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

Hi Emily,

the seed parameter on the disease model is obsolete and not used. The seed on the stochastic solver can be set to anything you like. If you start a simulation with the same seed twice you're expected to get the same results in the outputs. Different seeds in two runs and you'd expect to get different result. Hope this helps, Cheers, Stefan

Stefan Edlund
Research Software Engineer - Industrial and Applied Genomics
IBM Research - Almaden
(408) 927-1766 sedlund@xxxxxxxxxx


Inactive hide details for Emily Nixon ---05/04/2017 01:48:45 AM---Hi Jamie, Thanks, that's all very helpful.Emily Nixon ---05/04/2017 01:48:45 AM---Hi Jamie, Thanks, that's all very helpful.

From: Emily Nixon <emily.nixon@xxxxxxxxxxxxx>
To: STEM developer mailing list <stem-dev@xxxxxxxxxxx>
Date: 05/04/2017 01:48 AM
Subject: Re: [stem-dev] stem-dev Digest, Vol 97, Issue 2
Sent by: stem-dev-bounces@xxxxxxxxxxx




Hi Jamie,

Thanks, that's all very helpful. 

One of my models will be stochastic so I will need to use a seed. The default seed on the disease models seems to be 1, whereas it is 17 on the stochastic solver. Does the number itself make a difference or is it just an ID code? Should I set the seed number for the disease model and the stochastic solver to be the same? Once I've run a model with a particular seed, do I then need to pick a new number when running another model? 

Best wishes,

Emily


On 3 May 2017 at 18:15, James Kaufman <jhkauf@xxxxxxxxxx> wrote:
    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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    Date:            05/03/2017 09:00 AM
    Subject:            stem-dev Digest, Vol 97, Issue 2
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      1. Non-linearity coefficient and random seed parameters (Emily Nixon)


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    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
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    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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--
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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