Related papers: WinBioinfTools: Bioinformatics Tools for Windows H…
Since the advent of next-generation sequencing in the early 2000s, the volume of bioinformatics software tools and databases has exploded and continues to grow rapidly. Documenting this evolution on a global and time-dependent scale is a…
A range of computational biology software (GROMACS, AMBER, NAMD, LAMMPS, OpenMM, Psi4 and RELION) was benchmarked on a representative selection of HPC hardware, including AMD EPYC 7742 CPU nodes, NVIDIA V100 and AMD MI250X GPU nodes, and an…
Developing complex biomolecular workflows is not always straightforward. It requires tedious developments to enable the interoperability between the different biomolecular simulation and analysis tools. Moreover, the need to execute the…
Simulation, machine learning, and data analysis require a wide range of software which can be dependent upon specific operating systems, such as Microsoft Windows. Running this software interactively on massively parallel supercomputers can…
Background SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. Findings The first version appeared online twelve years ago and has been maintained and further developed ever since,…
Motivation: The rapid growth of biological data has intensified the need for transparent, reproducible, and well-documented computational workflows. The ability to clearly connect the steps of a workflow in the code with their description…
With high-throughput biotechnologies generating unprecedented quantities of data, researchers are faced with the challenge of locating and comparing an exponentially growing number of programs and websites dedicated to computational…
Study reproducibility is essential to corroborate, build on, and learn from the results of scientific research but is notoriously challenging in bioinformatics, which often involves large data sets and complex analytic workflows involving…
Computational models have great potential to accelerate bioscience, bioengineering, and medicine. However, it remains challenging to reproduce and reuse simulations, in part, because the numerous formats and methods for simulating various…
Summary: Accurate phenotype prediction from genomic sequences is a highly coveted task in biological and medical research. While machine-learning holds the key to accurate prediction in a variety of fields, the complexity of biological data…
To reproduce eScience, several challenges need to be solved: scientific workflows need to be automated; the involved software versions need to be provided in an unambiguous way; input data needs to be easily accessible; High-Performance…
In year 2006 Bio-Linux with the work of Tim Booth and team gives its rising and provide an operating system that was and still specialized in providing a bioinformatic specific software environment for the working needs in this corner of…
This work-in-progress research paper explores the effectiveness of tutorials in interdisciplinary learning environments, specifically focusing on bioinformatics. Tutorials are typically designed for a single audience, but our study aims to…
Bioinformatics and Computational Biology are two fields that have been exploiting GPUs for more than two decades, being CUDA the most used programming language for them. However, as CUDA is an NVIDIA proprietary language, it implies a…
Summary: With the rapid development of long-read sequencing technologies, the era of individual complete genomes is approaching. We have developed wgatools, a cross-platform, ultrafast toolkit that supports a range of whole genome alignment…
The openPC is a set of open source tools that realizes a parallel machine and distributed computing environment divisible into several independent blocks of nodes, and each of them is remotely but fully in any means accessible for users…
IT based scientific research requires high computational resources. The limitation on funding and infrastructure led the high performance computing era from supercomputer to cluster and grid computing technology. Parallel application…
Low-cost, high-throughput DNA and RNA sequencing (HTS) data is the backbone of the life sciences. Genome sequencing is now becoming a part of Predictive, Preventive, Personalized, and Participatory (termed 'P4') medicine. All genomic data…
Programming is ubiquitous in applied biostatistics; adopting software engineering skills will help biostatisticians do a better job. To explain this, we start by highlighting key challenges for software development and application in…
Motivation: Accurate detection of sequence similarity and homologous recombination are essential parts of many evolutionary analyses. Results: We have developed SimPlot++, an open-source multiplatform application implemented in Python,…