Blog
Hiring again
Posted on 3 November 2009 by None
We’re looking for more software engineers to work on the Galaxy project. See our updated job ad.
Windshield splatter analysis
Posted on 19 October 2009 by James Taylor
The Galaxy team’s new paper is now available online, featuring new tools and a pipeline for analyzing metagenomic datasets. In addition to showing off the tools and workflow system, this paper includes the first use of the new Galaxy page system to publish an online supplement that fully documents every detail of the analysis and allows direct access to all of the data and methods used. This work has been featured in wired news, genomeweb, and the Chronicle.
EDIT: More at Emory eScienceCommons
New Lab Members
Posted on 17 August 2009 by James Taylor
July and August have seen many additions to our lab.
In the news and blogs
Posted on 17 August 2009 by James Taylor
- An article in Bioinform, on the growing importance of data management, references the recent Data and Analysis Management SIG at ISMB.
- Brad Chapman is looking at Galaxy and continues to provide useful examples of using bx-python
- Ido Tamir is starting to blog about hacking Galaxy internals
- Fungus growing ant genomics is underway
Galaxy: Big in Japan?
Posted on 3 April 2009 by James Taylor
I was privileged to have been invited to Biohackathon 2009 in Tokyo and Okinawa. Greg von Kuster and myself from the Galaxy team attended. It was a very interesting event, part hackathon and part unconference, with a lot of satellite discussions and informal talks. While I didn’t end up doing as much hacking as I hoped, the opportunity to discuss some big challenge areas from a technical perspective was useful. The venue was incredible, and DBCLS/OIST were incredibly generous in hosting us for so long in such amazing accommodations…
Profile in Genome Technology
Posted on 31 December 2008 by James Taylor
Genome Technology magazine’s annual feature “Tomorrow’s PIs” included a profile describing our efforts to facilitate more accessible, transparent, and reproducible computational analysis through Galaxy.
The pipeline analysis model
Posted on 3 October 2008 by James Taylor
Titus recently posted some thoughts on the “unix” scripting/pipeline model for analysis. The model is essentially one of discrete components that do one thing and produce and consume standard (or at least easily parsed) data formats. The components are naturally reusable, and are chained together to perform more complex analysis. Higher level facilities such as make) facilitate reproducibility.
This model has a lot of nice features. In particular, it makes reuse easy and thus encourages the development of reusable components. In fact, this is exactly the analysis model that Galaxy makes available to non-computational users. In doing so we tackle several of the “deficiencies” of this model that Titus mentions…
The state of python and bioinformatics
Posted on 27 September 2008 by James Taylor
Chris Lasher and Titus Brown recently posted on bioinformatics in python, briefly igniting the same old discussion on the biology-in-python list. The usual questions and concerns: “why is Perl ‘winning’ in bioinformatics”, “why don’t people like / use / contribute to BioPython”, “let’s make a new BioPython, I’m sure it will work better this time!”…
Genome Informatics 2008
Posted on 15 September 2008 by James Taylor
The joint CSHL / Wellcome Trust meeting on Genome Informatics is one of my favorite meetings, particularly because the presentations generally contain an excellent mix of cool biology and informatics. This year’s meeting was no exception, and my session (Data Management, Mining & Curation), though likely among of the least biological in overall content, turned out very well. All of the talks were excellent, and I was happy to see an (unexpected) theme among many of them: putting more power in the hands of biologists without informatics support…