S4: Easing the integration of bioinformatics software and services

Easing the integration of bioinformatics software and services with the ELIXIR bio.tools registry

S4: Easing the integration of bioinformatics software and services, OpenTox Euro 2017

Herve Menager


Bioinformatics Hub of the Centre de Bioinformatique


Research Engineer


Over the last few years, bioinformatics has played a major role in the field of biology, raising the issue of best practices in software development. These practices include facilitating the discovery, and usage of tools, and several helpful solutions are available. Tool discovery is facilitated by various online catalogs and registries. The bio.tools registry is an effort funded by the ELIXIR european research infrastructure. This registry describes bioinformatics software and services. It is based on extensive metadata descriptions, supported by the EDAM ontology. On the other hand, workbench and workflow systems such as Galaxy, Tavern or Chipster allow the execution and composition of bioinformatics tools in integrated environments which aim at improved​ ​usability,​ ​interoperability​ ​and​ ​reproducibility. 

One of the goals of bio.tools registry is to facilitate the access to bioinformatics tools, i.e. their execution once they have been identified with the registry. We develop this axis of the project through​ ​an​ ​integration​ ​with​ ​workbench​ ​environments​ ​using​ ​two ​strategies:​

  • 1. The automated publication of bioinformatics tools available on Galaxy instances on bio.tools using a utility called ReGaTE, to enable a direct access to available online workbench ​ environments.​ 
  • 2. The semi-automated integration of tools described in the bio.tools registry into workbench environments, through the "ToolDOG" (Tool DescriptiOn Generator) software. The goal here is to enhance the quality of the tool descriptions provided in workbench​ ​environments​ ​using​ ​the​ ​curated​ ​descriptions​ ​provided​ ​by​ ​bio.tools.
These two developments provide complementary approaches to improve the contents of both the​ ​bio.tools​ ​registry.