Related papers: WinBioinfTools: Bioinformatics Tools for Windows H…
We present an application, Superplot, for calculating and plotting statistical quantities relevant to parameter inference from a "chain" of samples drawn from a parameter space, produced by e.g. MultiNest. A simple graphical interface…
While GUI agents have shown impressive capabilities in common computer-use tasks such as OSWorld, current benchmarks mainly focus on isolated and single-application tasks. This overlooks a critical real-world requirement of coordinating…
Compendium Manager is a command-line tool written in Python to automate the provisioning, launch, and evaluation of bioinformatics pipelines. Although workflow management tools such as Snakemake and Nextflow enable users to automate the…
One of the more complex tasks for researchers using HPC systems is performance monitoring and tuning of their applications. Developing a practice of continuous performance improvement, both for speed-up and efficient use of resources is…
Almost all applications stop scaling at some point; those that don't are seldom performant when considering time to solution on anything but aspirational/unicorn resources. Recognizing these tradeoffs as well as greater user functionality…
Dynamic programming (DP) based algorithms are essential yet compute-intensive parts of numerous bioinformatics pipelines, which typically involve populating a 2-D scoring matrix based on a recursive formula, optionally followed by a…
We report SInC (SNV, Indel and CNV) simulator and read generator, an open-source tool capable of simulating biological variants taking into account a platform-specific error model. SInC is capable of simulating and generating single- and…
A bioinformatics platform is introduced aimed at identifying models of disease-specific pathways, as well as a set of network measures that can quantify changes in terms of global structure or single link disruptions.The approach integrates…
Objective of this work is to integrate high performance computing (HPC) technologies and bioacoustics data-mining capabilities by offering a MATLAB-based toolbox called Raven-X. Raven-X will provide a hardware-independent solution, for…
In-Network Computing (INC) has found many applications for performance boosts or cost reduction. However, given heterogeneous devices, diverse applications, and multi-path network typologies, it is cumbersome and error-prone for application…
The key to speeding up applications is often understanding where the elapsed time is spent, and why. This document reviews in depth the full array of performance analysis tools and techniques available on Linux for this task, from the…
Scientific research frequently involves the use of computational tools and methods. Providing thorough documentation, open-source code, and data -- the creation of reproducible computational research -- helps others understand a…
High Performance Computing (HPC) applications are essential for scientists and engineers to create and understand models and their properties. These professionals depend on the execution of large sets of computational jobs that explore…
To turn environmentally derived metabarcoding data into community matrices for ecological analysis, sequences must first be clustered into operational taxonomic units (OTUs). This task is particularly complex for data including large…
Medical image processing is often limited by the computational cost of the involved algorithms. Whereas dedicated computing devices (GPUs in particular) exist and do provide significant efficiency boosts, they have an extra cost of use in…
Summary: Biospectrogam is an open-source software for the spectral analysis of DNA and protein sequences. The software can fetch (from NCBI server), import and manage biological data. One can analyze the data using Digital Signal Processing…
In today's world of big data, computational analysis has become a key driver of biomedical research. Recent exponential growth in the volume of available omics data has reshaped the landscape of contemporary biology, creating demand for a…
The RooStats toolkit, which is distributed with the ROOT software package, provides a large collection of software tools that implement statistical methods commonly used by the High Energy Physics community. The toolkit is based on RooFit,…
Future computing systems, from handhelds to supercomputers, will undoubtedly be more parallel and heterogeneous than todays systems to provide more performance and energy efficiency. Thus, GPUs are increasingly being used to accelerate…
With the growing complexity of computational and experimental facilities, many scientific researchers are turning to machine learning (ML) techniques to analyze large scale ensemble data. With complexities such as multi-component workflows,…