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Empowering communities with open* principles

Yo Yehudi, Bérénice Batut, Malvika Sharan, Emmy Tsang
2021 Zenodo  
Talk on the Open Life Science program at InCoB 2021
doi:10.5281/zenodo.5651491 fatcat:qrnfyxasybgrzkoofbz5gzfsfe

Empowering communities with open* principles

Yo Yehudi, Bérénice Batut, Malvika Sharan, Emmy Tsang
2021 Zenodo  
Talk on the Open Life Science program at InCoB 2021
doi:10.5281/zenodo.5651492 fatcat:ert3ulsc75fjdpfmm4sbxalgp4

Open Life Science Application To Code for Science & Society (successful) [article]

Yo Yehudi, Malvika Sharan, Bérénice Batut
2021 Zenodo  
OLS was developed and launched in 2019 through Mozilla Open Leaders X by us: Yo Yehudi, Malvika Sharan, and Bérénice Batut.  ...  Batut • Galaxy Community Conference, Germany. 2019: https://galaxyproject.org/events/gcc2019/ • Galaxy Training Network training and resource development sprints, online and Germany, 2019: https:  ... 
doi:10.5281/zenodo.4777229 fatcat:5gh7h3bhmnatneiundefc2umya

Open Life Science - Wellcome Trust Open Research Fund Application 2021 [article]

Malvika Sharan, Yo Yehudi, Emmy Tsang, Bérénice Batut
2021 Zenodo  
Bérénice Batut, Open Life Science Role: Content development and data strategy -Dr Batut will develop and maintain a robust and scalable data architecture for the OLS community; establish content and data  ...  Sharan, Batut and Tsang will bring key skills to the programme from their professional background, areas of expertise and personal networks.  ... 
doi:10.5281/zenodo.5267933 fatcat:twwkvlbj2vdsvchjq63qeunbh4

RNA-Seq Data Analysis in Galaxy

Bérénice Batut, Marius van den Beek, Maria A Doyle, Nicola Soranzo
2021 Msphere  
A complete RNA-Seq analysis involves the use of several different tools, with substantial software and computational requirements. The Galaxy platform simplifies the execution of such bioinformatics analyses by embedding the needed tools in its web interface, while also providing reproducibility. Here, we describe how to perform a reference-based RNA-Seq analysis using Galaxy, from data upload to visualization and functional enrichment analysis of differentially expressed genes.
doi:10.1007/978-1-0716-1307-8_20 pmid:33835453 fatcat:7rgme3uzyfgx3eqiio5r3x5ope

Open Life Science's successful Grant Application from the First EOSC-Life Training Call [article]

Bérénice Batut, Yo Yehudi, Malvika Sharan
2020 Zenodo  
Within the 1st EOSC-Life Training Open Call, Open Life Science was awarded the training grant to develop mentoring and training opportunities for EOSC Research Infrastructures Open Life Science (OLS) is a 16-week long personal mentorship and cohort-based training for individuals who would like to develop and lead Open Research projects in their communities. OLS will open a call for mentors and project leads from EOSC RIs for their third cohort, which is expected to take place from February to
more » ... y 2021. In each cohort, the participants of this program will: share their expertise and gain knowledge essential to create, lead, and sustain an Open Science project connect with members across different projects, communities, backgrounds, and identities empower each other to become effective Open Science ambassadors in their communities
doi:10.5281/zenodo.4060367 fatcat:lofohmyldvbxjme7uembylrz5q

Open Life Science: Empowering early career researchers to become open science leaders

Malvika Sharan, Yo Yehudi, Bérénice Batut
2020 Zenodo  
Motivation: As scientists, we are provided training and guidance in how to conduct research in the lab, design algorithms, analyse data and publish them. However, scientists are rarely expected to apply important skills such as open science principles for tooling and road mapping their projects, planning reproducible workflows, involving others in their work, and leading an inclusive community. Modern bioinformatics communities stand in the interface of computational and biological research.
more » ... s interdisciplinary position requires us to develop collaborative projects by implementing such "open by design" principles in our research projects systematically -- skills that aren't necessarily taught at university or graduate school level. About the project: Open Life Science (OLS) is a volunteer-driven training and mentoring program aimed at empowering early career researchers and potential academic leaders to become open science ambassadors. Participants join OLS with a proposal to work on an open science project and attend a series of one-on-one mentoring calls over 16 weeks, alternating with full cohort calls that provide training on specific open science and leadership skills. OLS's work is underpinned by a community of over 50 mentors and expert guest speakers. Cohort calls cover a broad spectrum of topics relevant to leading an open project, ranging from open science topics, community building, project and contribution management of GitHub repositories, and caring both for yourself and others in your community. Calls are designed to be interactive and engaging, utilising a mix of Zoom's break-out room features to facilitate group discussion, collaborative document editing, and guest speakers from academia and industry giving short talks. The program is modelled on the exact principles we teach, and hence, all materials, including syllabus, call notes, and slides, are shared under the CC-BY licence. Cohort calls are recorded and shared openly on YouTube. Third-party organisation [...]
doi:10.5281/zenodo.4459417 fatcat:vfltbw5wrbfdrdlmf6zu4x3wty

Open Life Science - Training and Mentoring programme - Website release 2019-2021 [article]

Bérénice Batut, Yo Yehudi, Malvika Sharan, Emmy Tsang, Open Life Science Community
2021 Zenodo  
The Open Life Science (OLS) program helps individuals and stakeholders in research to become Open Science ambassadors. About This is a 16-week long personal mentorship and cohort-based training, where participants (organisers, hosts, mentors and project leads/mentees) of this program will: share their expertise and gain knowledge essential to create, lead, and sustain an Open Science project connect with members across different projects, communities, backgrounds, and identities empower each
more » ... er to become effective Open Science ambassadors in their communities
doi:10.5281/zenodo.5636584 fatcat:oy5r6jrwavcd5dx3f7gplvocmm

ASaiM: a Galaxy-based framework to analyze microbiota data

Bérénice Batut, Kévin Gravouil, Clémence Defois, Saskia Hiltemann, Jean-François Brugère, Eric Peyretaillade, Pierre Peyret
2018 GigaScience  
doi:10.1093/gigascience/giy057 pmid:29790941 pmcid:PMC6007547 fatcat:guy4ocqx3vhgfn2pk7nd5jmnda

ASaiM: a Galaxy-based framework to analyze raw shotgun data from microbiota [article]

Bérénice Batut, Kévin Gravouil, Clémence Defois, Saskia Hiltemann, Jean-François Brugère, Eric Peyretaillade, Pierre Peyret
2017 bioRxiv   pre-print
New generation of sequencing platforms coupled to numerous bioinformatics tools has led to rapid technological progress in metagenomics and metatranscriptomics to investigate complex microorganism communities. Nevertheless, a combination of different bioinformatic tools remains necessary to draw conclusions out of microbiota studies. Modular and user-friendly tools would greatly improve such studies. We therefore developed ASaiM, an Open-Source Galaxy-based framework dedicated to microbiota
more » ... analyses. ASaiM provides a curated collection of tools to explore and visualize taxonomic and functional information from raw amplicon, metagenomic or metatranscriptomic sequences. To guide different analyses, several customizable workflows are included. All workflows are supported by tutorials and Galaxy interactive tours to guide the users through the analyses step by step. ASaiM is implemented as Galaxy Docker flavour. It is scalable to many thousand datasets, but also can be used a normal PC. The associated source code is available under Apache 2 license at https://github.com/ASaiM/framework and documentation can be found online (http://asaim.readthedocs.io/). Based on the Galaxy framework, ASaiM offers sophisticated analyses to scientists without command-line knowledge. ASaiM provides a powerful framework to easily and quickly explore microbiota data in a reproducible and transparent environment.
doi:10.1101/183970 fatcat:ibolunrhlzc4nldbpj2pbof56m

In silico experimental evolution: a tool to test evolutionary scenarios

Bérénice Batut, David P Parsons, Stephan Fischer, Guillaume Beslon, Carole Knibbe
2013 BMC Bioinformatics  
Comparative genomics has revealed that some species have exceptional genomes, compared to their closest relatives. For instance, some species have undergone a strong reduction of their genome with a drastic reduction of their genic repertoire. Deciphering the causes of these atypical trajectories can be very difficult because of the many phenomena that are intertwined during their evolution (e.g. changes of population size, environment structure and dynamics, selection strength, mutation
more » ... .). Here we propose a methodology based on synthetic experiments to test the individual effect of these phenomena on a population of simulated organisms. We developed an evolutionary model -aevol -in which evolutionary conditions can be changed one at a time to test their effects on genome size and organization (e.g. coding ratio). To illustrate the proposed approach, we used aevol to test the effects of a strong reduction in the selection strength on a population of (simulated) bacteria. Our results show that this reduction of selection strength leads to a genome reduction of~35% with a slight loss of coding sequences (~15% of the genes are lost -mainly those for which the contribution to fitness is the lowest). More surprisingly, under a low selection strength, genomes undergo a strong reduction of the noncoding compartment (~55% of the noncoding sequences being lost). These results are consistent with what is observed in reduced Prochlorococcus strains (marine cyanobacteria) when compared to close relatives.
doi:10.1186/1471-2105-14-s15-s11 pmid:24564457 pmcid:PMC3851946 fatcat:2ycxoeqlxbdixpkbkjrcazl7pa

An alife game to teach evolution of antibiotic resistance

Guillaume Beslon, Berenice Batut, David Parsons, Dominique Schneider, Carole Knibbe
2013 Advances in Artificial Life, ECAL 2013  
The emergence of antibiotic resistant bacteria is a major threat to public health and there is a constant need for education to limit dangerous practices. Here, we propose to use alife software to develop training media for the public and the physicians. On the basis of the Aevol model we have been developing for more than six years, we built a game in which players fight bacterial infections using antibiotics. In this game the bacteria can evolve resistance traits, making the infection more
more » ... more difficult to cure. The game has been tested with automatic treatment procedures, showing that it behaves correctly. It has been demonstrated during the French "Nuit des Chercheurs" in October 2012.
doi:10.7551/978-0-262-31709-2-ch007 dblp:conf/ecal/BeslonBPSK13 fatcat:viomlaxx5rdivkses7w6ndtgcq

FAIR Training in ELIXIR Europe

Mateusz Kuzak, Leyla García Castro, Bérénice Batut, Ricardo Arcila, Niall Beard, Melissa Burke, Denise Carvalho-Silva, Victoria Dominguez Del Angel, Kim Gurwitz, Pascal Kahlem, Paula Martinez, Sarah Morgan (+5 others)
2019 Zenodo  
Leyla Garcia 1,2 , Berenice Batut 3,4,5 , Mateusz Kuzak 6,7 , Ricardo Arcila 1 , Niall Beard 8,9 , Melissa Burke 1 , Denise Carvalho-Silva 1 , Victo Angel 10,11 , Kim Gurwitz 9,12 , Pascal Kahlem 2 , Paula  ... 
doi:10.5281/zenodo.3349846 fatcat:z67seyd445crteupitx6h275ry

Environmental Pollutant Benzo[a]Pyrene Impacts the Volatile Metabolome and Transcriptome of the Human Gut Microbiota

Clémence Defois, Jérémy Ratel, Sylvain Denis, Bérénice Batut, Réjane Beugnot, Eric Peyretaillade, Erwan Engel, Pierre Peyret
2017 Frontiers in Microbiology  
Benzo[a]pyrene (B[a]P) is a ubiquitous, persistent, and carcinogenic pollutant that belongs to the large family of polycyclic aromatic hydrocarbons. Population exposure primarily occurs via contaminated food products, which introduces the pollutant to the digestive tract. Although the metabolism of B[a]P by host cells is well known, its impacts on the human gut microbiota, which plays a key role in health and disease, remain unexplored. We performed an in vitro assay using 16S barcoding,
more » ... nscriptomics and volatile metabolomics to study the impact of B[a]P on two distinct human fecal microbiota. B[a]P exposure did not induce a significant change in the microbial structure; however, it altered the microbial volatolome in a dosedependent manner. The transcript levels related to several metabolic pathways, such as vitamin and cofactor metabolism, cell wall compound metabolism, DNA repair and replication systems, and aromatic compound metabolism, were upregulated, whereas the transcript levels related to the glycolysis-gluconeogenesis pathway and bacterial chemotaxis toward simple carbohydrates were downregulated. These primary findings show that food pollutants, such as B[a]P, alter human gut microbiota activity. The observed shift in the volatolome demonstrates that B[a]P induces a specific deviation in the microbial metabolism.
doi:10.3389/fmicb.2017.01562 pmid:28861070 pmcid:PMC5559432 fatcat:c263nd5zivgy5fort7htrkh5jy

Fostering accessible online education using Galaxy as an e-learning platform

Beatriz Serrano-Solano, Melanie C. Föll, Cristóbal Gallardo-Alba, Anika Erxleben, Helena Rasche, Saskia Hiltemann, Matthias Fahrner, Mark J. Dunning, Marcel H. Schulz, Beáta Scholtz, Dave Clements, Anton Nekrutenko (+3 others)
2021 PLoS Computational Biology  
The COVID-19 pandemic is shifting teaching to an online setting all over the world. The Galaxy framework facilitates the online learning process and makes it accessible by providing a library of high-quality community-curated training materials, enabling easy access to data and tools, and facilitates sharing achievements and progress between students and instructors. By combining Galaxy with robust communication channels, effective instruction can be designed inclusively, regardless of the students' environments.
doi:10.1371/journal.pcbi.1008923 pmid:33983944 fatcat:xe5lwcf66fbpbpqixfs5ok7a6e
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