The JigCell Problem Solving Environment (PSE)
Marc Vass and Nick AllenDepartment of Computer Science
Virginia Tech
Computational Molecular Biology
Conversions are done by hand
CdkCycB
Cdh1 CK
I
ClnCdk
Cdc20 +APC
Molecular network
+APCd CDK
dt = k1 - (v2’ + v2” . Cdh1 ) . CDK
d Cdh1dt =
(k3’ + k3” . Cdc20A) (1 - Cdh1) J3 + 1 - Cdh1 -
(k4’ + k4” . CDK . M) Cdh1 J4 + Cdh1
d IEPdt = k9
. CDK . M . (1 – IEP ) – k10 . IEP
d Cdc20T
dt = k5’ + k5” (CDK . M)4
J54 + (CDK . M)4 - k6
. Cdc20T
d Cdc20A
dt = k7
. IEP (Cdc20T - Cdc20A) J7 + Cdc20T - Cdc20A
- k8
. MAD Cdc20A
J8 + Cdc20A - k6
. Cdc20T
Differential equations
growth
RENT
Lte1
Clb5MBF
P Sic1 SCFSic1Swi5
Clb2Mcm1
APC
Cdc14
Cdc14
CDKs
Cln2SBF
?
andCln3
Bck2
DNA synthesis
Inactive trimer
Inactive trimer
P
Clb2
Budding
Cdc20
Cdc20
Cdh1
Cdh1
Mcm1
Mad2
unaligned chromosomes
Cdc14
SBF
Esp1 Esp1Pds1
Pds1
Net1
Net1P
PPX
Cdc15/MENTem1-GDP
Tem1-GTPBub2
unaligned chromosomesCdh1
Sister chromatid separation
Mcm1
IEP
Cln2Clb2Clb5
Cdc20
The JigCell PSE
Why we need a PSE Representing a model Making a prediction based on the
model Validating a model
Without a PSE
Impossible to move beyond simple hand built models
Evaluating models is repetitive and time consuming
Leads to more errors
Performing a Comparison
Identify experimental results of interest
Define a simulation with equivalent conditions
Massage simulation results into a usable form
Run an objective evaluation
Conclusions
JigCell allows modelers to produce truly useful computer representations of molecular regulatory systems
JigCell also allows modelers to quickly evaluate and re-evaluate changes to their models against experimental data
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