16 August 2010

PARRIS analysis: Is there evidence of positive selection anywhere in my alignment?

Running instance of Galaxy where you can play with SLAC can be found here.
Please be patient because PARRIS computation takes some time.

20 July 2010

Dynamic job creation in the SLAC analysis

In the last post I've presented you the SLAC analysis.

SLAC output

Clicking "details" link triggers additional computation and displays details of each substitution.

Substitution details

There is no support for this kind of on-demand computation in Galaxy so what I had to do was:
  • Create a hidden tool (invisible in the tool menu)
  • Execute this tool in the request controller
  • Hide job's history association from the History Box
  • Create a jQuery UI displaying job's status
jQuery UI

I encourage you to play with my demo instance:

14 July 2010

SLAC analysis: Which codon sites are under diversifying positive or negative selection?

Sorry for the lack of posts recently but there was nothing significant to report. Most of the time we (my mentors and I) were designing and improving the implementation pattern.

Now it's time to introduce you to the SLAC analysis.

The general workflow with phylogenetics tools is:
  • Upload your data via "Get Data"->"Upload File"
  • Validate your data via "Phylogenetics"->"Data Reader"
  • Run analysis e.g. SLAC via "Phylogenetics"->"SLAC"
SLAC analysis creates an HTML table report. Rows with substitutions can be unfolded to show details of each substitution.

I've also provided some documentation on running SLAC and understanding its output.

Running instance of Galaxy where you can play with SLAC can be found here.

10 May 2010


In my proposal I've suggested implementing the following set of analyses from datamonkey.org:
  • SLAC analysis
  • FEL analysis
  • IFEL analysis
  • REL analysis
  • PARRIS analysis
  • GARD analysis
  • SBP analysis
  • Model analysis
  • Codon Model Selection analysis
(Analyses are shortly described on the homepage of http://www.datamonkey.org).

This is the majority of those on datamonkey and of course I don't insist on integrating this particular subset. I would really appreciate any feedback on this matter.


As a part of my proposal I've mplemented a sample integration of SimpleGlobalFitter.

My code can be found here.

I've also taken an existing initial Datamonkey integration code, played a little bit with it and hooked to my demo.

I've instantiated Galaxy on my university's server:


I've provided a description of this demo in the Galaxy's welcome page


Galaxy is a popular web based interface for integrating biological tools and analysis pipelines. HyPhy provides a popular package for molecular evolution and sequence statistical analysis. Integrating those tools will make Galaxy even more powerful and useful. Hence probably increase its popularity.

The goal of my GSoC project is to integrate the relevant tools into Galaxy. Functional tests will be developed for tools and workflows, along with high level documentation for end users.