Bioinformatics

The ARTbio Bioinformatics platform provides support and environments for big data analyses. We primarily accompany any type of analyses of high throughput sequencing datasets. We are open to projects involving statistics, modeling and image analysis. The team offers its services through scientific collaborations. For needs out of our expertise, we will orient researchers to more appropriate bioinformatics platforms or laboratories.

We are web-service oriented, and adhere to the manifesto of Agile software development and to the notion of continuous delivery which involve short cycles of question/resolution as well as face-to-face interactions with researchers. Through deployment of Galaxy web servers, we provide our users with access to softwares and help in setting up, streamlining, and running analysis workflows. We offer solutions to record analyses in every detail, for sharing or publication. We also offer online environments for statistics (Rstudio) and programming (iPython).

The platform is involved in tool development for small RNA biology, mRNA de novo assembly and metagenomics as well as in tool integration in the Galaxy framework. We ensure training in bioinformatics and Galaxy use, through courses and development of knowledge databases.

Services

The ARTbio bioinformatics analysis platform provides support to biologists in their analyses, at the IBPS and beyond. We have five main objectives:
1. Galaxy servers maintained at state of the art. We maintain our Galaxy server instances in configuration close to the highest standards which continuously evolve thanks to the Galaxy development community. Along this line, we are closely following progresses in methodologies such as continuous integration and delivery, automatic testing and deployment as well as environment virtualization. Users with sufficient skill to autonomously conduct analysis using Galaxy will directly benefit from our public mississippi Galaxy instance (https://mississippi.snv.jussieu.fr). Another Galaxy instance (https://lbcd41.snv.jussieu.fr/) is available to IBPS researchers or users with appropriate credentials.
2. Analysis project support. We accompany NGS analysis projects through the use of the Galaxy interface. Interacting with biologists through the Galaxy framework is currently one of the best ways to give them consistent access to bioinformatics tools or complex workflows and to help them to perform reproducible and transparent analyses. We have experience in this activity and we propose more effective support to projects focusing on:
- Small RNA and RNA biology
- Epigenetics analyses
- Virus detection and discovery
- Variant and snp analyses
- Metagenomics
3. Tool development. We develop Galaxy tools. In a competitive context of a growing offer for highly relevant standalone or online software, focusing development to our area of biological expertise is the best way to deliver outstanding tools.
4. Training. Analyses are better performed with educated users. Therefore, we participate to Galaxy training efforts. We also work at extensive tutorials to help users in their analyses.
5. Cloud Infrastructure. We took the option to have a light hardware infrastructure for the platform, while keeping a maximum of our means to focus on tool development and user analysis projects. This implies working at migrating our services in cloud infrastructures, which we are doing primarily in collaboration with the Institut Français de Bioinformatique (IFB).

Methodological developments

Project support: Over the past year we provided advanced support to many NGS analysis projects including works aimed at understanding epigenetic functions of piRNAs (1), antiviral RNA interference (2) or roles of miRNAs in stem cell differentiation (3).

Tools: We developed and made publicly available the mississippi suite of tools for mining small RNA sequencing datasets (4). We are currently releasing a set of Galaxy workflows aimed at detecting viruses or identifying new viral species from small RNA sequencing datasets (5). Another example of tool development is our DockerToolFactory tool that allows everyone to execute customized R, python, perl or bash scripts without leaving the Galaxy interface (6).

Methodology developments: We are closely following progresses in methodologies such as continuous integration and delivery (utilizing Galaxy-specific tools such as bioblend (7), Planemo (8) and our own developments through the Jenkins CI server (9)), automatic testing and deployment as well as environment virtualization (e.g. Docker (10))

1. Nature. 490, 112–115 (2012).

2. Nucleic Acids Res. (2015), doi:10.1093/nar/gkv590.

3. RNA. 18, 253–264 (2012).

4. https://testtoolshed.g2.bx.psu.edu/view/mvdbeek/mississippi_toolsuite/

5. https://toolshed.g2.bx.psu.edu/view/drosofff/suite_visitor2/

6. https://bitbucket.org/mvdbeek/dockertoolfactory

7. Bioinformatics. 29, 1685–1686 (2013).

8. https://github.com/galaxyproject/planemo

9. https://jenkins-ci.org/

10. https://www.docker.com/whatisdocker/