RE: [Swarm-Modelling] modelling antibody binding

[Virginia Nivar]

Hi Caroline,

I am also a biologist and I have been using Repast to model the interactions of the cells of the immune system.  There may be an audible groan from the Repast crowd when I say this, but you could begin with code from the "HeatBugs" demo model, using agents to represent the antibodies moving ramdomly in a "world" that is the dish.  You wouldn't need the signal generation part of the code.  The agents could have two arm variables (or objects) with whatever specificity and other properties that you want to give them.  You could also give them Fc variables or objects.  The RBC's could also be represented as randomly moving agents with antigen variables/objects.  People often use randomly generated strings of bits to represent antigen specificity.  You can search the work of Stephanie Forrest for examples of this.  You didn't mention your level of expertise in Java programming, but a good knowledge of Java is necessary to use Repast.  There is another software tool called NetLogo that people who don't know how to program can use to create some pretty impressive models (see the work of Gary An).  I have never used Swarm so I don't have any suggestions for it.  Fell free to contact me for more information.

Virginia Folcik

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From:  "Caroline Buckee" <address@hidden>
Reply-To:  address@hidden, Agent-based modeling <address@hidden>
To:  address@hidden
Subject:  [Swarm-Modelling] modelling antibody binding
Date:  Thu, 13 Jul 2006 09:08:36 +0300

Hello,

I am a biologist, and would like to use swarm to model the dynamics of

antibody agglutination (I'll explain). Does anyone have any advice as to

how to go about it or where to find similar code (in java)? The

agglutination reaction involves antibodies of a particular type binding

to red blood cells of a corresponding type (there can be several

different types). Antibodies have two 'arms', and sometimes bind two

different red blood cells, one with each arm - effectively sticking the

them together into an 'agglutinate'. The antibodies and cells are moving

(due to rotation of the plate in the lab) so that over time, different

size agglutinates form, each made up of different types of

cells+antibodies (ranging from two up to a thousand cells).

Any advice? Any 'sticking agents together' code would be useful...

Thanks,

Caroline

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