WAVES




Summary

WAVES is a web application dedicated to bioinformatic tool integration. It provides an efficient way to implement a service for any bioinformatic software. Such services are automatically made available in three ways: web pages, web forms to include in remote websites, and a RESTful web services API to access remotely from applications. In order to fulfill the service’s computational needs, WAVES can perform computation on various resources and environments, such as Galaxy instances.

Availability and implementation

WAVES was developed with Django, a Python-based web framework. It was designed as a reusable web application. It is fully portable, as only a Python installation is required to run Django. It is licensed under GNU General Public License version 3.

WAVES components

WAVES-core

This is the main WAVES component.

WAVES-Galaxy

This is a WAVES adapter dedicated to Galaxy. Using the BioBlend python library, this adapter enables Galaxy services import into WAVES-core. WAVES-Galaxy automatically recognizes the tools available in a Galaxy instance.

WAVES-demo

This is a custom WAVES instance for demo purpose. It was created to show what could be done with Django functionalities to custom a WAVES installation.

The changes that have been made are:

  • Use a different skin for the back-office interface.
  • Custom front-end interface.
  • Override the Service class.
  • Override the Authentication class.

Please note that anyone can login the back-office administration interface and create new services. Thus, for security reasons, we intentionally deactivated the jobs running procedure.

WAVES Singularity image

This is a Singularity container with a functional WAVES installation including two pre-configured services (‘Hello world’ and ‘PhyML’). For testing purpose.

Contact

You may contact the WAVES support by e-mail : waves [at] lirmm.fr

WAVES WAVES Papers & contacts

TIDE

TIDE

What is TIDE? TIDE is the orchestration platform behind ATGC online bioinformatics services. It provides a unified web interface and a public REST API to submit analyses, monitor jobs, and retrieve results across a growing catalog of phylogenetic and sequence-analysis tools. TIDE is a modernized redesign of WAVES, an older tool previously developped by ATGC…

Sequence analysis Software engineering Service discovery Service invocation Service management Job identifier Tool metadata HTML JSON
PhyML 3.0

PhyML 3.0

Overview: new algorithms, methods and utilities PhyML is a software package that uses modern statistical approaches to build phylogenetic trees from the analysis of alignments of nucleotide or amino acid sequences. The main tool in this package builds phylogenies under the maximum likelihood criterion. It implements a large number of substitution models coupled to efficient…

Phylogenetics Phylogenomics Phylogenetic inference (AI methods) FASTA PHYLIP format
DExTER

DExTER

Overview DExTER (Domain Exploration To Explain gene Regulation) is a bioinformatics tool designed to automatically identify genomic regions whose nucleotide composition correlates with gene expression levels. Unlike traditional approaches focusing on short transcription factor binding sites (6-12 bp), DExTER detects Long Regulatory Elements (LREs) that can span tens to hundreds of nucleotides. This makes it…

Gene expression Gene regulation Sequence analysis Expression correlation analysis Regression analysis Sequence analysis Sequence motif discovery Gene expression matrix Nucleotide code Sequence motif (nucleic acid) CSV FASTA TSV
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