Expasy, the Swiss Bioinformatics Resource Portal, as designed by its users

S Duvaud, C Gabella, F Lisacek… - Nucleic acids …, 2021 - academic.oup.com
Abstract The SIB Swiss Institute of Bioinformatics (https://www. sib. swiss) creates, maintains
and disseminates a portfolio of reliable and state-of-the-art bioinformatics services and …

Towards FAIR principles for research software

AL Lamprecht, L Garcia, M Kuzak, C Martinez… - Data …, 2020 - content.iospress.com
The FAIR Guiding Principles, published in 2016, aim to improve the findability, accessibility,
interoperability and reusability of digital research objects for both humans and machines …

Resources and tools for rare disease variant interpretation

L Licata, A Via, P Turina, G Babbi… - Frontiers in Molecular …, 2023 - frontiersin.org
Collectively, rare genetic disorders affect a substantial portion of the world's population. In
most cases, those affected face difficulties in receiving a clinical diagnosis and genetic …

Evaluating LC-HRMS metabolomics data processing software using FAIR principles for research software

X Du, F Dastmalchi, H Ye, TJ Garrett, MA Diller, M Liu… - Metabolomics, 2023 - Springer
Background Liquid chromatography-high resolution mass spectrometry (LC-HRMS) is a
popular approach for metabolomics data acquisition and requires many data processing …

Ten quick tips for building FAIR workflows

C de Visser, LF Johansson, P Kulkarni… - PLoS Computational …, 2023 - journals.plos.org
Research data is accumulating rapidly and with it the challenge of fully reproducible
science. As a consequence, implementation of high-quality management of scientific data …

WorkflowHub: a registry for computational workflows

OJR Gustafsson, SR Wilkinson, F Bacall… - arXiv preprint arXiv …, 2024 - arxiv.org
The rising popularity of computational workflows is driven by the need for repetitive and
scalable data processing, sharing of processing know-how, and transparent methods. As …

WOMBAT-P: benchmarking label-free proteomics data analysis workflows

D Bouyssié, P Altıner, S Capella-Gutierrez… - Journal of proteome …, 2023 - ACS Publications
The inherent diversity of approaches in proteomics research has led to a wide range of
software solutions for data analysis. These software solutions encompass multiple tools …

ChannelsDB 2.0: a comprehensive database of protein tunnels and pores in AlphaFold era

A Špačková, O Vávra, T Raček, V Bazgier… - Nucleic Acids …, 2024 - academic.oup.com
ChannelsDB 2.0 is an updated database providing structural information about the position,
geometry and physicochemical properties of protein channels—tunnels and pores—within …

Implementing FAIR data management within the German Network for Bioinformatics Infrastructure (de. NBI) exemplified by selected use cases

G Mayer, W Müller, K Schork, J Uszkoreit… - Briefings in …, 2021 - academic.oup.com
This article describes some use case studies and self-assessments of FAIR status of de. NBI
services to illustrate the challenges and requirements for the definition of the needs of …

Developing and reusing bioinformatics data analysis pipelines using scientific workflow systems

M Djaffardjy, G Marchment, C Sebe, R Blanchet… - Computational and …, 2023 - Elsevier
Data analysis pipelines are now established as an effective means for specifying and
executing bioinformatics data analysis and experiments. While scripting languages …