Category Archives: oa.biology

Bioleft: open-source seeds for low-input farming systems – ScienceOpen

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Abstract:  This article describes Bioleft, an ‘open source’, highly collaborative seed breeding initiative, in order to encourage reflection on potential synergies with fair trade ideas and practices. Bioleft aims to develop and redistribute collective agency over seed breeding, as a response to the emergence of an oligopolistic seed industry. It is experimenting with novel approaches to seed innovation that increase the diversity of crop varieties, in order to support agricultural practices that are ignored by mainstream seed firms, particularly small- scale family farming and more ecologically and socially sustainable agricultural practices. More generally it is experimenting with new forms of social and productive organization based on norms of sharing and solidarity.

Open Science Policies as Regarded by the Communities of Researchers from the Basic Sciences in the Scientific Periphery

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Abstract:  This paper explores the different open science policy effects on the knowledge generation process of researchers in basic sciences: biology, chemistry, and physics.

This paper uses a qualitative methodology with a content analysis approach. It uses seventeen semi-directed interviews.

The main perceived effect of open science is access to research inputs, with open access, open research data and code reuse as primary sources. Another issue is the increase of collaboration with other colleagues in terms of the ability to collaborate faster and the encouraging the exchange of ideas. However, this benefit does not translate to the division of labor in large transnational teams. Time spent on tasks like cleaning up data and code, scooping and other ethical issues are unfavorable aspects noted.

Policymakers could use it to enhance current open science policies in the countries.

It analyzes perspectives of basic sciences researchers from two countries about open science policies. The main conclusion is the fact that open science policies should focus on the research process itself -rather than research outputs- in order to effectively tackle inequalities in science.

AI writes summaries of preprints in bioRxiv trial

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“The bioRxiv pilot is part of a broader trend of using LLMs to help researchers — and the public — keep afloat in the tsunami of scientific literature. The physics-focused preprint server arXiv uses AI to generate audio summaries of some papers, and publishers and funders are starting to roll out features that allow users to ‘talk to a paper’ through a chatbot….

Before rolling out the service, Sever and his colleagues evaluated several dozen summaries produced by the tool. Most were pretty good, he says, and some were even better than the abstracts scientists had written. Others included clear falsehoods. “We know there are going to be errors in these things,” Sever says….

If the pilot becomes a fully fledged service, bioRxiv might look at routinely involving authors in proofreading and approving the content, Sever says. For now, to minimize the consequences of errors, the pilot is not being rolled out to medRxiv, a sister medical-research preprint server run by Cold Spring Harbor Laboratory Press, the London-based publisher BMJ and Yale University in New Haven, Connecticut. MedRxiv studies typically have clinical relevance, and errors could guide patient behaviour. By limiting the pilot to bioRxiv, says Sever, “the consequences of being wrong are more that somebody might feel misled or misunderstand a fairly arcane study in cell biology”. …”

OPIA: an open archive of plant images and related phenotypic traits | Nucleic Acids Research | Oxford Academic

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Abstract:  High-throughput plant phenotype acquisition technologies have been extensively utilized in plant phenomics studies, leading to vast quantities of images and image-based phenotypic traits (i-traits) that are critically essential for accelerating germplasm screening, plant diseases identification and biotic & abiotic stress classification. Here, we present the Open Plant Image Archive (OPIA, https://ngdc.cncb.ac.cn/opia/), an open archive of plant images and i-traits derived from high-throughput phenotyping platforms. Currently, OPIA houses 56 datasets across 11 plants, comprising a total of 566 225 images with 2 417 186 labeled instances. Notably, it incorporates 56 i-traits of 93 rice and 105 wheat cultivars based on 18 644 individual RGB images, and these i-traits are further annotated based on the Plant Phenotype and Trait Ontology (PPTO) and cross-linked with GWAS Atlas. Additionally, each dataset in OPIA is assigned an evaluation score that takes account of image data volume, image resolution, and the number of labeled instances. More importantly, OPIA is equipped with useful tools for online image pre-processing and intelligent prediction. Collectively, OPIA provides open access to valuable datasets, pre-trained models, and phenotypic traits across diverse plants and thus bears great potential to play a crucial role in facilitating artificial intelligence-assisted breeding research.

 

 

The Biochemical Society and the Big Ten Academic Alliance sign Read & Publish agreement in support of open access

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“The Biochemical Society and the Big Ten Academic Alliance (BTAA) are delighted to announce a Read & Publish agreement that supports the open sharing of research and knowledge from across the molecular biosciences.

The agreement guarantees uncapped, fee-free open access (OA) publishing for corresponding authors at participating institutions, alongside full read access to all Biochemical Society journals (published by the Society’s publishing arm, Portland Press).  

With this agreement, thirteen BTAA institutions across the United States join more than 200 others around the world already taking advantage of Read & Publish benefits. The agreement covers over 50 campuses, supporting hassle-free OA for US-based authors publishing across all areas of molecular bioscience….”

Broadening audience, increasing understanding

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“Many biomedical research papers are readily understood only by those who know as much about the topic as their authors do. There are understandable reasons for this. Science is increasingly specialized, which means that aficionados of specific fields develop terminologies, nomenclatures, and even technologies that can make the work feel impenetrable. So even working scientists reading outside their own area of expertise can struggle to understand what was actually done and why it is important.

As a preprint server that costs nothing to read, bioRxiv has a massive, worldwide audience that views and downloads millions of articles each month. We don’t track readers or ask them to register but we have anecdotal evidence for who they are. Enormous numbers of professional scientists, clearly, but many other kinds of readers too, including undergraduate and medical students, teachers at every level, journalists, patients and their advocates, and members of the public who are intellectually curious about our world and biology. These more general readers must also grapple with articles not written with them in mind….”

Biochemical Society launches innovative Subscribe to Open model for its journals

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“The Biochemical Society (and its trading arm, Portland Press Ltd) is delighted to announce the launch of Subscribe to Open (S2O) for five of its world-leading research and review journals. This move marks another significant step in the Society’s commitment to making research accessible while maintaining the highest standards of quality….”

Portland Press supplies full-text articles to Publications Router – Research

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“Full-text articles from Portland Press are now being deposited automatically into UK institutional repositories via a live feed into Jisc’s Publications Router service.”

Analytical code sharing practices in biomedical research | Sciety

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Abstract:  Data-driven computational analysis is becoming increasingly important in biomedical research, as the amount of data being generated continues to grow. However, the lack of practices of sharing research outputs, such as data, source code and methods, affects transparency and reproducibility of studies, which are critical to the advancement of science. Many published studies are not reproducible due to insufficient documentation, code, and data being shared. We conducted a comprehensive analysis of 453 manuscripts published between 2016-2021 and found that 50.1% of them fail to share the analytical code. Even among those that did disclose their code, a vast majority failed to offer additional research outputs, such as data. Furthermore, only one in ten papers organized their code in a structured and reproducible manner. We discovered a significant association between the presence of code availability statements and increased code availability (p=2.71×10 ?9 ). Additionally, a greater proportion of studies conducting secondary analyses were inclined to share their code compared to those conducting primary analyses (p=1.15*10 ?07 ). In light of our findings, we propose raising awareness of code sharing practices and taking immediate steps to enhance code availability to improve reproducibility in biomedical research. By increasing transparency and reproducibility, we can promote scientific rigor, encourage collaboration, and accelerate scientific discoveries. We must prioritize open science practices, including sharing code, data, and other research products, to ensure that biomedical research can be replicated and built upon by others in the scientific community.

 

A conceptual framework for nomenclatural stability and validity of medically important fungi: a proposed global consensus guideline for fungal name changes supported by ABP, ASM, CLSI, ECMM, ESCMID-EFISG, EUCAST-AFST, FDLC, IDSA, ISHAM, MMSA, and MSGERC | Journal of Clinical Microbiology

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Abstract:  The rapid pace of name changes of medically important fungi is creating challenges for clinical laboratories and clinicians involved in patient care. We describe two sources of name change which have different drivers, at the species versus the genus level. Some suggestions are made here to reduce the number of name changes. We urge taxonomists to provide diagnostic markers of taxonomic novelties. Given the instability of phylogenetic trees due to variable taxon sampling, we advocate to maintain genera at the largest possible size. Reporting of identified species in complexes or series should where possible comprise both the name of the overarching species and that of the molecular sibling, often cryptic species. Because the use of different names for the same species will be unavoidable for many years to come, an open access online database of the names of all medically important fungi, with proper nomenclatural designation and synonymy, is essential. We further recommend that while taxonomic discovery continues, the adaptation of new name changes by clinical laboratories and clinicians be reviewed routinely by a standing committee for validation and stability over time, with reference to an open access database, wherein reasons for changes are listed in a transparent way.

 

Transforming health and well?being through publishing computable biomedical knowledge (CBK) – Koru – 2023 – Learning Health Systems – Wiley Online Library

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Abstract:  Computable biomedical knowledge artifacts (CBKs) are software programs that transform input data into practical output. CBKs are expected to play a critical role in the future of learning health systems. While there has been rapid growth in the development of CBKs, broad adoption is hampered by limited verification, documentation, and dissemination channels. To address these issues, the Learning Health Systems journal created a track dedicated to publishing CBKs through a peer-review process. Peer review of CBKs should improve reproducibility, reuse, trust, and recognition in biomedical fields, contributing to learning health systems. This special issue introduces the CBK track with four manuscripts reporting a functioning CBK, and another four manuscripts tackling methodological, policy, deployment, and platform issues related to fostering a healthy ecosystem for CBKs. It is our hope that the potential of CBKs exemplified and highlighted by these quality publications will encourage scientists within learning health systems and related biomedical fields to engage with this new form of scientific discourse.

 

OBF » Call for the third round of OBF Event Fellowship 2023 & overview of the second 2023 round. » Call for the third round of OBF Event Fellowship 2023 & overview of the second 2023 round.

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“The call for applications for the OBF Event Fellowship 2023, round 3, is now open. The deadline for this round is 1 December 2023….

The OBF Event Fellowship program aims to increase diverse participation at events that promote open-source bioinformatics and/or open science. We invite applications from candidates seeking financial support to attend relevant scientific events from January 2024 to August 2024. These events include conferences, workshops, code fests, hackathons, training courses, collaborative sprints, informal meet-ups or other skill-building and networking events. For more details, please read our OBF Event Fellowship policy document….”

PLOS Biology at 20: Exploring possible futures | PLOS Biology

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“Twenty years ago this month, PLOS Biology was launched, helping to catalyze a movement that has transformed publishing in the life sciences. In this issue, we explore how the community can continue innovating for positive change in the next decades….”