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Simulators
available:
Simulator005
"WorldRatchet"
simulates
Muller's ratchet in a single asexual population to determine rates
of genomic decay for several parameter combinations of mutation
rate, selection coefficient and population size. Download program
and input run-files.
If you want to
get a email whenever a new simulator for your platform is available,
please register.
To participate, you do not need to register, just submit results.
You may want
to get an overview
over how
simulators help to model biological reality and how they work practically.
Here is a description
of our lates project:
Project
3 enters the long-term computing phase (30 Jan 2006)
More than 3.5 years
of CPU time have been submitted since the start of Project 3. For
the moment the simple tasks have been computed with enough accuracy.
Now computation will have to focus on the more complex tasks that
will take several CPU-decades to resolve.
Project 3 looks at the
effects of Muller's ratchet if combined with another ratchet process
that has different mutational parameters. A thorough analysis requires
the computation of a very large number of parameter combinations
(See here
for statistics). Since most of these processes will be operating
in fairly large populations in nature, their computational modelling
is again a challenge worthy of evolution@home.
New
project for Simulator005 looks at the combined effects of two types
of mutations (1 Nov 2005)
Thanks
to your contributions the first major project of Simulator005 has
been completed to an acceptable degree. Now it is time to extend
the very simple observations of mutation accumulation from the first
project towards the more complicated case, where two types of mutations
can potentially accumulate in the same population. This is an important
step towards understanding more realistic situations as those faced
by real organisms.
The first major simulation
project of Simulator005 has been declared complete. With more than
83 years of contributed computing time and over 100 000 simulation
results enough statistical power has been accumulated for the analyses
that are being carried out at the moment. Those of you, who still
want to contribute to that project can continue to do so and you
should certainly submit the results you have already computed, as
this will further increase the statistical power of future analyses.
Some results from this project are being written up and others are
under peer-review. As the scientific review of the results is beeing
completed, you will read about it on this website.
Those of you who want
to start new run-files can get them here.
In these tasks Simulator005
looks at what happens, if two different Muller's ratchet processes
operate in the same population at the same time. This collection
of run-files contains 21680 simulations of an estimated CPU-time
of less than 1 month with a total of 98.7 years most probable CPU-time
and 714 simulations of an estimated CPU-time of more than 1 month
with a total of 97.1 years most probable CPU-time. Since some of
the run-files are quite long, some of you might want to consider
editing them manually to compute some of the parameter combinations
from the back sooner than their original order.
Muller's ratchet is already
hard to understand if all mutations have the same effect; however,
when two different types of mutations (occurring at different rates
and having different effects) start to interact, then it becomes
even harder to predict the rate of mutation accumulation. Since
the estimate of the most likely computing time strongly depends
on the rate of mutation accumulation, some of the predicted computing
times will be very inaccurate. If that is the case and you counted
on a simulation to complete at a certain date, then just stop the
simulation. The incomplete result of that simulation will eventually
end up in the results-file, so that it will be submitted with your
next results submission. On the long run simulations like these
will be used to improve computing time predictions.
The careful readers among
you will have noted that this new project is the third, where as
the last big project was the first. Between these two there was
a small project that explored the upper limit of population sizes
that can be computed on 32-bit CPUs. This project 2 contains only
a limited parameter range of some very large simulations. Those
of you, who enjoy exploring simulations with extremely large RAM
requirements are invited to explore these run-files.
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