Publications related to Workflow engine

Orchestrating chromosome conformation capture analysis with Bioconductor

Genome-wide chromatin conformation capture assays provide formidable insights into the spatial organization of genomes. However, due to the complexity of the data structure, their integration in multi-omics workflows remains challenging. We present data st ...

Nature Research2024

Data and Workflow to: Three-dimensional buoyant hydraulic fractures: finite volume release (Möri and Lecampion, (2023))

Brice Tanguy Alphonse Lecampion, Andreas Möri

This upload contains the relevant scripts, notebooks, and datasets to reproduce the numerically obtained results of the Journal article "Three-dimensional buoyant hydraulic fractures: finite volume release" by Möri and Lecampion, (2023). ...

Zenodo2023

Building a Knowledge Graph of Chinese Kung Fu Masters From Heterogeneous Bilingual Data

Lin Yuan, Yumeng Hou

Various endeavours into semantic web technologies and ontology engineering have been made within the organisation of cultural data, facilitating public access to digital assets. Although models for conceptualising objects have reached a certain level of ma ...

2023

Formation of carbonyl compounds during ozonation of lake water and wastewater: Development of a non-target screening method and quantification of target compounds

Urs von Gunten, Joanna Maria Houska

Ozonation of natural waters is typically associated with the formation of carbonyl compounds (aldehydes, ketones and ketoacids), a main class of organic disinfection byproducts (DBPs). However, the detection of carbonyl compounds in water and wastewater is ...

PERGAMON-ELSEVIER SCIENCE LTD2023

Data and Workflow to: Three-dimensional buoyant hydraulic fracture growth: constant release from a point source (Möri and Lecampion, (2022))

Brice Tanguy Alphonse Lecampion, Andreas Möri

This upload contains the relevant scripts, notebooks, and datasets to reproduce the numerically obtained results of the Journal article "Three-dimensional buoyant hydraulic fracture growth: constant release from a point source" by Möri and Lecampion, (2022 ...

2022

Combining hypothesis- and data-driven neuroscience modeling in FAIR workflows

Daniel Keller

Modeling in neuroscience occurs at the intersection of different points of view and approaches. Typically, hypothesis-driven modeling brings a question into focus so that a model is constructed to investigate a specific hypothesis about how the system work ...

2022

A conceptual simulation workflow to guide design decisions regarding the effects of daylight on occupants' alertness

Marilyne Andersen, Clotilde Marie A Pierson, Victoria Eugenia Soto Magán

Recent developments in the lighting research field have demonstrated the importance of a proper exposure to light to mediate several of our behavioral and physiological responses. However, we spend nowadays around 90% of our time indoors with an often quit ...

IOP PUBLISHING LTD2021

Clouseau: Blockchain-based Data Integrity for HDFS Clusters

Ioannis Mytilinis

As the volume of produced data is exponentially increasing, companies tend to rely on distributed systems to meet the surging demand for storage capacity. With the business workflows becoming more and more complex, such systems often consist of or are acce ...

IEEE COMPUTER SOC2021

Proteomics of Human Milk: Definition of a Discovery Workflow for Clinical Research Studies

Loïc Dayon

Milk is a complex biological fluid composed mainly of water, carbohydrates, lipids, proteins, and diverse bioactive factors. Human milk represents a unique tailored source of nutrients that adapts during lactation to the specific needs of the developing in ...

2021

A computational workflow for the expansion of heterologous biosynthetic pathways to natural product derivatives

Vassily Hatzimanikatis, Jasmin Maria Hafner

Plant natural products (PNPs) and their derivatives are important but underexplored sources of pharmaceutical molecules. To access this untapped potential, the reconstitution of heterologous PNP biosynthesis pathways in engineered microbes provides a valua ...

Nature Research2021

AiiDA 1.0, a scalable computational infrastructure for automated reproducible workflows and data provenance

Nicola Marzari, Giovanni Pizzi, Nicolas Frank Mounet, Martin Uhrin, Andrea Cepellotti, Boris Kozinsky, Fernando Gargiulo, Christoph Leopold Talirz, Leonid Kahle, Aliaksandr Yakutovich, Sebastiaan Philippe Huber, Snehal Pramod Kumbhar, Andrius Merkys, Conrad Johnston, Casper Welzel Andersen, Spyros Zoupanos, Elsa Passaro, Carl Simon Adorf, Francisco Fernando Ramirez

The ever-growing availability of computing power and the sustained development of advanced computational methods have contributed much to recent scientific progress. These developments present new challenges driven by the sheer amount of calculations and d ...

2020

Workflows in AiiDA: Engineering a high-throughput, event-based engine for robust and modular computational workflows

Nicola Marzari, Giovanni Pizzi, Martin Uhrin, Sebastiaan Philippe Huber

Over the last two decades, the field of computational science has seen a dramatic shift towards incorporating high-throughput computation and big-data analysis as fundamental pillars of the scientific discovery process. This has necessitated the developmen ...

2020

Artificial Intelligence in Musculoskeletal Imaging: Review of Current Literature, Challenges, and Trends

Tobias Kober, Jonas Richiardi

Artificial intelligence (AI) has gained major attention with a rapid increase in the number of published articles, mostly recently. This review provides a general understanding of how AI can or will be useful to the musculoskeletal radiologist. After a bri ...

THIEME MEDICAL PUBL INC2019

Scaling Out Bioinformatics in the Data Center

Sam David Whitlock

Whole Genome Sequencing is a process in the field of bioinformatics that transforms biological samples of DNA into an electronic dataset of genetic bases. The process consists of two sequential components. First, the laboratory process of sequencing transf ...

EPFL2019

A digital workflow to quantify regenerative urban design in the context of a changing climate

Pietro Florio, Parag Rastogi, Emanuele Naboni

The regenerative approach to design goes beyond limiting the environmental impact of the built environment and towards the enrichment of the ecosystem, adaptation to climate change, and the improvement of human health. This concept is being applied to buil ...

2019

Provenance, workflows, and crystallographic tools in materials science: AiiDA, spglib, and seekpath

Giovanni Pizzi, Boris Kozinsky

The near-exponential expansion in computing resources over the last few decades has enabled a rapid increase in the capabilities of computational science, including applications to materials research. In order to harness the available resources and acceler ...

CAMBRIDGE UNIV PRESS2018

Automated construction of symmetrized Wannier-like tight-binding models from ab initio calculations

Quansheng Wu

Wannier tight-binding models are effective models constructed from first-principles calculations. As such, they bridge a gap between the accuracy of first-principles calculations and the computational simplicity of effective models. In this work, we extend ...

AMER PHYSICAL SOC2018

Reconstruction and visualization of large-scale volumetric models of neocortical circuits for physically-plausible in silico optical studies

Henry Markram, Felix Schürmann, Marwan Muhammad Ahmed Abdellah, Juan Bautista Hernando Vieites, Stefan Eilemann, Nicolas Antille

Background: We present a software workflow capable of building large scale, highly detailed and realistic volumetric models of neocortical circuits from the morphological skeletons of their digitally reconstructed neurons. The limitations of the existing a ...

2017

The Human Brain Project: Creating a European Research Infrastructure to Decode the Human Brain

Martin Telefont

Decoding the human brain is perhaps the most fascinating scientific challenge in the 21st century. The Human Brain Project (HBP), a 10-year European Flagship, targets the reconstruction of the brain's multiscale organization. It uses productive loops of ex ...

Cell Press2016

Comprehensive and Scalable Highly Automated MS-Based Proteomic Workflow for Clinical Biomarker Discovery in Human Plasma

Loïc Dayon, Martin Kussmann

Over the past decade, mass spectrometric performance has greatly improved in terms of sensitivity, dynamic range, and speed. By contrast, only limited progress has been accomplished with regard to automation, throughput, and robustness of the proteomic sam ...

Amer Chemical Soc2014