ReGaTE is a software component enabling the automated publication of Galaxy tools into the ELIXIR Tools and Data Services Registry
Upcoming Events : C3BI News – Galaxy Community Conference 2015
Date : 6-8th July 2015
Location : The Sainsbury Laboratory, Norwich, UK
REGATE, REGISTRATION OF GALAXY TOOLS IN ELIXIR
Olivia Doppelt-Azeroual1, Fabien Mareuil1, Eric Deveaud1, Matus Kalas2, Hervé Menager1
1 Center of Bioinformatics, Biostatistics and Integrative Biology, Institut Pasteur, Paris, France
2 Computational Biology Unit, University of Bergen, Norway
ReGaTE is a software component enabling the automated publication of Galaxy tools and workflows into the ELIXIR Tools and Data Services Registry (https://elixir-registry.cbs.dtu.dk/#/). This registry is a web portal for the exploration of bioinformatics resources, such as software packages, web services, websites, or reference databases. Through a dedicated interface, its users can search and locate relevant tools and data resources, and bioinformatics resource providers can enhance the visibility of their services. The registration of resources in the registry can be performed either manually, by filling a form on a web user interface, and providing the required description elements, or automatically by using the registry API.
ReGaTE uses the BioBlend API and the Registry API to completely automate the registration of the tools installed on any given Galaxy portal.
Central to the development of this tool is the mapping of the Galaxy datatype system to the EDAM Ontology. EDAM provides a controlled vocabulary for the description of scientific topics, software operations, types of data and data formats and it is used to describe the contents of the ELIXIR Registry. This mapping enables the automation of the registration of Galaxy tools by describing the format of their input and output data in the controlled vocabulary of the registry.
This mapping is being developed in collaboration with members of the Galaxy team, the EDAM ontology and the Common Workflow Language project.
ReGaTE is available at http://github.com/bioinfo-center-pasteur-fr/ReGaTE
Working Group : Best Practices and the particularities of mammalian genomes
Date : Thursday 16th April 2015 – 2PM
Location : Retrovirus room – Lwoff building – ground floor
Speakers : Bernd JAGLA
Best Practices and the particularities of mammalian genomes
A potential list of topics to be discussed during these meetings :
– Recent papers related to this subject (see e.g. http://www.biomedcentral.com/1471-2164/16/97)
– Difference between the different versions of the genomes and annotations
– How to handle reads (from a sequencing machine) that align to multiple places in the genome
– How to handle different individuals (e.g. from sequencing multiple patients), from a reference genome point of view
– How to deal with transcripts / differential analysis of splice variants.