Any population geneticists out there? interested in a Ruby SIG?

[Phil Rhoades]

People,

I have previously done all my simulation work in C/C++ (as a C++
exercise really) but it would be nice to do further work in Ruby
(although I am concerned about performance for big simulations - might
need a C interface?). Using Ruby for large scale redevelopments is
probably not going to be possible until I get the thesis finished but it
would be good if I had some idea if there are other people doing things
of interest who are interested in chatting about stuff.

Regards,

Phil.
--
Philip Rhoades

Pricom Pty Limited (ACN 003 252 275 ABN 91 003 252 275)
GPO Box 3411
Sydney NSW 2001
Australia
E-mail: (e-mail address removed)

 

[Joel VanderWerf]

People,

I have previously done all my simulation work in C/C++ (as a C++
exercise really) but it would be nice to do further work in Ruby
(although I am concerned about performance for big simulations - might
need a C interface?). Using Ruby for large scale redevelopments is
probably not going to be possible until I get the thesis finished but it
would be good if I had some idea if there are other people doing things
of interest who are interested in chatting about stuff.

I'm very interested in simulation with ruby (and C), though probably
using very different constructs than you are. What sorts of models do
you use? Is any part of it continuous dynamics, ODEs?

 

[Michael Linfield]

Lately I'm down for anything, let me know some details and I'll tell you
what I think.

 

[M. Edward (Ed) Borasky]

People,

I have previously done all my simulation work in C/C++ (as a C++
exercise really) but it would be nice to do further work in Ruby
(although I am concerned about performance for big simulations - might
need a C interface?). Using Ruby for large scale redevelopments is
probably not going to be possible until I get the thesis finished but it
would be good if I had some idea if there are other people doing things
of interest who are interested in chatting about stuff.

Regards,

Phil.

"Simulation" is a pretty broad term, including discrete-event
simulation, for example. What sort of simulations do population
geneticists do?

 

[Phil Rhoades]

I'm very interested in simulation with ruby (and C), though probably
using very different constructs than you are. What sorts of models do
you use? Is any part of it continuous dynamics, ODEs?

DNA, specifically microsatellite replication, generations of organisms,
mutation etc - modelling thratened populations. So they are Individual
Based Models rather than say a Differential Equation Model.

Regards,

Phil.

--
Philip Rhoades

Pricom Pty Limited (ACN 003 252 275 ABN 91 003 252 275)
GPO Box 3411
Sydney NSW 2001
Australia
E-mail: (e-mail address removed)

 

[Axel Etzold]

-------- Original-Nachricht --------

Datum: Thu, 15 May 2008 14:12:37 +0900
Von: Phil Rhoades <[email protected]>
An: (e-mail address removed)
Betreff: Re: Any population geneticists out there? interested in a Ruby SIG?

DNA, specifically microsatellite replication, generations of organisms,
mutation etc - modelling thratened populations. So they are Individual
Based Models rather than say a Differential Equation Model.

Regards,

Phil.

--
Philip Rhoades

Pricom Pty Limited (ACN 003 252 275 ABN 91 003 252 275)
GPO Box 3411
Sydney NSW 2001
Australia
E-mail: (e-mail address removed)

Philip,

if you have individual problems of many different kinds, maybe you get
the best input by posting on a general list ... eg, this one.

There is some software for genetic algorithms in Ruby, like:

http://gga4r.rubyforge.org/

or constraint programming,

http://conssolv.rubyforge.org/
http://gecoder.rubyforge.org/

A good place to look for Ruby and science in general is :

http://sciruby.codeforpeople.com/

If you want to use C/C++ code from Ruby, you might be interested in following this project:

http://rubyforge.org/projects/rbplusplus/

Best regards,

Axel