Sinatra

The problem The R community has a package distribution thing called CRAN just like Ruby has Rubygems, and Python has Pypi, etc. On all packages on CRAN, the CRAN maintainers run checks on each package on multiple versions of R and on many operating systems. They report those results on a page associated with the package, like this one. You might be thinking: okay, but we have Travis-CI and friends, so who cares about that? Well, it’s these checks that CRAN runs that will determine if your package on CRAN leads to emails to you asking for changes, and possibly the package being taken down if e.g., they email and you don’t respond for a period of time. ...

GBIDS API is back Back in March this year I wrote a post about a new API for working with GenBank IDs. I had to take the API down because it was too expensive to keep up. Expensive because the dump of data is very large (3.8 GB compressed), and I need disk space on the server to uncompress that to I think about 18 GB, then load into MySQL, which is another maybe 30 GB or so. Anyway, it’s not expensive because of high traffic - although I wish that was the case - but because of needing lots of disk space. ...

GenBank IDs, accession numbers and GI identifiers, are the two types of identifiers for entries in GenBank. (see this page for why there are two types of identifiers). Actually, recent news from NCBI is that GI identifiers will be phased out by September this year, which affects what I’ll talk about below. There are a lot of sequences in GenBank. Sometimes you have identifiers and you want to check if they exist in GenBank, or want to get one type from another (accession from GI, or vice versa; although GI phase out will make this use case no longer needed), or just get a bunch of identifiers for software testing purposes perhaps. ...