AuBi platform for biologists and bioinformaticians at UCA Mesocentre

International audienceThe Mesocentre as part of Clermont Auvergne University (UCA) is delivering services in sciences data computing (HPC, VM, …) and short-term storage through a network of technology core facilities. These offers are done to assist multi-disciplinary scientists in their computing projects. At that time, we are hosting a computer farm with about 800 cores, 40 nodes for moderate memory usage (<256 Gb) and a SMP supercomputer made of 384 cores and 12 To memory in addition to a CEPH storage of at least 1 To capacity by user. Hosted by the Mesocentre, the Auvergne bioinformatics (AuBi) platform is a member of the French Bioinformatics Institute (IFB, https://www.france-bioinformatique.fr/en/platforms/AUBI). AuBi platform aims at sharing expertises and knowledge in large-scale data treatments and analysis by supplying a complete computing environment with hardware and software infrastructures for 9 research laboratories. AuBi platform is then involved in various projects belonging to genomics, metagenomics, transcriptomics, modeling and imaging fields amongst others [1,2,3]. Furthermore, we provide support to UCA laboratories and Associates in their effort to maintain and enhance their scripts and pipelines used on our infrastructure.Another aspect of AuBi platform work is to facilitate computing access to non-bioinformatician biologists by the way of a Galaxy server released in the upcoming weeks. We are also organizing training sessions to help our users, either biologists or bioinformaticians to optimize computing resources usage through command line interface and Galaxy environment.References1. Amato P., Joly M., Besaury L. Oudart A., Taib N., Moné A., Deguillaume L., Delort A.M. and Debroas D. (2017). Active microorganisms thrive among extremely diverse communities in cloud water. PLoS ONE 12(8):e0182869.2. Gasc C, Constantin A, Jaziri F, Peyret P: OCaPPI-Db: an oligonucleotide probe database for pathogen identification through hybridization capture. Database (Oxford) 2017, 2017.3. Parisot N, Peyretaillade E, Dugat-Bony E, Denonfoux J, Mahul A, Peyret P: Probe Design Strategies for Oligonucleotide Microarrays. Methods Mol Biol 2016, 1368:67-82

A Newly Opened Galaxy Platform at Clermont Auvergne University

The Mesocentre as part of Clermont Auvergne University (UCA) is delivering services in sciences data computing (HPC, VM, …) and short-term storage through a network of technology core facilities. These offers are done to assist multi-disciplinary scientists in their computing projects. At that time, we are hosting a computer farm with about 800 cores, 40 nodes for moderate memory usage (<256 GB) and a SMP supercomputer made of 384 cores and 12 TB memory in addition to a scalable storage cluster managed with Ceph of at least 1 TB capacity per user, with a total of 1.2 PB.Hosted by the Mesocentre, the AuBi (Auvergne bioinformatics) platform is a member of IFB (French Bioinformatics Institute, https://www.france-bioinformatique.fr/). AuBi platform aims at sharing expertises and knowledge in large-scale data treatments and analysis by supplying a complete computing environment with hardware and software infrastructures for UCA research laboratories. To fit this goal, a Galaxy server was installed as a facilitator for a computing access to non-bioinformatician biologists. As AuBi platform is involved in various projects, roughly 50 tools related to genomics, metagenomics, transcriptomics and epigenetics were installed to the Galaxy instance as well as homemade tools from a local toolshed.From an informatics infrastructure point of view, our Galaxy server is behind a reverse proxy server, galaxy.mesocentre.uca.fr. A virtual machine, with an extensible disk on a scalable storage cluster (RBD / Ceph), runs the server. It is connected to the HPC facilities through a NFS server in order to allow Galaxy to benefit from the Mesocentre empowered computing and storage capabilities. Users authenticate through a shared LDAP directory between the Galaxy server and the cluster. In addition, BioMaJ1 framework was deployed for sharing databanks access to both Galaxy and cluster.In the future, we plan to expand our access to the users from the IFB community via an eduGAIN connection. Finally, we expect a significant contribution from UCA laboratories into migrating local tools to the IUC toolshed

Auvergne Bioinformatics platform at UCA Mesocentre

Le mésocentre, qui fait partie de l'Université de Clermont Auvergne (UCA), fournit des services de calcul haute performance pour les données scientifiques et le stockage à court terme grâce à un réseau d'installations technologiques de base. Ces offres sont faites pour aider les scientifiques pluridisciplinaires dans leurs projets de calcul. Nous hébergeons actuellement une ferme informatique d'environ 800 cœurs ; 40 nœuds pour une utilisation modérée de la mémoire (<256 Go) ; un supercalculateur SMP composé de 384 cœurs et de 12 To de mémoire ; plus une technologie GPU (8 GPU de 5120 cœurs chacun) ; une plateforme de cloud computing - basée sur la technologie Openstack - avec un total de 960 cœurs physiques et 9 To de mémoire ; et un stockage CEPH d'une capacité d'au moins 1 To par utilisateur. Hébergée par le Mésocentre, la plateforme de bio-informatique d'Auvergne (AuBi) est membre de l'Institut français de bio-informatique (IFB, https://www.france-bioinformatique.fr/en/platforms/AUBI). La plate-forme AuBi vise à partager les expertises et les connaissances en matière de traitement et d'analyse de données à grande échelle en fournissant un environnement informatique complet avec des infrastructures matérielles et logicielles pour 9 laboratoires de recherche. La plate-forme AuBi est ensuite impliquée dans différents projets appartenant aux domaines de la génomique, de la métagénomique, de la transcriptomique, de la modélisation et de l'imagerie, entre autres [1,2,3]. De plus, nous soutenons les laboratoires de l'UCA et leurs associés dans leurs efforts pour maintenir et améliorer leurs scripts et pipelines utilisés sur notre infrastructure, ainsi qu'un accès facile aux banques de données publiques reflétées par le BioMAJ [4].Un autre aspect du travail de la plateforme AuBi consiste à faciliter l'accès au calcul par le biais de Galaxy [5] et d'une installation de stockage des métadonnées d'images par le biais d'un serveur OMERO [6]. Nous organisons également des sessions de formation pour aider nos utilisateurs, qu'ils soient biologistes ou bioinformaticiens, à optimiser l'utilisation des ressources informatiques via l'interface de ligne de commande ou l'environnement Galaxy.References [1] Pierre Amato, Ludocic Besaury, Muriel Joly, Benjamin Penaud, Laurent Deguillaume and Anne-Marie Delort. Metatranscriptomic exploration of microbial functioning in clouds. Scientific Reports 9: 4383, 2019. [2] François Balfourier, Sophie Bouchet, Sandra Robert, Romain De Oliveira, Hélène Rimbert, Jonathan Kitt, Frédéric Choulet, IWGS Consortium, BreedWheat Consortium and Etienne Paux. Worldwide phylogeography and history of wheat genetic diversity. Science Advances 5(5): eaav0536, 2019 [3] Caroline Pont, Thibault Leroy, Michael Seidel, Alessandro Tondelli, Wandrille Duchemin, David Armisen, Daniel Lang, Daniela, Bustos-Korts, Nadia Goué, François Balfourier, Márta Molnár-Láng, Jacob Lagen Benjamin Kilian, Hakan Özkan, Darren Waite, Sarah Dyer, Letellier Thomas, Michael Alaux, WHEALBI consortium, Joanne Russel, Beat Keller, Fred van Eeuwijk, Manuel Spannagl, Klaus Mayer, Robbie Waugh, Nils Stein, Kuigi Cattivelli, Georg Haberer, Gilles Charmet and Jérôme Salse. Tracing the ancestry of modern bread wheats. Nature Genetics, (51): 905-911, 2019 [4] Olivier Filangi, Yoann Beausse, Anthony Assi, Ludovic Legrand, Jean-Marc Larré, Véronique Martin, Olivier Collin, Christophe Caron, Hugues Leroy, David Allouche. BioMAJ: A flexible framework for databanks synchronization and processing. Bioinformatics, 24(16): 1823-1825, 2008. [5] Enis Afgan, Dannon Baker, Bérénice Batut, Marius van den Beek , Dave Bouvier, Martin Cech, John Chilton, Dave Clements, Nate Coraor, Björn Grüning, Aysam Guerler, Jennifer Hillman-Jackson, Saskia Hiltemann, Vahid Jalili, Helena Rasche, Nicola Soranzo, Jeremy Goecks, James Taylor, Anton Nekrutenko and Daniel Blankenberg. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses : 2018 update. 46(W1) : W537-W544, 2018. [6] http://www.openmicroscopy.org

Supports for imaging projects toward Open Science at AuBi platform

International audience1. IntroductionHosted by the Clermont Auvergne Mesocenter [1], the Auvergne Bioinformatics (AuBi) platform is member of the French Institute of Bioinformatics (IFB) [2]. We aim at sharing expertise and knowledge in large-scale data analysis with computing and storage facilities for biology and health research laboratories located at Clermont Auvergne University (UCA). Among axis of interest is imaging for which OMERO [3] a tool for data visualization and metadata storage as well as a bio-analysis platform Galaxy [4] have been deployed.2. A web portal to orchestrate the tools around the FAIR dataWith the recent advances towards Open Science, data flows, tools and workflow analysis need to be orchestrated in order to help scientists to navigate across projects and collaborate together. To initiate this structuration around the data projects and based on FAIR principles, we started working on a web portal accessible from the Mesocenter hub. This portal shall give access to several services : (1) a unique corresponding address to help scientists feeding Data Management Plan (DMP) and HAL publication referencing system leaded by University library ; (2) mature web services for meta-data and image storing system, as well as images workflow analysis ; (3) a high performance calculation and storage infrastructureprovided by the Mesocenter. Our objective is to be able to link these tools through data projects. This is why we are working together with OpenLink team [5] to develop a service meeting our biologists and bioinformatics communities, the Mesocenter and UCA requirements.3. ConclusionThis Open Science project gives an opportunity for laboratories associated with AuBi platform to get involved in national IFB projects such as MuDiS4LS. This is the case for iGReD [6] and i ts confocal microscopy facility CLIC (CLermont Imagerie Confocal) by contributing to the implementation Study for the elaboration of the structure DMP dedicated to imaging. This is challenging laboratories with imaging projects to mutualize storage resources like the storage server bought in 2021 all together with four Mixed Research Units : GDEC, iGReD, PIAF and UNH [6]. This project is initiated on imaging data and once on track, other data types will be orchestrated and linked together.References[1] www.mesocentre.uca.fr[2] www.france-bioinformatique.fr[3] http://www.openmicroscopy.org/[4] Afgan E. et al. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses : 2018update. 46(W1) : W537-W544, 2018.[5] https://gitlab.com/igbmc/openlink[6] https://ressources.france-bioinformatique.fr/fr/plateformes/aub

From Sensor to Cloud: An IoT Network of Radon Outdoor Probes to Monitor Active Volcanoes

International audienceWhile radon in soil gases has been identified for decades as a potential precursor of volcanic eruptions, there has been a recent interest for monitoring radon in air on active volcanoes. We present here the first network of outdoor air radon sensors that was installed successfully on Mt. Etna volcano, Sicily, Italy in September 2019. Small radon sensors designed for workers and home dosimetry were tropicalized in order to be operated continuously in harsh volcanic conditions with an autonomy of several months. Two stations have been installed on the south flank of the volcano at~3000 m of elevation. A private network has been deployed in order to transfer the measurements from the stations directly to a server located in France, using a low-power wide-area transmission technology from Internet of Things (IoT) called LoRaWAN. Data finally feed a data lake, allowing flexibility in data management and sharing. A first analysis of the radon datasets confirms previous observations, while adding temporal information never accessed before. The observed performances confirm IoT solutions are very adapted to active volcano monitoring in terms of range, autonomy, and data loss

DéBAT : Analyse de Diversité d'un panel de pré-breeding de Blé tendre par une approche Transcriptomique-projet FSOV 2018 M

Rapport du projet FSOV-DeBat 2018 MDéBAT : Analyse de Diversité d'un panel de pré-breeding de Blé tendre par une approche Transcriptomique-projet FSOV 2018

FAIRing Research Data to Live @AuBi Platform

International audienceHosted by the Mésocentre Clermont-Auvergne [1], the Auvergne Bioinformatique (AuBi) platform is member of the Institut Français de Bioinformatique (IFB) [2]. Around 15 labs contributes to AuBi activities with scientific questions related to health, microbes, agronomy and environment disciplines. Despite a high diversity a research questioning, data that are produced, processed and analyzed belongs to four main categories : sequences, images, qualitative and quantitative data and digital models. We aim at sharing expertise and knowledge in handling these kind of large-scale data with computing and storage facilities administrated at Mesocentre.An update of general services are presented here in terms of computing and storage as well as our prospects in the coming months. Recently opened services like jupyter notebooks and gitlab server for code tracking are keys points towards reproducible sciences. In addition, our concern about security and safety data storage guided us for proposing a new storage services accessible from any labs on our campus. Among services administrated for biologists and bioinformaticians are mature tools, an OMERO [3] server for data visualization and (meta)-data storage as well as the bio-analysis platform Galaxy [4]. In addition to the administration and technical support, we are contributing to scientific projects, such as the microservice web portal for the PlateForme d’Exploration du métabolisme. The project started a year ago and we are offering an infrastructure and our expertise in tool development to improve metabolomic annotation and analysis from a cloud infrastructure. In addition, through the IFB, we interact with FAIRChecker [5] development team to improve the FAIRness of our microservices web services. A poster to specifically detail the project has been submitted.Considering the data lifecycle, we are collaborating on 3 main IFB project. Firstly, one project initiated with the Projet-flash ANR machine-actionable DMP for Life Sciences (maDMP4LS) and the Institut de l’lnformation Scientifique et Technique (INIST) team ended up into the produce a web form connected to OPIDoR DMP, to help users to estimate project cost on the Mesocentre. Secondly, as part of the MuDiS4LS project, Data Stewart Wizard project was used to develop DMP dedicated to platforms: images produced and annotated on the CLermont Imagerie Confocal platform [6] as well as images stored and analyzed on omero.mesocentre.uca.fr. Thirdly, we contributed to the previously OpenLink project renamed as MadBot [7] offering a web portal orchestrating project information from data production to data publication with a view and link to where data are stored (Galaxy, OMERO, ...)To support users towards open science, FAIR principles and reproducibility, we are working together with the “Open Science Unit” and the IFB training team, investing in training sessions. Training are oriented toward best practices in using the Mesocenter infrastructures as well as raising awareness about the proper use of metadata while storing image data. We are also offering training sessions for bioinformaticians for best practices (FAIR-bioinfo) and for biologists with the Galaxy Training Network with topics of interest for the AuBi community.All our actions are Open Science oriented. This is challenging as actions have to be coordinated and in agreement with the University and research Institutes strategies, the Information Systems Management and the GDPR regulations, and considering diversity of research programs and various types of produced and stored data.AcknowledgementsINIST, maDMP4LS, IS1-MuDiS4LS and MadBot teamsReferences1.www.mesocentre.uca.fr2.www.france-bioinformatique.fr3.http://www.openmicroscopy.org/4.Afgan et al. (2018) https://doi.org/10.1093/nar/gky3795.Gaignard et al. (2023) https://doi.org/10.1186/s13326-023-00289-56.https://ressources.france-bioinformatique.fr/fr/plateformes/aubi7.https://www.france-bioinformatique.fr/science-ouverte

Analyse de diversité d'un panel de pré-breeding de blé tendre par une approche transcriptomique

Projet FSOV DeBat 2018 MInternational audienc

FAIRing Research Data to Live @AuBi Platform

International audienceHosted by the Mésocentre Clermont-Auvergne [1], the Auvergne Bioinformatique (AuBi) platform is member of the Institut Français de Bioinformatique (IFB) [2]. Around 15 labs contributes to AuBi activities with scientific questions related to health, microbes, agronomy and environment disciplines. Despite a high diversity a research questioning, data that are produced, processed and analyzed belongs to four main categories : sequences, images, qualitative and quantitative data and digital models. We aim at sharing expertise and knowledge in handling these kind of large-scale data with computing and storage facilities administrated at Mesocentre.An update of general services are presented here in terms of computing and storage as well as our prospects in the coming months. Recently opened services like jupyter notebooks and gitlab server for code tracking are keys points towards reproducible sciences. In addition, our concern about security and safety data storage guided us for proposing a new storage services accessible from any labs on our campus. Among services administrated for biologists and bioinformaticians are mature tools, an OMERO [3] server for data visualization and (meta)-data storage as well as the bio-analysis platform Galaxy [4]. In addition to the administration and technical support, we are contributing to scientific projects, such as the microservice web portal for the PlateForme d’Exploration du métabolisme. The project started a year ago and we are offering an infrastructure and our expertise in tool development to improve metabolomic annotation and analysis from a cloud infrastructure. In addition, through the IFB, we interact with FAIRChecker [5] development team to improve the FAIRness of our microservices web services. A poster to specifically detail the project has been submitted.Considering the data lifecycle, we are collaborating on 3 main IFB project. Firstly, one project initiated with the Projet-flash ANR machine-actionable DMP for Life Sciences (maDMP4LS) and the Institut de l’lnformation Scientifique et Technique (INIST) team ended up into the produce a web form connected to OPIDoR DMP, to help users to estimate project cost on the Mesocentre. Secondly, as part of the MuDiS4LS project, Data Stewart Wizard project was used to develop DMP dedicated to platforms: images produced and annotated on the CLermont Imagerie Confocal platform [6] as well as images stored and analyzed on omero.mesocentre.uca.fr. Thirdly, we contributed to the previously OpenLink project renamed as MadBot [7] offering a web portal orchestrating project information from data production to data publication with a view and link to where data are stored (Galaxy, OMERO, ...)To support users towards open science, FAIR principles and reproducibility, we are working together with the “Open Science Unit” and the IFB training team, investing in training sessions. Training are oriented toward best practices in using the Mesocenter infrastructures as well as raising awareness about the proper use of metadata while storing image data. We are also offering training sessions for bioinformaticians for best practices (FAIR-bioinfo) and for biologists with the Galaxy Training Network with topics of interest for the AuBi community.All our actions are Open Science oriented. This is challenging as actions have to be coordinated and in agreement with the University and research Institutes strategies, the Information Systems Management and the GDPR regulations, and considering diversity of research programs and various types of produced and stored data.AcknowledgementsINIST, maDMP4LS, IS1-MuDiS4LS and MadBot teamsReferences1.www.mesocentre.uca.fr2.www.france-bioinformatique.fr3.http://www.openmicroscopy.org/4.Afgan et al. (2018) https://doi.org/10.1093/nar/gky3795.Gaignard et al. (2023) https://doi.org/10.1186/s13326-023-00289-56.https://ressources.france-bioinformatique.fr/fr/plateformes/aubi7.https://www.france-bioinformatique.fr/science-ouverte

FAIRing Research Data to Live @AuBi Platform

International audienceHosted by the Mésocentre Clermont-Auvergne [1], the Auvergne Bioinformatique (AuBi) platform is member of the Institut Français de Bioinformatique (IFB) [2]. Around 15 labs contributes to AuBi activities with scientific questions related to health, microbes, agronomy and environment disciplines. Despite a high diversity a research questioning, data that are produced, processed and analyzed belongs to four main categories : sequences, images, qualitative and quantitative data and digital models. We aim at sharing expertise and knowledge in handling these kind of large-scale data with computing and storage facilities administrated at Mesocentre.An update of general services are presented here in terms of computing and storage as well as our prospects in the coming months. Recently opened services like jupyter notebooks and gitlab server for code tracking are keys points towards reproducible sciences. In addition, our concern about security and safety data storage guided us for proposing a new storage services accessible from any labs on our campus. Among services administrated for biologists and bioinformaticians are mature tools, an OMERO [3] server for data visualization and (meta)-data storage as well as the bio-analysis platform Galaxy [4]. In addition to the administration and technical support, we are contributing to scientific projects, such as the microservice web portal for the PlateForme d’Exploration du métabolisme. The project started a year ago and we are offering an infrastructure and our expertise in tool development to improve metabolomic annotation and analysis from a cloud infrastructure. In addition, through the IFB, we interact with FAIRChecker [5] development team to improve the FAIRness of our microservices web services. A poster to specifically detail the project has been submitted.Considering the data lifecycle, we are collaborating on 3 main IFB project. Firstly, one project initiated with the Projet-flash ANR machine-actionable DMP for Life Sciences (maDMP4LS) and the Institut de l’lnformation Scientifique et Technique (INIST) team ended up into the produce a web form connected to OPIDoR DMP, to help users to estimate project cost on the Mesocentre. Secondly, as part of the MuDiS4LS project, Data Stewart Wizard project was used to develop DMP dedicated to platforms: images produced and annotated on the CLermont Imagerie Confocal platform [6] as well as images stored and analyzed on omero.mesocentre.uca.fr. Thirdly, we contributed to the previously OpenLink project renamed as MadBot [7] offering a web portal orchestrating project information from data production to data publication with a view and link to where data are stored (Galaxy, OMERO, ...)To support users towards open science, FAIR principles and reproducibility, we are working together with the “Open Science Unit” and the IFB training team, investing in training sessions. Training are oriented toward best practices in using the Mesocenter infrastructures as well as raising awareness about the proper use of metadata while storing image data. We are also offering training sessions for bioinformaticians for best practices (FAIR-bioinfo) and for biologists with the Galaxy Training Network with topics of interest for the AuBi community.All our actions are Open Science oriented. This is challenging as actions have to be coordinated and in agreement with the University and research Institutes strategies, the Information Systems Management and the GDPR regulations, and considering diversity of research programs and various types of produced and stored data.AcknowledgementsINIST, maDMP4LS, IS1-MuDiS4LS and MadBot teamsReferences1.www.mesocentre.uca.fr2.www.france-bioinformatique.fr3.http://www.openmicroscopy.org/4.Afgan et al. (2018) https://doi.org/10.1093/nar/gky3795.Gaignard et al. (2023) https://doi.org/10.1186/s13326-023-00289-56.https://ressources.france-bioinformatique.fr/fr/plateformes/aubi7.https://www.france-bioinformatique.fr/science-ouverte