generation of an active APC/CCdc20 complex. However, in case of an activated spindle assembly checkpoint, Mad2


Entity relationship diagrams mitotic progression. In early mitosis, Plk1 activity triggers the degradation of Emi1 via SCFß-TRCP, a prerequisite for the generation of an active APC/CCdc20 complex. However, in case of an activated spindle assembly checkpoint, Mad2


Activity flow diagrams mitotic progression. In early mitosis, Plk1 activity triggers the degradation of Emi1 via SCFß-TRCP, a prerequisite for the generation of an active APC/CCdc20 complex. However, in case of an activated spindle assembly checkpoint, Mad2


PD mitotic progression. In early mitosis, Plk1 activity triggers the degradation of Emi1 via SCFß-TRCP, a prerequisite for the generation of an active APC/CCdc20 complex. However, in case of an activated spindle assembly checkpoint, Mad2

ER

AF


Tutorial using celldesigner to create and edit models
Tutorial – using CellDesigner to create and edit models. mitotic progression. In early mitosis, Plk1 activity triggers the degradation of Emi1 via SCFß-TRCP, a prerequisite for the generation of an active APC/CCdc20 complex. However, in case of an activated spindle assembly checkpoint, Mad2

  • CellDesigner overview

  • Circadian clock model drawing and modelling

  • ‘Exit from mitosis diagram’.

  • ‘Bring your own’.

Goals:

Create a kinetic model in CellDesigner

Develop a working knowledge of SBGN-PD

Learn to use CellDesigner pathway editing/simulation software


CellDesigner <-> SBML mitotic progression. In early mitosis, Plk1 activity triggers the degradation of Emi1 via SCFß-TRCP, a prerequisite for the generation of an active APC/CCdc20 complex. However, in case of an activated spindle assembly checkpoint, Mad2

<reaction id="Reac_1" name="v1" reversible="false" fast="false">

<listOfReactants>

<speciesReference species="A"/>

</listOfReactants>

<listOfProducts>

<speciesReference species="B"/>

</listOfProducts>

<kineticLaw>

<math xmlns="http://www.w3.org/1998/Math/MathML"> <apply>

<apply>

<times/>

<ci> k1 </ci>

<ci> A </ci>

</apply>

</math>

</kineticLaw>

</reaction>

A

B


ad