Institut Français de Bioinformatique

Efficient utilization of low-grade waste heat is keyto reducingthe carbon footprint of cooling and water-harvesting technologies.Adsorption-based devices employing porous materials enable thermallydriven heat exchange and atmospheric water capture with low environmentalimpact. While zeotype materials such as SAPO-34 (commercially knownas FAM-Z02) have long been benchmarks in these systems due to theirstability and appropriate water uptake behavior, their relativelyhigh synthesis cost still limits their commercial deployment. Thisstudy addresses the need for alternative sorbents capable of achievinghigh water working capacities at lower regeneration temperatures underrealistic heat-pump and water-harvesting conditions. This study demonstrates,for the first time, a scalable, water-based synthesis of MIL-160,enabling production at industrially relevant scales for adsorptionheat transformation and water harvesting. We show that MIL-160 exhibitsa high water uptake (434 g kg–1 at 20 °C),a 15–70% increase in working capacity over the industrial benchmarkFAM-Z02, and, critically, an efficient regeneration at only 60 °C,corresponding to the temperature range of typical waste heat. Thislow-temperature desorption behavior translates directly into enhancedenergy efficiency and reduced operational costs for adsorption-basedcooling and water-harvesting systems, while the material maintainsexcellent hydrothermal and cyclic stability. This efficient low-temperatureregeneration highlights MIL-160s strong potential for energy-savingthermal management and adsorption-based cooling systems. By bridgingthe gap between laboratory-scale MOFs and industrially viable sorbents,this study advances the practical implementation of next-generation,low-carbon thermal management technologies.

The rapid evolution of bioinformatics and data-driven life sciences necessitates widespread, effective training solutions capable of transcending geographical and institutional boundaries. ELIXIR, as a pan-European bioinformatics research infrastructure, has strategically embraced e-learning methodologies to meet this challenge. This white paper systematically reviews the current landscape of e-learning initiatives across various ELIXIR Nodes and Communities, detailing both historical developments and contemporary practices. It identifies core attributes and desirable features of effective e-learning, presenting an analysis of diverse educational platforms and the deployment of Learning Management Systems (LMS) within ELIXIR's framework. Emphasis is placed on the interactive, open-access, and sustainable nature of these resources, exemplified by platforms such as the Training e-Support System (TeSS) and the ELIXIR-SI eLearning Platform (EeLP). The paper highlights critical advancements toward standardization and interoperability through initiatives such as the adoption of SCORM protocols, facilitating resource reuse across Nodes. Additionally, the integration of e-learning into broader educational strategies-such as hybrid learning environments and structured learning paths-is examined. Finally, future directions are discussed, including strategies for integrating e-learning with traditional training methods, enhancing trainer expertise, and further expanding the availability and FAIRification of bioinformatics training resources.

The Galaxy platform is a globally distributed environment for data-intensive research, providing thousands of analysis tools across major public servers. However, this decentralised ecosystem presents usability challenges for both users and administrators, particularly in surfacing relevant tools and workflows for specific communities. To improve discoverability and support global collaboration, the Galaxy project has employed community-driven "Galaxy Flavours"—subdomains with curated content for defined research domains. While conceptually valuable, Flavours suffer from critical limitations: they are statically deployed, difficult to replicate across servers, and often provide inconsistent and unintuitive user interfaces.To address these challenges, we developed the Galaxy Labs Engine (GLE), a service that enables the creation of Galaxy Labs. This new paradigm enables globally synchronised, domain-specific entry points built from structured, reusable web content. GLE separates content from deployment, allowing communities to define a shared canonical representation of their domain, while enabling individual Galaxy servers to locally customise presentation. Labs are designed to guide users through curated tools, workflows, and training resources, and are aimed at researchers who are new to the analytical methods or technologies specific to the domain.The Galaxy Labs Engine provides a consistent, customisable, and community-driven interface layer for the Galaxy ecosystem. By fostering FAIR principles, Labs offer a scalable improvement to Flavours and enhance Galaxy’s ability to support diverse research communities. GLE is open-source and currently deployed at https://labs.usegalaxy.org.au, with multiple Labs already supporting active user groups. This work strengthens Galaxy’s role as a collaborative platform for reproducible, user-centered science.

This document reports on the agenda, key points, and outcomes of the ELIXIR Microbiome Community's face-to-face and hybrid meeting, which took place on April 9-10, 2025, in Barcelona, Spain.

T-cell acute lymphoblastic leukemia (T-ALL) is a hematopoietic malignancy characterized by increased proliferation and incomplete maturation of T-cell progenitors, for which relapse is often of poor prognosis. To improve patient outcomes, it is critical to understand the chemoresistance mechanisms arising from cell plasticity induced by the bone marrow (BM) microenvironment. Single-cell RNA sequencing of human T-ALL cells from adipocyte-rich and adipocyte-poor BM revealed a distinct leukemic cell population defined by quiescence and high CD44 expression (Ki67neg/lowCD44high). During in vivo treatment, these cells evaded chemotherapy, and were further called Chemotherapy-resistant Leukemic Cells (CLCs). Patient sample analysis revealed Ki67neg/lowCD44high CLCs at diagnosis and during relapse, with each displaying a specific transcriptomic signature. Interestingly, CD44high expression in T-ALL Ki67neg/low CLCs was associated with E-selectin binding. Analysis of 39 human T-ALL samples revealed significantly enhanced E-selectin binding activity in relapse/refractory samples compared with drug-sensitive samples. These characteristics of chemoresistant T-ALL CLCs provide key insights for prognostic stratification and novel therapeutic options.

Created in 2021, UseGalaxy France (UseGalaxy.fr) is the first national UseGalaxy server. It is the French national instance hosted by the French Institute for Bioinformatics (IFB - ELIXIR-FR) Core Cluster (8300 CPU-cores, 52 TB of RAM, GPU cards) and maintained by IFB itself and by engineers from regional platforms. It offers 3k+ tools and several Interactive tools (GxIT) like Jupyter Notebook, AlphaFold, and Helixer. Since 2021, its 6k+ users ran 3.6M+ jobs. UseGalaxy.fr is well embedded within the French ecosystem. UseGalaxy.fr is involved in many national projects (e.g. ABRomics, the national platform for antimicrobial resistance surveillance) but also European efforts such as EuroScienceGateway . It hosts several community-specific subdomains : ecology, metabarcoding, proteore, covid19, workflow4metabolomics, MNHN, and Plants-pathogens. New subdomains are currently being integrated into UseGalaxy.fr. Several local servers (e.g. ABIMS, GenOuest/BIPAA, IGBMC) have decided to migrate to UseGalaxy.fr over the last few years. Other local servers from the French Galaxy Working Group have mentioned their interest in following the same pathway. Since the first day, UseGalaxy.fr has followed the wake of the UseGalaxy servers. It’s implemented as an Infrastructure as Code ( IaC ) infrastructure, stored on GitLab, managed by Ansible, and launched by GitLab-runner. The whole system is co-administered by a team of 6 IFB members from multiple regional platforms. The developments of UseGalaxy.fr are focused on the adoption of best practices for the deployment of UseGalaxy servers, in particular as one of the 7 national servers supported by the EuroScienceGateway project. As such, tools are installed using a standard GitLab repository and auto-updated by a bot (IFBOT) once a week. Tool dependencies are currently managed using Conda, but are progressively moving to be fully based on Apptainer. Data managers are automatically installed but are still manually launched, though this limitation should be solved by the planned adoption of IDC (Simon's Data Club) mechanism. Recently UseGalaxy.fr was configured to use the new Total Perspective Vortex (TPV), using community but also local rules to dynamically assign tool resources. As part of the EuroScienceGateway project, UseGalaxy.fr aims to integrate a European Pulsar network, allowing the execution of jobs from other UseGalaxy servers on the IFB infrastructure, but also the submission of UseGalaxy.fr jobs on other computing infrastructure, in France and abroad. A first French Pulsar node is already hosted on the GenOuest regional platform. UseGalaxy.fr also provides a Training Infrastructure as a Service ( TIaaS ). Since February 2022, this service has offered 550+ days of computing to 70+ events, reaching 1700+ learners. All support on UseGalaxy.fr is done as a community effort, using the public Discourse hosted by IFB ( https://community.france-bioinformatique.fr/ ). In this talk, we will present the UseGalaxy France server, a first successful implementation of a national UseGalaxy server, and share our plans for the future, in particular for better integration with the other UseGalaxy servers.

The COVID-19 pandemic has exemplified the importance of interoperable and equitable data sharing for global surveillance and to support research. While many challenges could be overcome, at least in some countries, many hurdles within the organizational, scientific, technical and cultural realms still remain to be tackled to be prepared for future threats. We propose to (i) continue supporting global efforts that have proven to be efficient and trustworthy toward addressing challenges in pathogen molecular data sharing; (ii) establish a distributed network of Pathogen Data Platforms to (a) ensure high quality data, metadata standardization and data analysis, (b) perform data brokering on behalf of data providers both for research and surveillance, (c) foster capacity building and continuous improvements, also for pandemic preparedness; (iii) establish an International One Health Pathogens Portal, connecting pathogen data isolated from various sources (human, animal, food, environment), in a truly One Health approach and following FAIR principles. To address these challenging endeavors, we have started an ELIXIR Focus Group where we invite all interested experts to join in a concerted, expert-driven effort toward sustaining and ensuring high-quality data for global surveillance and research.

A Gram-strain positive, aerobic, endospore-forming bacterial strain (JJ-246T) was isolated from the rhizosphere of Zea mays. The 16S rRNA gene sequence similarity comparisons showed a most closely relationship to Paenibacillus oenotherae DT7-4T (98.4%) and Paenibacillus xanthinolyticus 11N27T (98.0%). The pairwise average nucleotide identity and digital DNA-DNA hybridisation values of the JJ-246T genome assembly against publicly available Paenibacillus type strain genomes were below 82% and 33%, respectively. The draft genome of JJ-246T shared many putative plant-beneficial functions contributing (PBFC) genes, related to plant root colonisation, oxidative stress protection, degradation of aromatic compounds, plant growth-promoting traits, disease resistance, drug and heavy metal resistance, and nutrient acquisition. The quinone system of strain JJ-246T, the polar lipid profile and the major fatty acids were congruent with those reported for members of the genus Paenibacillus. JJ-246T was shown to represent a novel species of the genus Paenibacillus, for which the name Paenibacillus plantiphilus sp. nov. is proposed, with JJ-246T (= LMG 32093T = CCM 9089T = CIP 111893T) as the type strain.

Support for a 3h course to answer the question: How to make a bioinformatics project more reproducible?