I'm trying to find a better way to identify an 'equilibrium' genome score for our simulations of uptake sequence evolution. Ideally I would just let the runs go until the score was stable, but two factors complicate this. First, the scores are very noisy due to genetic drift, so there is no stable core. In principle this can be smoothed out by taking the mean score over a sufficiently long interval, but in practice the runs take a long time.
I have been working on complicated averaging strategies to deal with this, but for many runs I thought I could just stop trying to be economical of computer time. So I queue'd up a few very long runs, but this didn't really solve the problem, because the mean scores just drift up and down.
Finally I tried just plotting the 'grand mean' scores of the up-from-random-sequence-genome and down-from-seeded-sequence-genome runs ('up' and 'down' runs) on the same graph, and taking the average of the final values. The 'grand mean' score is the geometric mean of the genome scores at every cycle from the start of the run. For up runs it's a underestimate of the recent mean, and for the down runs it's an overestimate, but in both cases its much smoother than the recent mean. I'll paste a graph in later, but these give what look like pretty good stable estimates of equilibrium values. So I think I'll just state in the methods that runs were continued until the up and down grand mean scores differed by no more than two-fold, and then the final scores were averaged to give an equilibrium score.
- Home
- Angry by Choice
- Catalogue of Organisms
- Chinleana
- Doc Madhattan
- Games with Words
- Genomics, Medicine, and Pseudoscience
- History of Geology
- Moss Plants and More
- Pleiotropy
- Plektix
- RRResearch
- Skeptic Wonder
- The Culture of Chemistry
- The Curious Wavefunction
- The Phytophactor
- The View from a Microbiologist
- Variety of Life
Field of Science
-
-
Don't tell me they found Tyrannosaurus rex meat again!2 weeks ago in Genomics, Medicine, and Pseudoscience
-
-
-
Course Corrections4 months ago in Angry by Choice
-
-
The Site is Dead, Long Live the Site2 years ago in Catalogue of Organisms
-
The Site is Dead, Long Live the Site2 years ago in Variety of Life
-
Does mathematics carry human biases?4 years ago in PLEKTIX
-
-
-
-
A New Placodont from the Late Triassic of China5 years ago in Chinleana
-
Posted: July 22, 2018 at 03:03PM6 years ago in Field Notes
-
Bryophyte Herbarium Survey7 years ago in Moss Plants and More
-
Harnessing innate immunity to cure HIV8 years ago in Rule of 6ix
-
WE MOVED!8 years ago in Games with Words
-
-
-
-
post doc job opportunity on ribosome biochemistry!9 years ago in Protein Evolution and Other Musings
-
Growing the kidney: re-blogged from Science Bitez9 years ago in The View from a Microbiologist
-
Blogging Microbes- Communicating Microbiology to Netizens10 years ago in Memoirs of a Defective Brain
-
-
-
The Lure of the Obscure? Guest Post by Frank Stahl12 years ago in Sex, Genes & Evolution
-
-
Lab Rat Moving House13 years ago in Life of a Lab Rat
-
Goodbye FoS, thanks for all the laughs13 years ago in Disease Prone
-
-
Slideshow of NASA's Stardust-NExT Mission Comet Tempel 1 Flyby13 years ago in The Large Picture Blog
-
in The Biology Files
Not your typical science blog, but an 'open science' research blog. Watch me fumbling my way towards understanding how and why bacteria take up DNA, and getting distracted by other cool questions.
No comments:
Post a Comment
Markup Key:
- <b>bold</b> = bold
- <i>italic</i> = italic
- <a href="http://www.fieldofscience.com/">FoS</a> = FoS