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.
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Bridging the gap between modellers and biologists: Systems Biology Graphical Notation &
April 24th, 2012
"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
Cancer Cell - 2002, 2, 179-182
Mitotic exit in SBGN-PD
Entity relationship diagrams
Activity flow diagrams
Create a kinetic model in CellDesigner
Develop a working knowledge of SBGN-PD
Learn to use CellDesigner pathway editing/simulation software
CellDesigner <-> SBML
<reaction id="Reac_1" name="v1" reversible="false" fast="false">
<math xmlns="http://www.w3.org/1998/Math/MathML"> <apply>
<ci> k1 </ci>
<ci> A </ci>