Description
- Plasmodium falciparum
- Common name:
Description: any other discussion or useful background? (optional)
Note: Maybe you don't know a lot of the things below - but, that's OK!
The criteria are that (a) the choice is reasonable, and (b) the rationale is clear.
What we want is a "reasonable estimate" (or, "best guess") - if you were to use a number in a paper,
what would you use and how would you justify it to your collaborators?
For instance, for "generation time", best would be to cite a paper that actually measures
or estimates generation time. But most species don't have this;
next best would be to give a number used in the literature, and provide a citation that used it
(and hopefully the publication gives a justification also).
Lacking this, you might provide a number from a related species (and a citation for this).
Here is the checklist of things that we need to add a species to the catalogue.
Each thing should be provided, with a justification (maybe short) and a citation.
Demographic information:
- [] generation time in years
- [] "default" population size
Chromosome structure:
- [] ensembl assembly ID or, if the assembly is not in Ensembl, a list of chromosomes with name and length (in bp)
Note: species in Ensembl can be found in one of these lists:
vertebrates,
"metazoa",
plants,
fungi,
protists,
or bacteria.
Recombination rates:
- [] genetic map of recombination rates (as a hapmap or csv file)
- [] genome-wide mean recombination rate (which will be used as the default)
Mutation rate:
- [] genome-wide mean mutation rate
Demographic model:
- [] as a list of population sizes, growth rates, migration rates, etcetera. (optional)
- [] citation
Other information:
These are things we don't currently use, but will want to use in the future:
- [] sex determination system, and which chromosomes are the sex chromosome(s)
- [] ploidy