The Asparaginase Database: a comprehensive resource and classification of l-asparaginases

Abstract. l-Asparaginases have been essential anticancer biopharmaceuticals for nearly half a century, particularly in the treatment of acute lymphoblastic

academic.oup.com

Effective visualization of biomedical data using plot-misc

AbstractMotivation. Computational visualizations are prevalent in all disciplines of biomedical science, from wet-lab research, through clinical science to

academic.oup.com

MonBUG

monbug.ca

September - Jérome Waldispühl - MonBUG

monbug.ca

RUM/FILH: a standardized operational capability model for biodiversity databases

Abstract. The increasing reliance of biodiversity research on large-scale databases has brought significant progress in data accessibility but also new cha

academic.oup.com

STING-ExositeDB: An AI-assisted curated database of protein exosites for drug discovery

Abstract. Motivation: Protein exosites are secondary binding sites that recruit macromolecular partners and control molecular recognition across protein fa

academic.oup.com

bMINTY: enabling reproducible management of high-throughput sequencing analysis results and their metadata

Abstract. Due to the large scale of high-throughput sequencing data generation, the community has established standards that promote Findable, Accessible,

doi.org

Twelve quick tips for AI-assisted coding in science

While AI coding tools have demonstrated potential to accelerate software development, their use in scientific computing raises critical questions about code quality and scientific validity. In this pa...

journals.plos.org

TogoMCP: natural language querying of life-science knowledge graphs via schema-guided LLMs and the Model Context Protocol

Abstract. Querying the RDF Portal knowledge graph maintained by DBCLS—which aggregates ~60 life-science databases—requires proficiency in both SPARQL and d

academic.oup.com

OzButterflies – a high quality open database of multispectral images and spectra of tropical to temperate Australian butterflies

Abstract. Butterflies have been a model system for studying the evolution of colour. This is partly due to their complex patterns that reflect human-visibl

academic.oup.com

FRED enables standardized FAIR metadata generation and management for omics research - Scientific Reports

Scientific Reports - FRED enables standardized FAIR metadata generation and management for omics research

nature.com

Open access, unequal access: why publication fee waivers still exclude many researchers

The publish-or-perish paradigm puts pressure on academics worldwide to produce internationally visible research, with journal reputation, citation rates and open-access publications, which all togethe...

gh.bmj.com

Application of large language models to the annotation of cell lines and mouse strains in genomics data

Abstract. Accurate, consistent and comprehensive metadata are essential for the reuse of functional genomics data deposited in repositories such as the Gen

academic.oup.com

Eight quick tips for data-model integration in ecology

journals.plos.org

Eight quick tips for data-model integration in ecology

journals.plos.org

Advancing FAIR data towards comparable, organized, predictive AI-ready data for community validation - Communications Biology

This Perspective explores how updating static, FAIR data/databases can lead to COPE: Comparable, Organized (AI-ready) data that supports novel Predictions of biological systems ready for human-in-the-...

nature.com

How to SNIFF out Good Scientific Software

New PLOS Computational Biology paper: "Ten Quick Tips to SNIFF Out Sustainable and Secure Scientific Software"

blog.stephenturner.us

Ten quick tips to SNIFF out sustainable and secure scientific software

Modern computational biology depends heavily on open-source software tools, analysis pipelines, and containerized workflows developed and shared by the research community. While there is extensive gui...

journals.plos.org

Ten quick tips to SNIFF out sustainable and secure scientific software

Modern computational biology depends heavily on open-source software tools, analysis pipelines, and containerized workflows developed and shared by the research community. While there is extensive gui...

journals.plos.org

Goals and strategies for the indexing of publication types and study designs

Abstract. Major research and implementation efforts have been devoted to indexing articles according to the major topics discussed, but much less effort to

academic.oup.com

NORG - Nitrogen ORGanizer: a novel web-based system for cryopreservation and freezer management

Abstract. The preservation of samples, whether they are from humans, cell lines, animals, plants, or other resources, usually follows a similar process. Th

doi.org

IBDkb: an AI-enhanced integrative knowledge base for inflammatory bowel disease research and drug discovery

Abstract. IBDkb (Inflammatory Bowel Disease Knowledge Base; https://www.biosino.org/ibdkb) is a freely accessible, integrated web-based platform that syste

academic.oup.com