Related papers: HiTRACE-Web: an online tool for robust analysis of…
Motivation: Capillary electrophoresis (CE) of nucleic acids is a workhorse technology underlying high-throughput genome analysis and large-scale chemical mapping for nucleic acid structural inference. Despite the wide availability of…
HERITRACE is a semantic data management system tailored for the GLAM sector. It is engineered to streamline data curation for non-technical users while also offering an efficient administrative interface for technical staff. The paper…
High-throughput $ab$ $initio$ calculations are the indispensable parts of data-driven discovery of new materials with desirable properties, as reflected in the establishment of several online material databases. The accumulation of…
We present GobyWeb, a web-based system to facilitate the management and analysis of high-throughput sequencing (HTS) projects. The software provides integrated support for a broad set of HTS analyses and offers a simple plugin extension…
Powerful detectors at modern experimental facilities routinely collect data at multiple GB/s. Online analysis methods are needed to enable the collection of only interesting subsets of such massive data streams, such as by explicitly…
Just as in eukaryotes, high-throughput chromosome conformation capture (Hi-C) data have revealed nested organizations of bacterial chromosomes into overlapping interaction domains. In this chapter, we present a multiscale analysis framework…
HERITRACE is a data editor designed for galleries, libraries, archives and museums, aimed at simplifying data curation while enabling non-technical domain experts to manage data intuitively without losing its semantic integrity. While the…
Fast, incremental evolution of physics instrumentation raises the question of efficient software abstraction and transferability of algorithms across similar technologies. This contribution aims to provide an answer by introducing Track…
Digital pathology has become a standard in the pathology workflow due to its many benefits. These include the level of detail of the whole slide images generated and the potential immediate sharing of cases between hospitals. Recent…
HERITRACE is an open-source web application that enables users without Semantic Web expertise to curate RDF data through form-based interfaces with automatic provenance documentation and change tracking in RDF. It uses SHACL for data model…
By coupling peptides with DNA tags (i.e., 'barcodes'), it is now possible to harness high-throughput sequencing (HTS) technologies to enable highly multiplexed peptide-based assays, which have a variety of potential applications including…
In this thesis we investigate high throughput computational methods for processing large quantities of data collected from synchrotrons and their application to spectral analysis of powder diffraction data. We also present the main product…
The Hiperwalk package is designed to facilitate the simulation of quantum walks using heterogeneous high-performance computing, taking advantage of the parallel processing power of diverse processors such as CPUs, GPUs, and acceleration…
Objective: Medical relations are the core components of medical knowledge graphs that are needed for healthcare artificial intelligence. However, the requirement of expert annotation by conventional algorithm development processes creates a…
To provide the Cytoscape users the possibility of integrating ITM Probe into their workflows, we developed CytoITMprobe, a new Cytoscape plugin. CytoITMprobe maintains all the desirable features of ITM Probe and adds additional flexibility…
As High-Performance Computing (HPC) systems strive towards the exascale goal, studies suggest that they will experience excessive failure rates. For this reason, detecting and classifying faults in HPC systems as they occur and initiating…
High-level synthesis (HLS) accelerates FPGA design by rapidly generating diverse implementations using optimization directives. However, even with cycle-accurate C/RTL co-simulation, the reported clock cycles often differ significantly from…
In the rapidly growing field of wearable technology, optical devices are emerging as a significant innovation, offering non-invasive methods for analyzing skin and underlying tissue properties. Despite their promise, progress has been…
Advances in entity-graph based analysis of histopathology images have brought in a new paradigm to describe tissue composition, and learn the tissue structure-to-function relationship. Entity-graphs offer flexible and scalable…
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…