Tag Archives: Galaxy

GigaScienceĀ“s Impact Factor

Even though the editors of GigaScience don’t like Impact Factors (and I agree with them), GigaScience has received a very high Impact Factor, 7.46. I’m quite happy since we published a paper in GigaScience last year, Enhanced reproducibility of SADI web service workflows with Galaxy and Docker.

Tagged , , , , , , , , , , ,

The executable paper

This [1] is how all the papers should look like: an easy to execute workflow with all the datasets included, in order to be able to reproduce its science. It would avoid situations like the one described in this video.

[1] Dynamics of mitochondrial heteroplasmy in three families investigated via a repeatable re-sequencing study.

Tagged , , , ,

Galaxy tool for NCBO web services

We have developed a collection of Galaxy tools for executing NCBO web services as part of Galaxy (Available at the tool shed, in ontology manipulation). Available services:

  • Get ontology.
  • View.
  • Search.
  • Extract.
  • Annotator.
  • Recomendador.
  • Resource index.
Tagged ,

Taverna + Galaxy

Taverna workflows can now be executed as Galaxy workflows. Plus, Galaxy is a nice tool for teaching bioinformatics. It seems that Galaxy is gaining momentum!

Tagged , ,

Paper accepted at SWAT4LS

Our paper entitled “OPPL-Galaxy: Enhancing ontology exploitation in Galaxy with OPPL” has been accepted at SWAT4LS (First talk!). I will also help Simon with the Populous-OPPL tutorial.

Tagged , , , ,

Ontology Pre Processor Language for Galaxy

I have just released the first version of OPPL Galaxy, a wrapper of OPPL for the Galaxy platform. OPPL is an scripting language for manipulating ontologies; Galaxy is a platform for executing Bioinformatics workflows. Since ontologies are an important part of data analysis in Bioinformatics, it made sense to adapt OPPL to Galaxy. Plus it was really easy šŸ˜‰

You can find it in the Galaxy Tool Shed, under Ontology Manipulation.

OPPL Galaxy is built on top of OPPL API, OWL API and Pellet. Thanks to all of them!

Tagged , , , , , , , ,