Re: [stem-dev] stem-dev Digest, Vol 97, Issue 2

["James Kaufman" <jhkauf@xxxxxxxxxx>]

Hi Emily,
The nonlinearity coefficient is for
those that want to model the mass action term as (SI)y
where y is the nonlinearity exponent.
For all of your models you want y=1.0
(ie not a power law) so the interaction term is just SI
We can discuss why some models put this
in but I don't think it is something you will have to worry about.

Random seed will not matter if you are
running a deterministic model. For a stochastic model being able to set
the seed for the random number generator makes it possible to reproduce
a run (with noise) exactly, and of course to change it over multiple runs.
In fact, the new stochastic solver may set this seed separately. Stochasticity
used for be an optional part of DiseaseModel but it made more sense to
move it to the solver itself.


Best Regards,
Jamie

IBM Almaden Research Center, 650 Harry Rd.
San Jose, CA 95120-6099
email: jhkauf@xxxxxxxxxx
phone: (408) 927-2477  (tie 457-2477)





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 05/03/2017 09:00 AM
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   stem-dev Digest,
Vol 97, Issue 2
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Today's Topics:

   1. Non-linearity coefficient and random seed parameters (Emily
Nixon)


----------------------------------------------------------------------

Message: 1
Date: Wed, 3 May 2017 16:03:13 +0100
From: Emily Nixon <emily.nixon@xxxxxxxxxxxxx>
To: stem-dev@xxxxxxxxxxx
Subject: [stem-dev] Non-linearity coefficient and random seed
                
parameters
Message-ID:
                
<CAFsyUbzR6Bv2ckvOiWQvUDc-y+O=4SF-Q7xawNkOa1Ei0-WsNA@xxxxxxxxxxxxxx>
Content-Type: text/plain; charset="utf-8"

Hi all,

Could someone explain to me what the "Non-linearity coefficient"
and the
"Random seed" parameters for the disease models are? I was just
using the
default values for my test model, but I need to use more accurate values
now.

Best wishes,

Emily

-- 
*Emily Nixon*
*PhD Student*
Demonstrator

School of Biological Sciences

University of Bristol
Bristol Life Sciences Building
24 Tyndall Avenue
Bristol
BS8 1TQ

Tel +44 (0)117 394 41389
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