12 papers · ranked by Valyu relevance
Rafael Bravo, Mark Robertson-Tessi, Alexander R. A. Anderson
The Hybrid Automata Library (HAL) is a Java Library made of simple, efficient, generic components that can be used to model complex spatial systems. HAL’s components can broadly be classified into: on- and off-lattice agent containers, finite difference diffusion fields, a Gui building system, and additional tools and…
Federico Di Petta, Piermichele Rosati, Piero Hierro Canchari, Michela Quadrini + 1 more
Accurate annotation of RNA base-pairing interactions is essential for structural analysis, benchmarking, and data-driven RNA structure prediction. Several tools can extract RNA interactions from three-dimensional coordinates, but their outputs are heterogeneous and may disagree, particularly for non-canonical base…
Orges Koci, Richard K. Russell, M. Guftar Shaikh, Christine Edwards + 2 more
We have developed CViewer, a java-based framework to consolidate, visualize, and explore enormous amount of information recovered from shotgun sequencing experiments. This information includes and integrates all levels of gene products, mRNA, protein, metabolites, as well as their interactions in a single platform. The…
Olivia W Lang, Benjamin Beer, Dean Zhang, Courtney LeSon + 3 more
The growing diversity of genomic and epigenomic assays has driven a parallel expansion in data formats, analysis workflows, and figure-generation tools. However, tools for analyzing data and assembling publication-quality figures are often specialized to a specific assay, dramatically limiting their interoperability…
Caterina Fuster-Barceló, Carlos García López de Haro, Estibaliz Gómez-de-Mariscal, Wei Ouyang + 3 more
This manuscript showcases the latest advancements in deepImageJ, a pivotal Fiji/ImageJ plugin for bioimage analysis in the life sciences. The plugin, known for its user-friendly interface, facilitates the application of diverse pre-trained neural networks to custom data. The manuscript demonstrates a number of…
Göksel Mısırlı
The Synthetic Biology Open Language version 3 data standard provides a graph-based approach to exchange information about biological designs. The new data model has major updates and offers several features for software tools. Here, we present libSBOLj3 to facilitate data exchange and provide interoperability between…
Costanza Pascal, Herzeel Charlotte, Verachtert Wilfried
elPrep is an established multi-threaded framework for preparing SAM and BAM files in sequencing pipelines. To achieve good performance, its software architecture makes only a single pass through a SAM/BAM file for multiple preparation steps, and keeps sequencing data as much as possible in main memory. Similar to other…
Jamie Alnasir, Hugh P. Shanahan
The paper reviews the use of the Hadoop platform in Structural Bioinformatics applications. Specifically, we review a number of implementations using Hadoop of high-throughput analyses, e.g. ligand-protein docking and structural alignment, and their scalability in comparison with other batch schedulers and MPI. We find…
Shichen Qiao, Chen Shen
In this study, a web database application with the Flask framework was developed to implement three types of queries and visualize the results over a bioinformatical dataset from Alfalfa (Medicago sativa). A backend SQLite database was constructed from genome FASTA, population variations, transcriptome, and annotation…
Antonio Prestes García, Alfonso Rodríguez-Patón
In order to produce dependable results, the output of models must be carefully evaluated and compared to the experimental data. One of the main goals of analyzing a model is the understanding the effect of input factors on the model output. This task is carried out using a methodology known as sensitivity analysis. The…
Joséphine Abi-Ghanem, Djomangan Adama Ouattara
The need of digital tools for integrative analysis is today important in most scientific areas. It leads to several community-driven initiatives to standardize the sharing of data and computational workflows. However, there exists no open agnostic framework to model and implement computation workflows, in particular in…
Bjørn Fjukstad, Vanessa Dumeaux, Karina Standahl Olsen, Michael Hallet + 2 more
As the systems biology community generates and collects data at an unprecedented rate, there is a growing need for interactive data exploration tools to explore the datasets. These tools need to combine advanced statistical analyses, relevant knowledge from biological databases, and interactive visualizations in an…