# BIPAA, Bioinformatics Platform for the Agroecosystems Arthropods.

Stéphanie Robin, Fabrice Legeai, Anthony Bretaudieu

► To cite this version:

Stéphanie Robin, Fabrice Legeai, Anthony Bretaudieu. BIPAA, Bioinformatics Platform for the Agroecosystems Arthropods. JOBIM 2023 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2023, Plouzané (Brest Métropole), France. pp.1-1, 2023. hal-04176786

HAL Id: hal-04176786

https://hal.inrae.fr/hal-04176786

Submitted on 26 Jan 2024

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<figure><img src="image_1.png" /></figure>

Distributed under a Creative Commons Attribution 4.0 International License
# BIPAA, Bioinformatics Platform for the Agroecosystems Arthropods.

Stéphanie Robin, Fabrice Legeai, Anthony Bretaudieu

► To cite this version:

Stéphanie Robin, Fabrice Legeai, Anthony Bretaudieu. BIPAA, Bioinformatics Platform for the Agroecosystems Arthropods. JOBIM 2023 - Journées Ouvertes en Biologie, Informatique et Mathématiques, Jun 2023, Plouzané (Brest Métropole), France. pp.1-1, 2023. hal-04176786

HAL Id: hal-04176786

https://hal.inrae.fr/hal-04176786v1

Submitted on 26 Jan 2024

HAL is a multi-disciplinary open access
archive for the deposit and dissemination of sci-
entific research documents, whether they are pub-
lished or not. The documents may come from
teaching and research institutions in France or
abroad, or from public or private research centers.

L'archive ouverte pluridisciplinaire HAL, est
destinée au dépôt et à la diffusion de documents
scientifiques de niveau recherche, publiés ou non,
émanant des établissements d'enseignement et de
recherche français ou étrangers, des laboratoires
publics ou privés.

<figure><img src="image_1.png" /></figure>

Distributed under a Creative Commons Attribution 4.0 International License
<figure><img src="image_2.png" /></figure>

<figure><img src="image_3.png" /></figure>

<figure><img src="image_4.png" /></figure>

BIPAA is a bioinformatics platform from the **French National Institute for Agricultural, Food and Environment (INRAE)** to assist genomics and post-genomics programs developed on insects associated to agroecosystems. It is located in Rennes (France) and is integrated in **GenOuest** platform infrastructure (https://www.genouest.org/).

Contacts : bipaa@inrae.fr, https://bipaa.genouest.org/

## Data analysis

BIPAA supports a network of scientists from various french labs for analyzing their **genomics data**. BIPAA proposes personal guidance for developing scripts, running complex workflows on a computing cluster.

### Topics :

* Genome assembly and annotation

* Transcriptomics analysis and non coding RNA

* Transposable elements

* Genomes comparison (Orthology)

* Variant identification

* Genomics and epigenomics data integration

BIPAA contributes to the national **Galaxy** server usegalaxy.fr

<figure><img src="image_5.png" /></figure>

<figure><img src="image_6.png" /></figure>

## Information systems

BIPAA Information systems are based on the **BEAURIS project** https://gitlab.com/beaurls/beauris and **Galaxy Genome Annotation** https://galaxy-genome-annotation.github.io/

BEAURIS: How does it works?

<figure><img src="image_7.png" /></figure>

* Each genome is a multi-container application.

* This system permits automatic deployment of new genome and update.

* This is a reproducible, re-usable, modular and extensible system.

It organizes and manages genomics data generated by various international groups and offers **textual and graphical tools** for browsing and querying genomics data.

## BIPAA hosts multiple arthropod genomes

<figure><img src="image_8.png" /></figure>

SPODOPTERA LITURA

<figure><img src="image_9.png" /></figure>

ACYRTHOSIPHON PISUM

<figure><img src="image_10.png" /></figure>

HYPOSOETER DIDYMATOR

<figure><img src="image_11.png" /></figure>

HARMONIA AXYRIDIS

<figure><img src="image_12.png" /></figure>

ColeoDB

CrustaDB

<figure><img src="image_13.png" /></figure>

TickDB

For each genome, textual and graphical tools are available

Apollo (manual annotation)

<figure><img src="image_14.png" /></figure>

Program selection

PROGRAM

blastp (protein vs protein)

<figure><img src="image_15.png" /></figure>

SEARCH TYPE

Normal blastp

PSI-BLAST, PHI-BLAST and DELTA-BLAST can be used to find distantly related sequences

<figure><img src="image_16.png" /></figure>

Query sequence

PASTE YOUR
SEQUENCE

MPPPPPAGAGCDLRGAFTPASNNVAGQFSLGKKSLRRDPL

OR SELECT A FILE

FASTA format. Length is limited to 20Mb

Parcour... Aucun fichier sélectionné.

FASTA format. File size is limited to 20Mb

LepidoDB Aphidbase

17 lepidopterans 12 aphids

ParWaspDB

15 parasitoid wasps

<figure><img src="image_17.png" /><figcaption>Gene Ontology</figcaption></figure>

Rpa05639.t1-protein (polypeptide) Rhopalosiphum padi

You are viewing a polypeptide, more information available on the corresponding mRNA

page

Overview

Homology

The following BLAST results are available for this feature:

* BLAST of Rpa05639.t1 vs. genbank:protein

Analysis Date: 2017-07-12 (Blastp: Annotation v1.0 vs NR)

Total hits: 20

Homology

InterPro

Relationships

Sequences

ZOOM x1 POSITION 170N

Sequence

Sequence

XP_016657278.1

AQS60748.1

XP_016661171.1

XP_016661170.1

XP_016661169.1

AQS60751.1

XP_016661174.1

XP_016661168.1

XP_016661152.1

AQS60755.1

<caption>Sequence information</caption>

JBrowse

<figure><img src="image_18.png" /><figcaption>Genome browsers</figcaption></figure>

<figure><img src="image_19.png" /><figcaption>Orthology and synteny</figcaption></figure>

<caption>Blast</caption>

## Collaborations

* Involved in various bioinformatics research projects, in collaboration with teams in **Inria/IRISA** in Rennes :

**GenScale** (complex genome assembly, variant identification)

**Dyliss** (data integration and mining, Askomics)

<figure><img src="image_20.png" /></figure>

<figure><img src="image_21.png" /></figure>

* Associated with 3 national networks of INRAE : **BAPOA** (Biologie Adaptative des Pucerons et Organismes Associés), **ADALEP** (Adaptation à l'environnement biotique chez les lépidoptères) and **REacTION** (Réseau d'échange sur les mécanismes Épigénétiques qui façonnent les interacTIONS)

* Involved in international consortia and insect genome projects (i5k : sequencing of 5000 insect genomes)

* More than 700 users are currently listed

<figure><img src="image_22.png" /></figure>

## Trainings

BIPAA is involved in training sessions in partnership with the **GenOuest** bioinformatics platform and the **BARIC** (Bioinformatique pour l'Analyse, la Représentation et Intégration de Connaissances) community of INRAE, and in tutorials development in **Galaxy Training Network (GTN)**.

Project 2020-1-NL01-KA203-064717 is funded with the support of the Erasmus+ programme of the European Union. Their funding has supported a large number of tutorials within the GTN across a wide array of topics.

<figure><img src="image_23.png" /></figure>

With the support of the
Erasmus+ Programme
of the European Union