LecturesPart26

LecturesPart26 - Computational Biology Part 26 Virtual Cell...

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Unformatted text preview: Computational Biology, Part 26 Virtual Cell Robert F. Murphy Copyright © 2005,2006. Copyright All rights reserved. Virtual Cell - NRCAM http://www.nrcam.uchc.edu/vcellR4/login/login.jsp s Framework for building and running models Framework of cell biological processes of s Built in support for describing Built compartments, biochemical species, electrophysiological phenoma electrophysiological s Models can incorporate empirically derived Models geometries for compartments geometries s Models saved and calculated on the server Virtual Cell - To do s Create account s Read User Guide Virtual Cell - Hodgkin-Huxley s Versions of the models in “Computational Versions cell biology” by Fall et al have been implemented in Virtual Cell implemented s These are available as Public models s Within Virtual Cell, use Open/Biomodel s Then open Model Then Neighborhood/CompCell/Hodgkin-Huxley Neighborhood/CompCell/Hodgkin-Huxley Model Descriptions s Virtual Cell supports exporting (and to a Virtual limited extent, importing) model descriptions in various XML formats descriptions x SBML (Systems Biology Markup Language, SBML uses MathML) uses x CellML x VCML (Virtual Cell Markup Language) VCML required to re-import full model required SBML <sbml xmlns="http://www.sbml.org/sbml/level2" <sbml xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" level="2" version="1"> level="2" <notes> <notes> <body xmlns="http://www.w3.org/1999/xhtml"> <body <p>Models electrical behavior of the squid giant axon. Used to demonstrate interacting ion channels. Described in 2.5.</p> Described </body> </body> </notes> </notes> <model id="Hodgkin_Huxley"> <model <notes> <notes> <body xmlns="http://www.w3.org/1999/xhtml"> <body <p>Models electrical behavior of the squid giant axon. Used to demonstrate interacting ion channels. Described in 2.5.</p> Described </body> </body> </notes> </notes> <listOfUnitDefinitions> <listOfUnitDefinitions> SBML <listOfRules> <listOfRules> <assignmentRule variable="minf"> <assignmentRule <math xmlns="http://www.w3.org/1998/Math/MathML"> <math <apply> <apply> <times /> <times <cn>100.0</cn> <cn>100.0</cn> <ci>taum</ci> <ci>taum</ci> <apply> <apply> <plus /> <plus <cn>40.0</cn> <cn>40.0</cn> <ci>V</ci> <ci>V</ci> </apply> </apply> <apply> <apply> <divide /> <divide <cn>1.0</cn> <cn>1.0</cn> <apply> <apply> <plus /> <plus <cn>1.0</cn> <cn>1.0</cn> CellML <model xmlns="http://www.cellml.org/cellml/1.0#" name="unnamed"> name="unnamed"> <units name="uM"> <units <unit units="mole" prefix="-6" /> <unit <unit units="litre" exponent="-1" /> <unit </units> </units> <units name="uM.s-1"> <units <unit units="mole" prefix="-6" /> <unit <unit units="litre" exponent="-1" /> <unit <unit units="second" exponent="-1" /> <unit </units> </units> <units name="item" base_units="yes" /> <units <units name="molecules"> <units <unit units="item" /> <unit </units> </units> <units name="molecules.um-2.s-1"> <units <unit units="dimensionless" multiplier="1.0000000000000001E12" exponent="1" offset="0.0" /> offset="0.0" CellML <BioModel Name="Hodgkin-Huxley"> <BioModel <Annotation>Models electrical behavior of the squid giant axon. Used to demonstrate interacting ion channels. Described in 2.5.</Ann\ Described otation> <Model Name="unnamed"> <Model <Compound Name="K"> <Compound <Annotation>K</Annotation> <Annotation>K</Annotation> </Compound> </Compound> <Compound Name="h_o"> <Compound <Annotation>Na Channel H Gate (Open)</Annotation> <Annotation>Na </Compound> </Compound> <Compound Name="Na"> <Compound <Annotation>Na</Annotation> <Annotation>Na</Annotation> </Compound> </Compound> <Compound Name="m_o"> <Compound <Annotation>Na Channel M Gate (Open)</Annotation> <Annotation>Na </Compound> </Compound> Building a simulation s To illustrate building a new simulation, we To will build a model in which will x Prohormone is initially outside a cell, x Prohormone is internalized into the cell, x Prohormone is converted to hormone x Hormone is exported from the cell Building a simulation s Define a Cell compartment s Rename unnamed compartment to Rename Extracellular Extracellular s Add a species “prohormone” to Add Extracellular Extracellular s Add a species “hormone” to Extracellular s Copy species “prohormone” to Cell s Copy species “hormone” to Cell Building a simulation s s s s s Right (control) click on Cell membrane Define a flux for prohormone as Define “0.1*prohormone_Extracellular” “0.1*prohormone_Extracellular” Define a flux for hormone as “1.0*hormone_Cell” Right (control) click on Cell Define a reaction for prohormone to hormone with Define mass action forward rate=1.0 and reverse rate=0.0 mass Building a simulation s s s Define a new Application Give initial value for prohormone_Extracellular as Give 10.0 10.0 Run model Models that consider compartment geometry s Virtual Cell facilitated Ca-diffusion model Virtual from tutorial from Making a compartment map for Virtual Cell from a fluorescence microscope image Start from a fluorescence microscope image of a lysosomal protein (LAMP-2) (LAMP-2) Making a compartment map for Virtual Cell from a fluorescence microscope image s Use Matlab to create an image with values Use of zero for background, one for cytoplasm, and two for lysosomes and s Assume that the autofluorescence in the Assume lysosome image is sufficient to find a region corresponding to the cytoplasm corresponding Make contiguous cytoplasm image by averaging weak autofluorescence img=imread('r06aug97.h4b4.13--1---2.dat.png'); a=double(img); b=(a-min(min(a)))./(max(max(a))-min(min(a))); H=fspecial('average',13); c=imfilter(b,H,'replicate'); d=im2bw(c,0.004); imshow(d); max(max(d)) Combine with image of pixels with positive lysosomal staining e=im2bw(b,graythresh(b)); e=im2bw(b,graythresh(b)); imshow(e); f=d + e; imshow(f,[0 2]); g=uint8(f); imwrite(g,'geomap.tif','TIF','Compression','none'); Resulting image ...
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This note was uploaded on 01/13/2012 for the course BIO 101 taught by Professor Staff during the Fall '10 term at DePaul.

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