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Date: 2009/06/10 22:07:37, Link
Author: AnsgarSeraph
Hi, all —

I'm another migrant from TWeb; I've got Mendel's Accountant set up on a 32-bit and a 64-bit system. I certainly won't be much help with any actual knowledge but I'm very willing to run simulations for anyone who doesn't have/doesn't want Mendel set up on their computer.

I've found that Mendel will allow my 4GB setup to run small populations (~1000) for about 40,000 generations or larger populations (~10,000) for less than 10,000 generations. I plan on purchasing some extra RAM soon so I might be able to extend the runs a bit. I did not see much difference in latitude running a 64-bit setup but extra RAM might change that.

The user manual for Mendel's Accountant is here. If helpful, I can (hopefully) attach screen grabs of the advanced Mendel settings so people don't need to hunt through the manual.

—Sam

Date: 2009/06/10 22:10:43, Link
Author: AnsgarSeraph
Sorry. The manual is HERE:

Mendel's Accountant User Manual

There is also a Linux how-to but the SourceForge page does not have the tarball listed. Some advanced features of MENDEL require Linux. They are almost certainly unnecessary for a FAQ but I'll e-mail the maintainer of the code (Dr. Brewer, I think) and try to get that.

—Sam

Date: 2009/06/11 11:41:24, Link
Author: AnsgarSeraph
Quote (Wesley R. Elsberry @ June 11 2009,11:29)
So, how much "evolution sucks" verbiage was generated by the people running the pre-1.4.1 versions? Was there any notice that people should re-run their experiments due to a pretty drastic change in program behavior?

To be fair (to a shoddy program? How odd), v. 1.4.1 still "demonstrates" all the genetic entropy problems that Sanford makes noise about. Whatever they fixed in terms of beneficial mutations, our runs at TWeb using 1.4.1 indicate that it's nowhere near enough; a 90% beneficial mutation rate with default "maximal benefit effect" still reduces fitness in a linear manner.

—Sam

Date: 2009/06/11 11:45:52, Link
Author: AnsgarSeraph
Quote (Wesley R. Elsberry @ June 11 2009,11:29)
So, how much "evolution sucks" verbiage was generated by the people running the pre-1.4.1 versions? Was there any notice that people should re-run their experiments due to a pretty drastic change in program behavior?

To be fair (to a shoddy program? How odd), v. 1.4.1 still "demonstrates" all the genetic entropy problems that Sanford makes noise about. Whatever they fixed in terms of beneficial mutations, our runs at TWeb using 1.4.1 indicate that it's nowhere near enough; a 90% beneficial mutation rate with default "maximal benefit effect" still reduces fitness in a linear manner.

—Sam

Date: 2009/06/11 12:52:21, Link
Author: AnsgarSeraph
Quote (utidjian @ June 11 2009,12:17)
Is anyone else playing with the source (or even reading it)?
I also found this file in the Source folder:

Code Sample

      47469 max_tracked_mutn_per_indiv
         


Anything interesting in there?

-DU-

That number is considerably higher than the input parameters on my runs; ranging from a population of 1000 to a population of 10,000, I think the highest setting on my runs for that was ~25,000 tracked mutations per individual. I'm not sure how they calculate for that parameter. This might be one of the limiting factors in testing MENDEL, as I have already run up against a "Favorable mutation count exceeds limit" error.

—Sam

Date: 2009/06/11 13:23:45, Link
Author: AnsgarSeraph
Quote (Steve Schaffner @ June 11 2009,13:02)
For those who have the program running . . . Can it provide more output? Comparing results with theory would be much more straightforward if one could count only the number of mutations that have fixed, rather than all present in the population; it would also be useful to see the allele frequency spectrum. (And if it can't do those things, then it is of no interest as a population genetics tool.)

Is the allele frequency spectrum you're looking for in here?

Box.net - human1 sample Folder

I think what you're looking for might be titled "human1_plm.png".

The output files in MENDEL do give a count for the number of fixed alleles; it's near the bottom of the output file and looks like this:

Code Sample

Allele summary statistics (tracked mutations only):
   (Statistics are based on       891517 tracked deleterious mutations
                        and            0 tracked   favorable mutations.)
    Very rare   Polymorphic     Fixed      Total
      (0-1%)      (1-99%)      (100%)
       15107        8202           0       23309 deleterious
           0           0           0           0 favorable


—Sam

Date: 2009/06/11 20:50:29, Link
Author: AnsgarSeraph
Quote (Zachriel @ June 11 2009,20:41)
The program doesn't seem to use my available memory and quits well before the specified generations.

With a fitness level at 0.1, I'm sure your populations went extinct. I can't keep populations below 1000 alive for very long; they certainly won't last for more than 20,000 generations.

—Sam

Date: 2009/06/16 17:01:15, Link
Author: AnsgarSeraph
Quote (sledgehammer @ June 16 2009,14:42)
Maybe someone who has MA up and running (Zach, Sam?) could try this and report?

I was actually running simulations on this idea earlier today and will be posting some graphs up on TWeb within the next hour. The runs were identical, save that one run had a "maximal fitness effect" of 0.001 and the other a maximal fitness effect of 0.01. The first population, after ~6000 generations, had a fitness of 0.844. The second, after the same number of generations, had a fitness of 1.350. The number of beneficial mutations was cranked up to 75% to ensure the runs went for a significant number of generations.

I also received an e-mail from Dr. Sanford today, part of which dealt in this area . . . I am waiting to hear from him whether I have permission to forward his entire e-mail on forums; there wasn't any revelatory information, in any case. Dr. Sanford feels that 0.001 is an appropriate setting but is willing to discuss whether that is the case or not.

—Sam

Date: 2009/06/16 19:00:31, Link
Author: AnsgarSeraph
I didn't see an option for me to add to your Photobucket page, so I registered and created my own.

Here are the files. The first two are fitness graphs:






These are the distribution graphs for JSW507 (deleterious first, beneficial second):






And 508:







I've uploaded all the pictures, as well as the Input and Output files to my Box.net account, also:

MENDEL Run - JSW507, JSW508

—Sam

Date: 2009/06/16 19:51:21, Link
Author: AnsgarSeraph
Quote (Zachriel @ June 16 2009,19:38)
Is that with maximum beneficial effect equal to one versus default? Fraction favorable is set very high.

Consider this. If we use the defaults, then no beneficial mutation becomes fixed, which is contrary to fact. Even if you believe species are ultimately doomed to genetic meltdown, it still means the default parameters or the program itself has a problem.

The first run (JSW507) has a maximum beneficial effect of 0.01, while the second run (JSW508) is set to the default 0.001. There's only one order of magnitude between the two runs.

Sanford seems to be willing to give on the accuracy of the default parameters for the program . . . which is odd, in that those are the parameters he defends as biologically realistic in his papers. I think there are enough wrong parameters (and possibly a completely wrong coding paradigm) that any couple of parameters could be fixed and the population would still show fitness decline.

At the moment, I'm leaning toward the idea that the program is broken . . . but hopefully we can get Dr. Sanford on TWeb soon enough and have some clear back-n-forth.

—Sam

Date: 2009/06/24 21:24:37, Link
Author: AnsgarSeraph
I've been in touch with Dr. Wes Brewer, who maintains the MENDEL code. He's still working on the Linux flavors and hopes to have a production copy soon. He's not comfortable posting it on a public site, at the moment, but said that I could privately supply the link to people here who want it.

The "big deal" aspect of it is that this is version 1.4.5. It looks like the source code is packaged in "cgi-bin/cmendel" and "cgi-bin/fmendel" (but that's just from the README . . . I don't know code so I didn't open any files).

Anyone who wants this thing can email me @

whitebriar - gmail - com

—Sam

 

 

 

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