Science

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. ...

So I heard many people say after or during the recent ESA conference in Portland that they really enjoyed the converstations more than listening to talks or looking at posters. There was some chatter about doing an unconference associated with next year’s ESA conference in Minneapolis. And Sandra Chung (@sandramchung) got on it and started a wiki that we can all conribute ideas to. The wiki is here What is an unconference? The idea of an unconference is to have a community organized meetup in which interactions among people are emphasized over the traditional lecture and poster format. For example, many sessions may just be organized a single idea, and people attending have a discussion around the topic. The format can be decided by the community. ...