ASTERICS is an interactive and integrative data analysis tool for omics data. It uses Rserve and PyRserve with Flask and Vue.js in a Docker container to integrate omics data. The backend uses Rserve and PyRserve with Flask on the server side, while the frontend uses Vue.js. This architecture was chosen for its open source and light design. Data communication between Rserve and PyRserve is limited, requiring an object database. ASTERICS is deployed using three Docker containers for R, Python, and

1. Rserve, renv, flask, Vue.js dans un docker pour intégrer des
données omiques avec ASTERICS
Élise Maigné, Nathalie Vialaneix
nathalie.vialaneix@inrae.fr
http://www.nathalievialaneix.eu
R User Group Toulouse
19 octobre 2022

2. What is ASTERICS?
▶
▶ project (2020/2023) funded by
▶ with a case study contribution from
Tool designed for interactive and integrative data analysis,
oriented toward omics data.
R User Group Toulouse
19 octobre 2022 / Nathalie Vialaneix
p. 2

3. How does it work?
The most dangerous part of the talk: the live demo...
https://asterics.miat.inrae.fr
R User Group Toulouse
19 octobre 2022 / Nathalie Vialaneix
p. 3

4. Behind the scenes
Backend: and Rserve
R User Group Toulouse
19 octobre 2022 / Nathalie Vialaneix
p. 4

5. Behind the scenes
Backend: and Rserve
↕
PyRserve and
(with and on the server side)
R User Group Toulouse
19 octobre 2022 / Nathalie Vialaneix
p. 4

6. Behind the scenes
Backend: and Rserve
↕
PyRserve and
(with and on the server side)
↕
Frontend: and
R User Group Toulouse
19 octobre 2022 / Nathalie Vialaneix
p. 4

7. Behind the scenes
Backend: and Rserve
↕
PyRserve and
(with and on the server side)
↕
Frontend: and
Why this choice?
▶ Opensource & designed
to be light
▶ Vuejs: flexible and
modular programming
R User Group Toulouse
19 octobre 2022 / Nathalie Vialaneix
p. 4

8. Behind the scenes
Backend: and Rserve
↕
PyRserve and
(with and on the server side)
↕
Frontend: and
Why this choice?
▶ Opensource & designed
to be light
▶ Vuejs: flexible and
modular programming
Compared to shiny?
▶ could have been a bit
more flexible
▶ shiny deployment is hard
(free shiny server /
ShinyProxy)
▶ But: slower, more
complicated to program,
Rsessions are frequently
hijacking the application
R User Group Toulouse
19 octobre 2022 / Nathalie Vialaneix
p. 4

9. Main technical bottleneck from the side
Data communications between Rserve and PyRserve is restricted to characters,
numbers and vectors including these elements...!
R User Group Toulouse
19 octobre 2022 / Nathalie Vialaneix
p. 5

10. Main technical bottleneck from the side
Data communications between Rserve and PyRserve is restricted to characters,
numbers and vectors including these elements...!
Input arguments: dataset names (and not the actual object!) ⇒ need for an object
database + use of get and assign.
R User Group Toulouse
19 octobre 2022 / Nathalie Vialaneix
p. 5

11. Main technical bottleneck from the side
Data communications between Rserve and PyRserve is restricted to characters,
numbers and vectors including these elements...!
Input arguments: dataset names (and not the actual object!) ⇒ need for an object
database + use of get and assign.
R User Group Toulouse
19 octobre 2022 / Nathalie Vialaneix
p. 5

12. Deployment
First experience (for me) with
R User Group Toulouse
19 octobre 2022 / Nathalie Vialaneix
p. 6

13. Deployment
First experience (for me) with
R User Group Toulouse
19 octobre 2022 / Nathalie Vialaneix
p. 6

14. Deployment
First experience (for me) with
How does it work?
▶ three containers: (stabilized with renv), Python, and nginx
▶ docker-compose used to combine them
From a user point of view:
▶ Just pull the images from our registry
▶ ... and use our docker-compose file (just one command line)!
R User Group Toulouse
19 octobre 2022 / Nathalie Vialaneix
p. 6

15. Next steps
▶ a few bugs to fix
▶ a few other features to implement (metagenomics analyses are among them)
▶ test the deployment on other servers (with docker)
▶ upgrade , packages, python modules, ...
R User Group Toulouse
19 octobre 2022 / Nathalie Vialaneix
p. 7

16. Online application: https://asterics.miat.inrae.fr
User documentation:
https://asterics.pages.mia.inra.fr/user_documentation/
Code repository (with installation instructions):
https://forgemia.inra.fr/asterics/asterics
Suggest an issue:
https://forgemia.inra.fr/asterics/asterics-issues/-/issues or
asterics-tlse@inrae.fr
Want to contribute? Technical documentation:
https://asterics.pages.mia.inra.fr/doc_asterics/
R User Group Toulouse
19 octobre 2022 / Nathalie Vialaneix
p. 8