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To facilitate rational molecular and materials design, this research proposes an integrated computational framework that combines stochastic simulation, ab initio quantum chemistry, and molecular docking. The suggested workflow allows…
Open-source scientific software is a major driver of scientific progress, yet its development and reuse remain difficult in collaborative settings. Researchers repeatedly face four recurring challenges: discovering and reproducing existing…
A computational workflow, also known as workflow, consists of tasks that must be executed in a specific order to attain a specific goal. Often, in fields such as biology, chemistry, physics, and data science, among others, these workflows…
Advances in molecular technologies underlie an enormous growth in the size of data sets pertaining to biology and biomedicine. These advances parallel those in the deep learning subfield of machine learning. Components in the differentiable…
Background: With the rapid growth of massively parallel sequencing technologies, still more laboratories are utilizing sequenced DNA fragments for genomic analyses. Interpretation of sequencing data is, however, strongly dependent on…
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…
Deep learning has been postulated as a solution for numerous problems in different branches of science. Given the resource-intensive nature of these models, they often need to be executed on specialized hardware such graphical processing…
Recently proposed modifications of the standard particle-in-cell (PIC) method resolve long-standing limitations such as exact preservation of physically conserved quantities and unbiased ensemble down-sampling. Such advances pave the way…
The Common Workflow Language (CWL) is a widely adopted language for defining and sharing computational workflows. It is designed to be independent of the execution engine on which workflows are executed. In this paper, we describe our…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…
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…
Prototyping and implementing distributed algorithms, particularly those that address challenges related with fault-tolerance and dependability, is a time consuming task. This is, in part, due to the need of addressing low level aspects such…
Systems biology and whole-cell modelling are demanding increasingly comprehensive mathematical models of cellular biochemistry. These models require the development of simplified models of specific processes which capture essential…
In recent years, the research community has raised serious questions about the reproducibility of scientific work. In particular, since many studies include some kind of computing work, reproducibility is also a technological challenge, not…
Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modelling of such systems.…
We present FabSim, a toolkit developed to simplify a range of computational tasks for researchers in diverse disciplines. FabSim is flexible, adaptable, and allows users to perform a wide range of tasks with ease. It also provides a…
Database-search algorithms, that deduce peptides from Mass Spectrometry (MS) data, have tried to improve the computational efficiency to accomplish larger, and more complex systems biology studies. Existing serial, and high-performance…
The evolving landscape of scientific computing requires seamless transitions from experimental to production HPC environments for interactive workflows. This paper presents a structured transition pathway developed at OLCF that bridges the…
P-systems are abstract computational models inspired by the phospholipid bilayer membranes generated by biological cells. Illustrated here is a mechanism by which recursive liposome structures (multivesicular liposomes) may be…
Data processing pipelines need to be executed at scales ranging from small runs up through large production data release runs resulting in millions of data products. As part of the Rubin Observatory's pipeline execution system, BPS is the…