Community consensus on core open science practices to monitor in biomedicine | PLOS Biology

Abstract:  The state of open science needs to be monitored to track changes over time and identify areas to create interventions to drive improvements. In order to monitor open science practices, they first need to be well defined and operationalized. To reach consensus on what open science practices to monitor at biomedical research institutions, we conducted a modified 3-round Delphi study. Participants were research administrators, researchers, specialists in dedicated open science roles, and librarians. In rounds 1 and 2, participants completed an online survey evaluating a set of potential open science practices, and for round 3, we hosted two half-day virtual meetings to discuss and vote on items that had not reached consensus. Ultimately, participants reached consensus on 19 open science practices. This core set of open science practices will form the foundation for institutional dashboards and may also be of value for the development of policy, education, and interventions.

 

An iterative and interdisciplinary categorisation process towards FAIRer digital resources for sensitive life-sciences data | Scientific Reports

Abstract:  For life science infrastructures, sensitive data generate an additional layer of complexity. Cross-domain categorisation and discovery of digital resources related to sensitive data presents major interoperability challenges. To support this FAIRification process, a toolbox demonstrator aiming at support for discovery of digital objects related to sensitive data (e.g., regulations, guidelines, best practice, tools) has been developed. The toolbox is based upon a categorisation system developed and harmonised across a cluster of 6 life science research infrastructures. Three different versions were built, tested by subsequent pilot studies, finally leading to a system with 7 main categories (sensitive data type, resource type, research field, data type, stage in data sharing life cycle, geographical scope, specific topics). 109 resources attached with the tags in pilot study 3 were used as the initial content for the toolbox demonstrator, a software tool allowing searching of digital objects linked to sensitive data with filtering based upon the categorisation system. Important next steps are a broad evaluation of the usability and user-friendliness of the toolbox, extension to more resources, broader adoption by different life-science communities, and a long-term vision for maintenance and sustainability.

 

Open and reusable annotated mass spectrometry dataset of a chemodiverse collection of 1,600 plant extracts | GigaScience | Oxford Academic

Abstract:  As privileged structures, natural products often display potent biological activities. However, the discovery of novel bioactive scaffolds is often hampered by the chemical complexity of the biological matrices they are found in. Large natural extract collections are thus extremely valuable for their chemical novelty potential but also complicated to exploit in the frame of drug-discovery projects. In the end, it is the pure chemical substances that are desired for structural determination purposes and bioactivity evaluation. Researchers interested in the exploration of large and chemodiverse extract collections should thus establish strategies aiming to efficiently tackle such chemical complexity and access these structures. Establishing carefully crafted digital layers documenting the spectral and chemical complexity as well as bioactivity results of natural extracts collections can help prioritize time-consuming but mandatory isolation efforts. In this note, we report the results of our initial exploration of a collection of 1,600 plant extracts in the frame of a drug-discovery effort. After describing the taxonomic coverage of this collection, we present the results of its liquid chromatography high-resolution mass spectrometric profiling and the exploitation of these profiles using computational solutions. The resulting annotated mass spectral dataset and associated chemical and taxonomic metadata are made available to the community, and data reuse cases are proposed. We are currently continuing our exploration of this plant extract collection for drug-discovery purposes (notably looking for novel antitrypanosomatids, anti-infective and prometabolic compounds) and ecometabolomics insights. We believe that such a dataset can be exploited and reused by researchers interested in computational natural products exploration.

 

Galaxy Training: A powerful framework for teaching! | PLOS Computational Biology

Abstract:  There is an ongoing explosion of scientific datasets being generated, brought on by recent technological advances in many areas of the natural sciences. As a result, the life sciences have become increasingly computational in nature, and bioinformatics has taken on a central role in research studies. However, basic computational skills, data analysis, and stewardship are still rarely taught in life science educational programs, resulting in a skills gap in many of the researchers tasked with analysing these big datasets. In order to address this skills gap and empower researchers to perform their own data analyses, the Galaxy Training Network (GTN) has previously developed the Galaxy Training Platform (https://training.galaxyproject.org), an open access, community-driven framework for the collection of FAIR (Findable, Accessible, Interoperable, Reusable) training materials for data analysis utilizing the user-friendly Galaxy framework as its primary data analysis platform. Since its inception, this training platform has thrived, with the number of tutorials and contributors growing rapidly, and the range of topics extending beyond life sciences to include topics such as climatology, cheminformatics, and machine learning. While initially aimed at supporting researchers directly, the GTN framework has proven to be an invaluable resource for educators as well. We have focused our efforts in recent years on adding increased support for this growing community of instructors. New features have been added to facilitate the use of the materials in a classroom setting, simplifying the contribution flow for new materials, and have added a set of train-the-trainer lessons. Here, we present the latest developments in the GTN project, aimed at facilitating the use of the Galaxy Training materials by educators, and its usage in different learning environments.

 

 

Introducing Jot — a new open-source tool that help researchers with journal selection < Yale School of Public Health

“Say hello to Jot: a free, open-source web application that matches manuscripts in the fields of biomedicine and life sciences with suitable journals, based on a manuscript’s title, abstract, and (optionally) citations.

Developed by the Townsend Lab at the Yale School of Public Health, Jot gathers a wealth of data on journal quality, impact, fit, and open access options that can be explored through a dashboard of linked, interactive visualizations….”

New website compiles ocean data from landmark 19th-century scientific voyage | Illinois

“The HMS Challenger began a four-year voyage 150 years ago to explore the deep sea and the creatures that lived in it. The scientists aboard the ship discovered thousands of new species and recorded massive amounts of data about the oceans. The treasure trove of information they gathered is now available online in the first comprehensive database of the Challenger findings.

A new website devoted to the expedition and the database was launched Dec. 21 – the 150th anniversary of the beginning of the Challenger’s voyage. It is part of the Oceans 1876 project by Gillen D’Arcy Wood, a University of Illinois Urbana-Champaign English professor and a historian of 19th-century environmental history and science. Wood also is the associate director of the Institute for Sustainability, Energy, and the Environment, and the director of its environmental writing program….”

Preprints als Informationsquelle besser nutzbar machen – TH Köln

From Google’s English:  “In the project PIXLS – Preprint Information eXtraction for Life Sciences, TH Köln and ZB MED will develop an application over the next three years that automatically opens up the preprint server. This enables the research community to make better use of current information that was published on preprint servers – and therefore hardly appears in classic detection and search systems.

The German Research Foundation (DFG) is funding the project as part of the e-Research Technologies framework programme.”

FAIR service investigation survey

“The FAIR principles and “making data FAIR” have become common buzzwords in the biomedical field in recent years. Many organizations are striving to create fully FAIR data or to FAIRify existing data. In that process they often find themselves hindered by a range of challenges. To address those challenges, the FAIRplus consortium and other organizations have developed FAIR products and services in recent years. Now the question is: what is the need for new FAIR services or for improvement of the existing ones, in order to better serve life science organizations in their quest to accelerate biomedical research? To answer this, The Hyve run a survey to collect experience with the FAIR principles, main challenges and the products or services that help (or might have helped) to overcome those challenges….”

Publish and Read | Microbiology Society

“From 2023 all subscribers to the Society journals are invited to upgrade to a Publish and Read deal and quotes to do so will be sent with renewal notices. Institutions that buy a Publish and Read package are offered:

Unlimited OA: any article published in Society journals where the corresponding author is from a Publish and Read institution will be OA by default.
Unlimited usage: any user associated with a Publish and Read institution can access the entire archive of Society content, back to 1947, for reading and for text and data mining.

Following two successful pilot years, The Microbiology Society is extending its Publish and Read institutional licence so that more organisations and researchers can participate and benefit from Open Access (OA) publishing. 

Publish and Read is designed to offer a frictionless OA experience for authors, and provides maximum value for institutions, with minimum administration. It offers institutions an alternative to both subscriptions and article processing charges (APCs), although both of these routes will still be available….”

Microbiology’s transformation to fully Open Access | Microbiology Society

“Having published advances across the field of microbiology for 75 years, Microbiology – the Microbiology Society’s founding journal – has transitioned to fully Open Access (OA) for 2023. Find out more about the benefits of Open Access from the Editors of Microbiology in the video below….”

Introducing Jot — a new open-source tool that help researchers with journal selection < Yale School of Medicine

“Say hello to Jot: a free, open-source web application that matches manuscripts in the fields of biomedicine and life sciences with suitable journals, based on a manuscript’s title, abstract, and (optionally) citations….”

New project: Open science cloud infrastructure and training for communities in Latin America and Africa

“We are excited to share that the grant proposal that the IOI team contributed to, titled “A Collaborative Interactive Computing Service Model for Global Communities”, has been awarded funding by the Chan Zuckerberg Initiative….

The goal of this proposal is to create a collaborative cloud infrastructure service that enables community-based cloud-native workflows in the biosciences. Together with our collaborators, we will promote values of open and inclusive community practices, infrastructure that enables these practices, and a “train-the-trainers” approach that empowers community leaders to share expertise in cloud infrastructure with others in their communities. Our focus will be on communities in Latin America and Africa, and we hope to learn how this model could be extended to other global communities that are historically marginalized from large-scale scientific infrastructure projects….”

Kenyon | The Journal Article as a Means to Share Data: a Content Analysis of Supplementary Materials from Two Disciplines | Journal of Librarianship and Scholarly Communication

Abstract:  INTRODUCTION The practice of publishing supplementary materials with journal articles is becoming increasingly prevalent across the sciences. We sought to understand better the content of these materials by investigating the differences between the supplementary materials published by authors in the geosciences and plant sciences. METHODS We conducted a random stratified sampling of four articles from each of 30 journals published in 2013. In total, we examined 297 supplementary data files for a range of different factors. RESULTS We identified many similarities between the practices of authors in the two fields, including the formats used (Word documents, Excel spreadsheets, PDFs) and the small size of the files. There were differences identified in the content of the supplementary materials: the geology materials contained more maps and machine-readable data; the plant science materials included much more tabular data and multimedia content. DISCUSSION Our results suggest that the data shared through supplementary files in these fields may not lend itself to reuse. Code and related scripts are not often shared, nor is much ‘raw’ data. Instead, the files often contain summary data, modified for human reading and use. CONCLUSION Given these and other differences, our results suggest implications for publishers, librarians, and authors, and may require shifts in behavior if effective data sharing is to be realized.

 

The Design and Delivery of an Astrobiology Massive Open Online Class | Astrobiology

Abstract:  MOOCs, or massive open online classes have reached hundreds of millions of people around the world in the past decade with a model of free open access learning. They are an excellent vehicle for delivering science to lifelong learners. Building on experience in designing astronomy MOOCs for Udemy and Coursera, we have created an astrobiology MOOC for Coursera called “Astrobiology: Exploring Other Worlds” that launched in April 2019. As of early 2022, about 9000 people have started the course, and nearly 10% of those have completed it. The average user rating is 4.9 out of 5. The core content is 10?h of video lectures, divided into six modules, which cover the possibilities of life in the Solar System, the search for exoplanets, the concept of habitability, the definition of life and basics of biology, evolution of life on Earth, and the search for extraterrestrial intelligence. Pedagogy was designed around clear learning objectives and includes quizzes, writing assignments, and a final project that draws on all the concepts presented in the course where students design their own mission to characterize exoplanets. In this study, we describe the design, implementation, and subsequent success of our 2019 astrobiology MOOC.