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.

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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.

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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.
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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!

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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.

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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!

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