ResolveRef : looking at the logs
One of the nice features of Google App Engine is you can easily view logs for your application to quickly see requests generating errors. Browsing the logs of ResolveRef, I’ve been able to identify an...
View ArticleResolveRef updated : now with auto-suggest and source code
I updated ResolveRef last night and checked in the most current sourcecode to svn at Google Code. New features include: Suggest/autocomplete for journal title field, using the journal title lists...
View ArticleSoftware review: producing two dimensional diagrams of membrane proteins
I recently needed to make a simple, two dimensional figure of a beta-barrel membrane protein. I went hunting for programs that might take a sequence and/or structure and produce a pretty looking...
View ArticleSetting up NCBI wwwblast on Ubuntu 8.04 (Hardy), Apache 2
Recently I needed to install NCBI wwwblast on my local workstation to enable some software that needed to interface with BLAST via the web service. It was straightforward to install, but I took some...
View ArticleCount the number of sequences in a FASTA format file: a Unix shell snippet
Sometimes it’s nice to quickly check how many sequences are in a FASTA format sequence file. It barely warrants it’s own blog post, but here we go anyhow: my one-liner shell script for counting the...
View ArticleSearching bioinformatic databases with YubNub
You may already be familiar with YubNub; it describes itself as “the social command line for the web”. Most commands consist of two (or more) words … one for the search engine, the other for the query....
View ArticleNaming in molecular biology: get comfortable with meaninglessness !
I noticed an interesting post over on BoingBoing: “Comfort with meaninglessness the key to good programmers“. It outlines some research by Dehnadi and Bornat on attributes that can predict aptitude in...
View ArticleA proposal for encouraging user contributed annotations to Uniprot
Today I attended a presentation by Maria J Martin about Uniprot and various other EBI database services. At the end of the talk, someone asked something to the effect of “How about simplifying user...
View ArticleStack Exchange sites for science
Recently I’ve noticed the emergence of several Stack Overflow-style sites for science-related questions and answers. For those unfamiliar with Stack Overflow – it’s a question and answer ‘forum’ for...
View ArticleRunning a local JABAWS server for Jalview on Ubuntu (11.04 Natty)
The excellent Jalview sequence alignment visualization and editing tool has the ability to send a set of sequences to a multiple sequence alignment web service (“JABAWS”) and receive the results in a...
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