13 papers · ranked by Valyu relevance
Fabrice Bauget, Adama Ndour, Yann Boursiac, Christophe Maurel + 3 more
Drought is a significant factor in agricultural losses, making it imperative to understand how root system architecture (RSA) adapts to environmental condition like water deficit. HydroRoot is a functional-structural plant model (FSPM) aimed at analyzing and simulating hydraulic and solute transport of RSA. The model…
Subarna Sasmal, Martin McCullagh, Glen M. Hocky
Here we present a detailed workflow for clustering and enhanced sampling of biomolecular conformations using the ShapeGMM methodology. This approach fits a probabilistic model of biomolecular conformations rooted in the idea that the free energy can expressed in terms of local fluctuations in atomic positions around…
Subarna Sasmal, Martin McCullagh, Glen M. Hocky
Here we present a detailed workflow for clustering and enhanced sampling of biomolecular conformations using the ShapeGMM methodology. This approach fits a probabilistic model of biomolecular conformations rooted in the idea that the free energy can expressed in terms of local fluctuations in atomic positions around…
Haley Schuhl, Keely E. Brown, Hudanyun Sheng, Parag K. Bhatt + 58 more
PlantCV is an open-source Python project aimed at developing tools to address a range of image-based, plant phenotyping questions. PlantCV has been used for more than 10 years to automate trait collection from image data and the newest release, PlantCV version 4, continues to lower the barrier to entry for users…
Matteo De Matola, Giorgio Arcara
Convolutional neural networks (CNNs) are a class of artificial neural networks (ANNs). Since the early 2010s, they have been widely adopted as models of primate vision and classifiers of neuroimaging data, becoming relevant for a wealth of neuroscientific fields. However, the majority of neuroscience researchers come…
Sebastien Ravel, Nina Marthe, Camille Carrette, Mourdas Mohamed + 2 more
Pangenome variation graphs (PVGs), which represent genomic diversity through multiple genomes alignment, are powerful tools for studying genomic variations in populations. However, current tools often lack integration, efficiency, or require format conversions, to use them, hindering their usability. Here, we introduce…
Endre Bakken Stovner, Max Ticó, Ester Muñoz del Campo, Joan Pallarès-Albanell + 3 more
Sequence interval algebra is key to modern bioinformatics. Pyranges v1 offers a Python Pandas-based interface to a comprehensive palette of Rust-powered operations (e.g., overlap, count, slice intervals), enabling the intuitive development of efficient pipelines for diverse sequence data, including gene annotations…
Pranav Minasandra, Vivek H. Sridhar, Dominique G. Roche, Isaac Planas-Sitjà
Real-time tracking and automated response systems are essential for standardising experiments, reducing observer bias, and improving reproducibility in studies of movement and behaviour. However, existing solutions face significant challenges: AI-based tracking systems require expensive hardware and impose…
Annie G. Bryant
Recent years have seen an expanding repertoire of code-based tools for visualizing neuroimaging data, promoting reproducibility and interpretability of brain-mapping findings. However, most open-source visualization packages for the human brain are geared toward the cerebral cortex, and the comparatively few options…
Robert M. Salati, Geng Li, Spencer Williams, Benjamin J. Fregly
Personalized computational neuromusculoskeletal models have great potential for optimizing the design of clinical treatments for movement impairments. While many software tools address specific parts of the model personalization and treatment optimization processes, they typically require significant programming…
Jose L Figueroa, Richard Allen White
We now exist in the era of massive datasets from genomics, large language models, and all the known knowledge of humanity right at our fingertips. Much of this data is becoming more accessible; however, processing such data remains an ongoing issue across systems including high performance computing (HPC)…
Wade R. Boohar, Kayla Y. Xu, Nicole Black, Mahija Mogalipuvvu + 3 more
Computational methodology has become ubiquitous in biomedical research with the rise of big data analysis and popularity of artificial intelligence and machine learning. However, undergraduate bioinformatics education has largely struggled to keep pace with the demand for bioinformatics skills, due to a combination of…
Jayadev Joshi, Fabio Cumbo, Daniel Blankenberg
R is widely used in statistical computing, data analysis, and bioinformatics. A key contributor to its success in bioinformatics and computational biology is the open-source project Bioconductor. As of its latest release (3.20), the Bioconductor community offers 2,289 software packages for biomedical research…