Firefox and bioinformatics

I wondered who else might be working on bioinformatics related extensions for Firefox besides Firegoose. One interesting project is iHOPerator, which builds on Greasemonkey. And, there's a hint of something to come here.

It seems like there was a flurry of interest around 2005, in the early days of AJAX and mash-ups, which produced biobar along with two now-dead projects - bioFox and NCBI Search Toolbar. Back in those days, John Udell asked, How do you design a remixable Web application? Nifty developments like the REST API in EMBL's STRING 8.0 are starting to provide answers.

Bioinformatics as a Queryable Knowledge Map: the Pygr Project

Pygr is a hypergraph database in Python with applications in bioinformatics written by Christopher Lee, a faculty member at UCLA. There's a 30 minute video of talk about Pygr and a bunch of other resources on the Lee Lab website and Lee's thinking bioinformatics blog.

Thesis: Hypergraphs are a general model for bioinformatics and Python’s core models are already a good model of Bioinformatics Data

• Sequence: protein and nucleic acid sequences 
• Mapping / Graphs: alignment, annotation 
• Attributes: schema, i.e. relations between data 
• Namespace (import): the ontology of all bioinformatics data 

Pygr aims to show that these Pythonic patterns are a general and scalable solution for bioinformatics.

The general idea is not entirely different from the data types behind Gaggle, especially in the emphasis on basic data structures without a heavy semantic component.

Dr. Lee is also writing a textbook on probabilistic inference.

Dynamic Fusion of Web Data

I happened across a very cool project on web data integration at the University of Leipzig. Their paper Dynamic Fusion of Web Data is worth a look. They're working towards a theory of on-the-fly data integration for mashup applications that they refer to as dynamic data fusion. Data integration in mashups is dynamic in that it occurs as runtime. This provides for a pay-as-you-go model, rather than a large up-front semantic mapping task that limits the scalability of traditional data integration methods like data warehouses.

They describe mashups as workflow-like. Do they mean mashups are programmatic as opposed to declarative? In place of SQL, this group's iFuice system uses a scripting language with "set operations (e.g., union, intersection, and difference) and data transformation (e.g., fuse, aggregate) which can be used to post-process query results". Other key features are instance-level mapping and accommodation of structured and unstructured data.

This definitely gets at what Firegoose is good for - using the web as a channel for structured data - an approach that does for data integration what loose coupling does for software. Firegoose, part of the Gaggle framework, is a toolbar for Firefox that allows data to be exchanged between desktop software and the web. Firegoose can read microformats, call web services, query databases, or even perform nasty dirty screen scraping. Unlike a mashup, data integration in Firegoose and Gaggle requires user participation, although the user never deals with schemas, only instances of the Gaggle data types - mainly lists of identifiers, matrices of numeric data, networks, and tuples. The identifiers serve in a role somewhat analogous to primary keys.

More papers in a similar vein

• From Databases to Dataspaces: A New Abstraction for Information Management
• Web-scale Data Integration: You can only afford to Pay As You Go

Browsing genomes

I may as well come clean and admit that I'm developing a genome browser. What? Another genome browser? Why? You may well ask these questions. Well, it's a long story. But here is a completely non-exhaustive list of existing genome browsers.

• The classics: UCSC Genome Browser Home and paper and it's microbial sibling.
• Argo a Java rich-client genome browser built at the Broad Institute.
• Integrative Genomics Viewer also from Broad (see press release).
• Affymetrix spun out it's Integrated Genome Browser into an open source project, along with a library of re-usable components called GenoViz.
• GBrowse Lincoln Stein's Perl based genome browser, followed by the AJAXy javascripty JBrowse (with a paper, nicely written as usual from Lincoln Stein.).
• x:map an AJAX genome browser based on the Google Maps API.
• The biology of extemophiles lab at the University of Paris Sud have a nice little web based browser for Sulfolobus.
• NCBI has a new AJAX tool called Sequence Viewer
• Flash based OmicBrowse is apparently big in Japan.
• MochiView is really nice. Read the paper in BMC Biology.
• GenomeGraphs: integrated genomic data visualization with R
• GenomeView
• Visualization guru Ben Fry (of processing fame) wrote at least two:cd36 browser and a handheld genome browser
• A guy who calls himself Saaien Tist implemented a circular genome browser in ruby-processing
• Back in 2002, some canucks built BioViz an SVG based genome browser
• The Savant Genome Browser is a desktop visualization tool for genomic data. It was primarily developed for visualizing high throughput (aka next generation) sequencing data... Savant comes out of the Computational Biology Lab at the University of Toronto - also home of Cytoscape Web.

Note: updated in Sept. 2009 to reflect the fact that everyone and their uncle built a genome browser this past couple of years. See Brother, can you spare a genome browser?

Note: updated again in May of 2010 and again in Feb 2011 to add Savant.

UCSC Genome Browser

A while back, I wrote a little hack to to download and parse genome data from NCBI, but was flummoxed by NCBI's format for eukaryotes. A couple of local bioinformatics gurus directed me to UCSC as an alternate data source. UCSC's Genome Browser provides a nice interface to it's underlying data through a Table Browser. The main genome browser has data for eukaryotes, while archaea (and other prokaryotes) are in a separate project. The Table Browser for the archaeal genome browser is a little tricky to find, but it's there.

Better color chooser for Java Swing

I came across a color chooser that kicks the Swing JColorChooser's booty. It looks great and supports transparency. It's available at colorchooser.dev.java.net and on the developer's blog. It will soon be used in my genome browser. Thanks, Jeremy!

Free Icons

Who doesn't love icons?

• Crystal Project
• Tango
• Nuvola
• famfamfam
• California icon pack