From our News&Views with @rayanchikhi and @yoanndufresne
"[I]t is a good time to reinforce the standard that the output produced by a bioinformatics tool should be well defined...[W]hen a user has a pangenome reference in their hands, they should know what properties it has .... [P]angenome tool developers should ... minimize ad hoc heuristics and arbitrary parameters..."
"On the one hand, a population pangenome graph faithfully represents the complete variation of haplotypes present in some population of interest. On the other hand, an application-specific pangenome graph reflects only some of the population variability and is instead tailored toward maximizing the performance of application-specific downstream tools."
Gasarch on what counts as "closed form" and what does not, using the Ordered Bell numbers as an example: https://blog.computationalcomplexity.org/2024/05/what-is-closed-form-horse-numbers-are.html
He asks, in the form of a Platonic dialogue: is \(\tbinom{n}{i}\) or \(\tfrac{n!}{i!(n-i)!}\) closed form? What, if anything, makes that sort of formula different from the formula \(H(n)\), denoting the \(n\)th ordered Bell number?
@themaklin @EricPelletier @Pashadag
This is now published at PLOS CB!
https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1011920
Rob
0xDE
Pierre Lindenbaum
Luis Pedro Coelho
bioRxiv Bioinformatics