24 papers · ranked by Valyu relevance
Stephen R Piccolo, Zachary E Ence, Elizabeth C Anderson, Jeffrey T Chang + 3 more
'Jeffrey T Chang' 'Andrea H Bild' 'C Daniela Robles-Espinoza' 'Aleksandra M Walczak'] Command-line software plays a critical role in biology research. However, processes for installing and executing software differ widely. The Common Workflow Language (CWL) is a community standard that addresses this problem. Using…
Shixiang Wang
Bioinformatics analyses depend on workflow engines to coordinate dozens of computational tools across complex dependency chains. The most widely adopted engines—Snakemake, Nextflow, the Common Workflow Language (CWL), and the Workflow Description Language (WDL)—run on interpreted or just-in-time (JIT) compiled language…
Shadi A. Issa, Romeo Kienzler, Mohamed El-Kalioby, Peter J. Tonellato + 3 more
'Peter J. Tonellato' 'Dennis Wall' 'Rémy Bruggmann' 'Mohamed Abouelhoda'] Cloud computing provides a promising solution to the genomics data deluge problem resulting from the advent of next-generation sequencing (NGS) technology. Based on the concepts of “resources-on-demand” and “pay-as-you-go”, scientists with no or…
Ezio Bartocci, Flavio Corradini, Emanuela Merelli, Lorenzo Scortichini
'Lorenzo Scortichini'] Background An in-silico experiment can be naturally specified as a workflow of activities implementing, in a standardized environment, the process of data and control analysis. A workflow has the advantage to be reproducible, traceable and compositional by reusing other workflows. In order to…
Gaurav Kaushik, Sinisa Ivkovic, Janko Simonovic, Nebojsa Tijanic + 2 more
As biomedical data becomes increasingly easy to generate in large quantities, the methods used to analyze it have proliferated rapidly. However, for the insights gained from these analyses to be meaningful, the analysis methods themselves must be transparent and reproducible. To address this issue, numerous groups have…
Fabiana Fournier, Lior Limonad
We introduce the process harness, a new mechanism for uplifting legacy workflows into Agentic Business Process Management (Agentic BPM) without replacing the underlying workflow engine. A process harness places a policy-governed agentic layer around a deterministic workflow engine, intercepting designated control…
Akiharu Esashi, Pawissanutt Lertpongrujikorn, Kato, Shinji + 2 more
Function as a Service (FaaS) is poised to become the foundation of the next generation of cloud systems due to its inherent advantages in scalability, cost-efficiency, and ease of use. However, challenges such as the need for specialized knowledge, platform dependence, and difficulty in scalability in building…
Jöerg Evermann
—Blockchain technology provides an auditable and tamper-proof distributed storage infrastructure for information records. This can be leveraged to support distributed workflow management. Compared to proof-of-work consensus, popularized by Bitcoin and Ethereum, blockchains based on BFT (byzantine fault tolerance)…
Hirotaka Suetake, Tomoya Tanjo, Manabu Ishii, Bruno P. Kinoshita + 10 more
'Takeshi Fujino' 'Tsuyoshi Hachiya' 'Yuichi Kodama' 'Takatomo Fujisawa' 'Osamu Ogasawara' 'Atsushi Shimizu' 'Masanori Arita' 'Tsukasa Fukusato' 'Takeo Igarashi' 'Tazro Ohta'] The increased demand for efficient computation in data analysis encourages researchers in biomedical science to use workflow systems. Workflow…
Vojtech Huser, Luke V Rasmussen, Ryan Oberg, Justin B Starren
Background Workflow engine technology represents a new class of software with the ability to graphically model step-based knowledge. We present application of this novel technology to the domain of clinical decision support. Successful implementation of decision support within an electronic health record (EHR) remains…
Stephen R. Piccolo, Zachary E. Ence, Elizabeth C. Anderson, Jeffrey T. Chang + 1 more
Command-line software plays a critical role in biology research. However, processes for installing and executing software differ widely. The Common Workflow Language (CWL) is a community standard that addresses this problem. Using CWL, tool developers can formally describe a tool’s inputs, outputs, and other execution…
Alexandre Melo, Alessandra Faria-Campos, Daiane Mariele DeLaat, Rodrigo Keller + 2 more
'Rodrigo Keller' 'Vinícius Abreu' 'Sérgio Campos'] Background The need to manage large amounts of data is a clear demand for laboratories nowadays. The use of Laboratory Information Management Systems (LIMS) to achieve this is growing each day. A LIMS is a complex computational system used to manage laboratory data…
Long Thai, Adam Barker, Blesson Varghese, Özgür Akgün + 1 more
—When orchestrating Web service workflows, the geographical placement of the orchestration engine(s) can greatly affect workflow performance. Data may have to be transferred across long geographical distances, which in turn increases execution time and degrades the overall performance of a workflow. In this paper, we…
Maximilian Willer, Peter Ruckdeschel
It is motivated by the rapidly evolving field of algorithmic fairness — the PhD topic of the first author — where new metrics, mitigation strategies, and machine learning methods continuously emerge. A central challenge in fairness, but also far beyond, is that existing toolkits either focus narrowly on single…
Daniel J.B. Clarke, John Erol Evangelista, Zhuorui Xie, Giacomo B. Marino + 36 more
Many biomedical research projects produce large-scale datasets that may serve as resources for the research community for hypothesis generation, facilitating diverse use cases. Towards the goal of developing infrastructure to support the findability, accessibility, interoperability, and reusability (FAIR) of biomedical…
Mahnoor Zulfiqar, Michael R. Crusoe, Birgitta König-Ries, Christoph Steinbeck + 2 more
Scientific workflows facilitate the automation of data analysis tasks by integrating various software and tools executed in a particular order. To enable transparency and reusability in workflows, it is essential to implement the FAIR principles. Here, we describe our experiences implementing the FAIR principles for…
Eftychia Eva Kontou, Axel Walter, Timo Sachsenberg, Tilmann Weber + 5 more
Metabolomics experiments generate highly complex datasets, which are time and work-intensive, sometimes even error-prone if inspected manually. Therefore, new methods for automated, fast, reproducible, and accurate data processing and dereplication are required. Here, we present UmetaFlow, a computational workflow for…
J. Harry Moore, Matthias R. Bauer, Jeff Guo, Atanas Patronov + 2 more
We present Icolos, a workflow manager written in Python as a tool for automating complex structure-based workflows. Icolos can be used as a standalone tool, for example in virtual screening campaigns, or can be used in conjunction with deep learning-based molecular generation facilitated for example by REINVENT, a…
Ward Jaradat, Alan Dearle, Adam Barker
—Orchestrating service-oriented workflows is typically based on a design model that routes both data and control through a single point – the centralised workflow engine. This causes scalability problems that include the unnecessary consumption of the network bandwidth, high latency in transmitting data between the…
Michael J. Jackson, Edward Wallace, Kostas Kavoussanakis
Workflow management systems represent, manage, and execute multi-step computational analyses and offer many benefits to bioinformaticians. They provide a common language for describing analysis workflows, contributing to reproducibility and to building libraries of reusable components. They can support both incremental…
Authors not listed
High-throughput density functional theory (DFT) calculations have become a vital element of computational materials science, enabling materials screening, property database generation, and training of “universal” machine learning models. While several software frameworks have emerged to support these computational…
Authors not listed
The exponential growth of chemical literature necessitates the development of automated tools for extracting and curating molecular information from unstructured scientific publications into open-access chemical databases. Current optical chemical structure recognition (OCSR) and named entity recognition solutions…
Christopher Woods, Lester Hedges, Adrian Mulholland, Maturos Malaisree + 10 more
Sire is a Python/C++ library that is used to both prototype new algorithms and as an interoperability engine for exchanging information between molecular simulation programs. It provides a collection of file parsers and information converters that together make it easier to combine and leverage the functionality of…
Ulrich Pabst
The idea of peptide mass fingerprinting (PMF) was first introduced in 1989, when protein research was facing a serious issue with automated Edman-degradation taking nearly one hour per reaction cycle. There was a dire need for more streamlined and fast ways to analyse proteins and peptides. Since the first steps…