Quantcast
Channel: Your bones got a little machine » bioinformatics
Browsing latest articles
Browse All 10 View Live

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 Article



Image may be NSFW.
Clik here to view.

ResolveRef 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 Article

Image may be NSFW.
Clik here to view.

Software 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 Article

Image may be NSFW.
Clik here to view.

Setting 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 Article

Image may be NSFW.
Clik here to view.

Count 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 Article


Image may be NSFW.
Clik here to view.

Searching 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 Article

Image may be NSFW.
Clik here to view.

Naming 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 Article

Image may be NSFW.
Clik here to view.

A 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 Article


Image may be NSFW.
Clik here to view.

Stack 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 Article


Running 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...

View Article
Browsing latest articles
Browse All 10 View Live




Latest Images