Tipo de documento

Arguably, Python is one of the most widely used programming languages in data analytics, data mining, artificial intelligence, machine learning and deep learning (Nguyen et al., 2019). DEEPaaS API is a Python package that provides a REST API (Fielding, 2000) that can be used to easily expose the underlying model functionality over HTTP. Developers can plug their applications into DEEPaaS API with minimal requirements and modifications, allowing for easier interaction with the underlying..., This software has been developed within the DEEP-Hybrid-DataCloud (Designing and Enabling E-infrastructures for intensive Processing in a Hybrid DataCloud) project that has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 777435., Peer reviewed

32 páginas, 7figuras, 9 tablas. This project contains European Nucleotide Archive accession numbers for Illumina sequence data and associated metatdata, Two billion people are infected with Mycobacterium tuberculosis, leading to 10 million new cases of active tuberculosis and 1.5 million deaths annually. Universal access to drug susceptibility testing (DST) has become a World Health Organization priority. We previously developed a software tool, Mykrobe predictor, which provided offline species identification and drug resistance predictions for M. tuberculosis from whole genome sequencing (WGS) data. Performance was insufficient to support the..., ZI was funded by a Wellcome Trust/Royal Society Sir Henry Dale Fellowship, grant number 102541. MH was supported by Wellcome Trust/Newton Fund-MRC Collaborative Award [200205]; and Bill & Melinda Gates Foundation Trust [OPP1133541]. TMW is a Wellcome Trust Clinical Career Development Fellow, grant number 214560. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript., Peer reviewed

The ENMTools software package was introduced in 2008 as a platform for making measurements on environmental niche models (ENMs, frequently referred to as species distribution models or SDMs), and for using those measurements in the context of newly developed Monte Carlo tests to evaluate hypotheses regarding niche evolution. Additional functionality was later added for model selection and simulation from ENMs, and the software package has been quite widely used. ENMTools was initially..., DLW was funded by ARC DECRA award # DE140101675 and supported by subsidy funding to OIST. NJM was funded by Marsden grants 16‐UOA‐277 and 18‐UOA‐034, and U. Auckland FRDF #3722433. JCP is funded by a doctoral fellowship supported by the Agencia Canaria de la Investigación, Innovación y Sociedad de la Información and the European Social Fund (Operational Programme of the Canary Islands 2014‐2020). MC acknowledges support from Australian Research Council Discovery Project DP110103168., Peer reviewed

This is a PLOS Computational Biology Software paper., [Abstract] MIGNON is a workflow for the analysis of RNA-Seq experiments, which not only efficiently manages the estimation of gene expression levels from raw sequencing reads, but also calls genomic variants present in the transcripts analyzed. Moreover, this is the first workflow that provides a framework for the integration of transcriptomic and genomic data based on a mechanistic model of signaling pathway activities that allows a detailed biological interpretation of the results, including..., [Author summary] Currently, RNA massive sequencing RNA-seq is the most extensively used technique for gene expression profiling in a single assay. The output of RNA-seq experiments contains millions of sequences, generated from cDNA libraries produced by the retro-transcription of RNA samples, that need to be processed by computational methods to be transformed into meaningful biological information. Thus, a number of bioinformatic workflows and pipelines have been proposed to produce different..., JD has received these grants: SAF2017-88908-R from the Ministerio de Economía y Competitividad and PT17/0009/0006 from the Instituto de Salud Carlos III, as well as an FP7 People Marie-Curie Actions 813533 and and Horizon 2020 Framework Programme 676559., Peer reviewed

[EN] This article presents Q-Facies, an open-source Python package for quantitative analysis of hydrochemical facies (HF). HF is widely used to interpret the chemical characteristics of groundwater. However, it is difficult to analyse its spatial or temporal variability due to its qualitative nature and the small number of classes. To avoid these limitations, Q-Facies performs the parametrization of HF based on the calculation of five statistical indices on the Piper diagram: Blau, Standard..., This work has been carried out within the framework and the grant of the SIGLO-PRO project, Spain (Ref. PID2021-128021OB-I00), State R + D + I Program (Challenges of Society 2021) funded by the State Research Agency, Spain (AEI) and the European Regional Development Fund (ERDF) ., Peer reviewed

Climate change affects biodiversity in a variety of ways, necessitating the exploration of multiple climate dimensions using appropriate metrics. Despite the existence of several climate change metrics tools for comparing alternative climate change metrics on the same footing are lacking. To address this gap, we developed ‘climetrics' which is an extensible and reproducible R package to spatially quantify and explore multiple dimensions of climate change through a unified procedure. Six..., Peer reviewed

The Temperature Dependent Effective Potential (TDEP) method is a versatile and efficient approach to include temperature in ab initio materials simulations based on phonon theory. TDEP can be used to describe thermodynamic properties in classical and quantum ensembles, and several response properties ranging from thermal transport to Neutron and Raman spectroscopy. A stable and fast reference implementation is given in the software package of the same name described here. The underlying..., F.K. and O.H. acknowledge support from the Swedish Research Council (VR) program 2020- 04630, and the Swedish e-Science Research Centre (SeRC). Work at Boston College was supported by the U.S. Department of Energy (DOE), Office of Science, Basic Energy Sciences (BES) under Award #DE-SC0021071. M.J.V., A.C., and J.P.B. acknowledge funding by ARC project DREAMS (G.A. 21/25-11) funded by Federation Wallonie Bruxelles and ULiege, and by Excellence of Science project CONNECT number 40007563 funded..., Peer reviewed

[Refers to:] BioIntertidal Mapper software: A satellite approach for NDVI-based intertidal habitat mapping, https://doi.org/10.1016/j.softx.2023.101520, BioIntertidal Mapper 2.0 is a user-friendly tool with a graphical user interface that automates Sentinel-2 processing (since 2017) for intertidal habitat mapping in Google Earth Engine (GEE) using the Normalized Difference Vegetation Index (NDVI). Unlike version 1.0, low-tide scenes are no longer selected using the WorldTides API; instead, images are screened by estimating the proportion of water pixels using the Normalized Difference Water Index. Reflectance inputs were updated to the Sentinel..., This work was co-funded by the European Union’s CLIMAREST project (Grant Agreement No. 101093865). S.H. was supported by a regional postdoctoral fellowship (DGP_POST_2024_00524) funded by the Junta de Andalucía / CUII and the European Social Fund Plus (ESF+), and by the VIII Mares Circulares Awards (Chelonia Association). The authors acknowledge the assistance of Jonathan Jiménez Reina in developing the code., Peer reviewed

The presented program aims at speeding up the brute force computation of the so-called $L_d$ norm of a matrix $M$ using graphics processing units (GPUs). Alternatives for CPUs have also been implemented, and the algorithm is applicable to any parallel environment. The $n\times m$ matrix $M$ has real elements which may represent coefficients of a bipartite Bell expression or those of a linear prepare-and-measure (PM) witness. In this interpretation, the $L_1$ norm is the local bound of the given..., We thank Tamás Vértesi, Kai-Siang Chen and Hsin-Yu Hsu for valuable input and fruitful discussions. The authors thank Csaba Hruska for providing technical assistance in the GPU computations. This paper was supported by the EU (CHIST-ERA MoDIC) and the National Research, Development and Innovation Office NKFIH (No. 2023-1.2.1-ERA_NET-2023-00009 and No. K145927). I.M. was supported by the János Bolyai Research Scholarship of the Hungarian Academy of Sciences. G.D. acknowledges support from the EU..., Peer reviewed

[Data availability statement] GLOSSA is developed openly on GitHub (https://github.com/iMARES-group/glossa), with releases archived on Zenodo (https://doi.org/10.5281/zenodo.17161715; Mestre-Tomás et al., 2025a). The R package glossa is also available via the Comprehensive R Archive Network (CRAN; https://cran.r-project.org/package=glossa). Documentation is available at https://imares-group.github.io/glossa/. Data and code used in the examples are available on Zenodo (https://doi.org/10.5281/..., Special Feature: Conservation, Ecology and Artificial Intelligence — Advances and Symbiotic Solutions, 1. Species distribution models (SDMs) are one of the most common statistical methods to assess species occupancy and geographic distribution patterns. With the increasing complexity and availability of ecological data in the marine context, many methodological approaches have been developed to support SDM analysis. However, their application often requires expertise in data analysis, statistical modelling and programming, which limits their accessibility for broader use., 2. Here we introduce GLOSSA, an open-source R package and Shiny application designed to make marine species distribution modelling more accessible. GLOSSA provides a user-friendly interface for fitting Bayesian Additive Regression Trees (BART) SDMs using species occurrence and environmental data., 3. GLOSSA guides users through key SDM steps, including data uploading, filtering occurrence data, harmonizing environmental layers, generating pseudo-absences, tuning BART complexity, performing spatial and temporal block cross-validation, visualizing predictions and uncertainty and exporting configuration files to ensure reproducibility., 4. We demonstrate the functionality of GLOSSA through three marine case studies, addressing a range of ecological scenarios at regional and global scales. Along with detailed documentation, examples and tutorials, GLOSSA provides an example of how an intuitive graphical interface can make species distribution modelling accessible to a broad audience., We would like to thank the iMARES group for their helpful feedback on the app design. This study is part of the ProOceans project (PID2020-118097RB-I00) funded by the Spanish Ministry of Science and Innovation. We also acknowledge support from the SOSPen (PID2021-124831OA-I00) project funded by the Spanish Ministry of Science and Innovation and the GES4SEAS project (grant agreement no. 101059877) funded by the European Union under the Horizon Europe program. The authors also acknowledge the..., With funding form the Spanish government through the "Severa Ochoa Centre of Excellence" accreditation (CEX2024-001494-S)., Peer reviewed