Bioproductions
Projets financés
Méthodologies et outils transversaux
Galaxy-BioProd

Galaxy-BioProd

Un portail opérationnel pour la production de produits biosourcés.

Le projet Galaxy-BioProd vise à fournir des outils et des ressources génériques et partagés pour concevoir, exécuter et suivre d'autres projets du programme. À cette fin, un portail centralisé fournira des outils logiciels ainsi que des ressources de calcul et de stockage.

La technologie DBTL (Design-Build-Test-Learn) est le mode opératoire en R&D pour les biotechnologies industrielles (biofonderies) pour pallier le long et coûteux processus traditionnel d'essais-erreurs.

Cette technologie combine protocoles manuels et robotisés avec logiciels, mais est complexe à mettre en oeuvre. Il existe de nombreux outils et ressources développés au travers de projets européen (IBISBA, ELIXIR (Galaxy and Microbial Biotech Communities), BioRoBoost) et Nationaux (MetaboHUB, Equipex+(Aladin,MetEx+).

Cependant, il existe aujourd'hui un manque de pratiques partagées, avec des projets et biofonderies qui ont déployé leurs propres pipelines.

Les objectifs du projet :

Outils et ressources

« FARification » d’outils et ressources informatiques au travers du système de workflow Galaxy :

  • Interface simple et efficace pour construire des workflows ;
  • Couplage de nouveaux outils avec ceux déjà présents dans le ToolShed ’ de Galaxy en génomique, transcriptomique, métabolomique, apprentissage machine ;
  • Formation en ligne pour l’utilisation et la création d’outils Galaxy.
Outils inter-projets 

Développement de nouveaux outils pour répondre aux besoins spécifiques des axes "Caractérisation de la biomasse" et "Nouveaux schémas de transformation de la biomasse" du programme Bioproductions :

  • Standardiser les méthodes de caractérisation de la biomasse ;
  • Réduire le temps de conception et d’ingénierie des bioprocédés pour la production de produits biosourcés ;
  • Coupler la modélisation multi-échelle de bioprocédés avec l’analyse de cycle de vie (ACL).

 

Le consortium :
 

Établissements d'enseignement supérieur
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Instituts de recherche
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Titre-image Publications

HAL : Dernières publications

  • [hal-04673511] Artificial Intelligence Methods and Models for Retro-Biosynthesis: A Scoping Review

    [...]

    ano.nymous@ccsd.cnrs.fr.invalid (Guillaume Gricourt) 20 Aug 2024

    https://hal.science/hal-04673511v1
  • [hal-04603192] Artificial Intelligence Methods and Models for Retro-Biosynthesis

    Retrosynthesis aims to efficiently plan the synthesis of desirable chemicals by strategically breaking down molecules into readily available building block compounds. Having a long history in chemistry, retro-biosynthesis has also been used in the fields of biocatalysis and synthetic biology. Artificial intelligence (AI) is driving us towards new frontiers in synthesis planning and the exploration of chemical spaces, arriving at an opportune moment for promoting bioproduction that would better align with green chemistry, enhancing environmental practices. In this review, we summarize the recent advancements in the application of AI methods and models for retrosynthetic and retro-biosynthetic pathway design. These techniques can be based either on reaction templates or generative models and require scoring functions and planning strategies to navigate through the retrosynthetic graph of possibilities. We finally discuss limitations and promising research directions in this field.

    ano.nymous@ccsd.cnrs.fr.invalid (Guillaume Gricourt) 06 Jun 2024

    https://hal.science/hal-04603192v1
  • [hal-04351679] Galaxy-SynBioCAD — An Automated Pipeline for Synthetic Biology Design and Engineering

    There’s a substantial number of tools released around Synthetic Biology and Metabolic Engineering- related questions and needs. This population of tools is difficult to comprehend and use together, main reasons being complexity and interoperability issues. Indeed, a high level of expertise could be required for installing codes, and execution for real life use cases could be computationally resource demanding. Plus some tools, although complementary, use different inputs and outputs which prevent easy chaining. The SynBioCAD-Galaxy portal [1] is a growing toolshed for synthetic biology, metabolic engineering, and industrial biotechnology. The tools and workflows currently shared on the portal enable one to build libraries of strains producing desired chemical targets covering an end-to-end metabolic pathway design and engineering process: from the selection of strains and targets, the design of DNA parts to be assembled, to the generation of scripts driving liquid handlers for plasmid assembly and strain transformations. Tools are made available on GitHub, anaconda.org and the Galaxy Tool Shed, opening to the greatest number access and utilization throughout the SynBio community, and significant effort has been granted for adopting FAIR principles. As a community effort helped by funded projects, the scope covered by tools is expected to expand over time. The poster will give an overview of the SynBioCAD-Galaxy portal in the context of prediction and construction of E. coli lycopene-producing pathways. The poster will open the discussion around good practices guiding releases of tools through continuous integration. A – lightweight – testing instance of SynBioCAD-Galaxy is available at https://galaxysynbiocad.org.

    ano.nymous@ccsd.cnrs.fr.invalid (Joan Hérisson) 18 Dec 2023

    https://hal.science/hal-04351679v1
  • [hal-04644779] Exploring the richness of the French Galaxy Ecosystem

    The French Bioinformatics Community has embraced Galaxy since its inception, with a pivotal moment being the Galaxy Tour de France led by Nate Coroar, Anton Nekrutenko, and James Taylor in 2012. This adoption has led to the establishment of over 10 Galaxy servers across France, catering to diverse local needs and specialized thematic areas such as ecology, biodiversity, NGS, proteomics, and more. Among these servers, UseGalaxy.fr stands out as the flagship national instance, launched in 2021 and hosted by the French Institute for Bioinformatics (IFB - ELIXIR-FR). With robust infrastructure boasting 8300 CPU cores, 52 TB of RAM, and GPU cards, UseGalaxy.fr offers a comprehensive suite of over 3,000 tools, including interactive options like Jupyter Notebook, AlphaFold, and Helixer. Notably, it has garnered over 6,000 users who have collectively executed over 3.6 million jobs. Moreover, UseGalaxy.fr hosts specialized subdomains catering to various community needs, such as ecology, metabarcoding, and COVID-19 research, with ongoing integration of new subdomains. The community's commitment to collaboration and consolidation is evident as several local servers have migrated to UseGalaxy.fr in recent years, with others expressing interest in doing the same. The French Galaxy community is deeply engaged in a multitude of projects at national, European, and global levels, including EOSC FAIR EASE, EuroScienceGateway, ATLASea and ABRomics. To foster cohesion and synergy within the community, a Galaxy Working Group led by the French Bioinformatics Institute facilitates regular interactions. This group serves to connect Galaxy users across France, share knowledge, support UseGalaxy.fr, and combat misconceptions about Galaxy within the French scientific community. In this poster presentation, we provide an overview of the dynamic French Galaxy ecosystem, highlighting its diverse servers, engaged researchers, ongoing projects, and collaborative efforts. Through this exploration, we aim to showcase the vibrancy and impact of Galaxy within the French bioinformatics landscape.

    ano.nymous@ccsd.cnrs.fr.invalid (Bérénice Batut) 11 Jul 2024

    https://hal.science/hal-04644779v1

Date de modification : 18 septembre 2024 | Date de création : 08 novembre 2023 | Rédaction : B-BEST