11 papers · ranked by Valyu relevance
Mark P Waller, Thomas Dresselhaus, Jack Yang
Here, we present just a collection of beans (JACOB): an integrated batch-based framework designed for the rapid development of computational chemistry applications. The framework expedites developer productivity by handling the generic infrastructure tier, and can be easily extended by user-specific scientific code.…
Andreas Holzinger, Mario Zupan
Background Professionals in the biomedical domain are confronted with an increasing mass of data. Developing methods to assist professional end users in the field of Knowledge Discovery to identify, extract, visualize and understand useful information from these huge amounts of data is a huge challenge. However, there…
Elishai Ezra Tsur
Databases are imperative for research in bioinformatics and computational biology. Current challenges in database design include data heterogeneity and context-dependent interconnections between data entities. These challenges drove the development of unified data interfaces and specialized databases. The curation of…
Diego Alonso, Francisco Sánchez-Ledesma, Pedro Sánchez, Juan A. Pastor + 1 more
'Juan A. Pastor' 'Bárbara Álvarez'] The use of frameworks and components has been shown to be effective in improving software productivity and quality. However, the results in terms of reuse and standardization show a dearth of portability either of designs or of component-based implementations. This paper, which is…
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…
Andrei Olaru, Monica Pricope, Roberto Teti
Current multi-agent frameworks usually use centralized, fixed communication infrastructures for the entities that are deployed using them. This decreases the robustness of the system but is less challenging when having to deal with mobile agents that can migrate between nodes. We introduce, in the context of 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…
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…