- The subsystem count at the bottom of the organism summary page is no longer be active as a link. Previously, this took the user into the SEED and there was no real way to get back from that. It was easier to simply disable the link in NMPDR than convert the entire subsys_vector script.
- The downloads page presents an FTP directory when the user clicks the FTP link. When the user clicks the HTTP link, a ZIP file of the directory is downloaded to the user's hard drive.
- There is now an Operon search. Like the drug search, it's available on an orphaned page not generally visible to the public. The user specifies a genome and some tuning parameters and is presented with the genes in the genome grouped by operon. In addition to the standard search results fields, the operon search also displays the feature location and the feature's upstream DNA. For forward operons, the genes are presented in the normal order. For backward operons, the genes are presented in the reverse order so that the upstream data for the first gene of an operon is always upstream of the entire operon. This is almost what Ron Taylor wanted, the exception being that the downloaded file only includes the subsystem names and not the links. My goal here was to prove I could create a custom search in one day. It was one-and-a-half days, but I'm getting closer every time.
All of this has been moved to the staging server, and the links herein are staging server links.
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