Publications associées à ChemCalc: a building block for tomorrow’s chemical infrastructure

Adding Color to Mass Spectra of Biopolymers: Charge Determination Analysis (CHARDA) Assigns Charge State to Every Ion Peak

Yury Tsybin, Laure Menin, Anton Kozhinov, Natalia Gasilova, Konstantin Nagornov

Traditionally, mass spectrometry (MS) output is the ion abundance plotted versus the ionic mass-to-charge ratio m/z. While employing only commercially available equipment, Charge Determination Analysis (CHARDA) adds a third dimension to MS, estimating for ...

Amer Chemical Soc2024

BigNeuron: a resource to benchmark and predict performance of algorithms for automated tracing of neurons in light microscopy datasets

Pascal Fua, Sean Lewis Hill, Amos Sironi, Jiancheng Yang, Jian Zhou, Siqi Liu, Xiang Li, Jie Zhou

BigNeuron is an open community bench-testing platform with the goal of setting open standards for accurate and fast automatic neuron tracing. We gathered a diverse set of image volumes across several species that is representative of the data obtained in m ...

2023

Identification of human milk oligosaccharide positional isomers by combining IMS-CID-IMS and cryogenic IR spectroscopy

Thomas Rizzo, Ahmed Ben Faleh, Stephan Warnke, Ali H Abikhodr, Vasyl Yatsyna

High-resolution ion mobility spectrometry (IMS) coupled with cryogenic infrared spectroscopy has proven to be a powerful technique for the identification of oligosaccharides. However, the need for an extensive database, combined with the scarcity of pure s ...

2023

Algorithms push forward the application of MALDI-TOF mass fingerprinting in rapid precise diagnosis

Hubert Girault, Yingdi Zhu

Macromolecular mass fingerprinting using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry is a quick tool for biochemical analysis. In combination with algorithms for automated data analysis and interpretation, it has wide appli ...

WILEY2023

OSSCAR, an open platform for collaborative development of computational tools for education in science

Giovanni Pizzi, Sara Bonella, Dou Du

In this paper we present the Open Software Services for Classrooms and Research (OSSCAR) platform. OSSCAR provides an open collaborative environment to develop and access educational resources in the form of web applications, for which various deployment m ...

ELSEVIER2023

DChannel: Accelerating Mobile ApplicationsWith Parallel High-bandwidth and Low-latency Channels

Haitham Al Hassanieh

Interactive mobile applications like web browsing and gaming are known to benefit significantly from low latency networking, as applications communicate with cloud servers and other users' devices. Emerging mobile channel standards have not met these needs ...

USENIX ASSOC2023

High-Throughput Sizing, Counting, and Elemental Analysis of Anisotropic Multimetallic Nanoparticles with Single-Particle Inductively Coupled Plasma Mass Spectrometry

Natalia Gasilova, Andreas Züttel, Wen Luo, Mo Li, Cedric David Koolen, Ayush Agarwal

Nanoparticles (NPs) have wide applications in physical and chemical processes, and their individual properties (e.g., shape, size, and composition) and ensemble properties (e.g., distribution and homogeneity) can significantly affect the performance. Howev ...

2022

ECCE: Entity-centric Corpus Exploration Using Contextual Implicit Networks

Maud Ehrmann, Matteo Romanello, Andreas Oliver Spitz

In the Digital Age, the analysis and exploration of unstructured document collections is of central importance to members of investigative professions, whether they might be scholars, journalists, paralegals, or analysts. In many of their domains, entities ...

ACM Digital Press2022

Surface Analysis by Secondary Ion Mass Spectrometry (SIMS): Principles and Applications from Swiss Laboratories

Thomas Bovay, Lukas Baumgartner, Anders Meibom, Stéphane Laurent Escrig, Florent Olivier Vivien Plane

Secondary Ion Mass Spectrometry (SIMS) extracts chemical, elemental, or isotopic information about a localized area of a solid target by performing mass spectrometry on secondary ions sputtered from its surface by the impact of a beam of charged particles. ...

SWISS CHEMICAL SOC2022

Supporting Developers in Creating Web Apps for Education via an App Development Framework

Denis Gillet, Sandy Ingram, Juan Carlos Farah

As more educational activities are conducted online, the need for interactive applications (apps) that can effectively support educators in their practice is increasing. These apps are often created by web developers or by researchers, educators, and even ...

Editorial Universitat Politècnica de València2022

A large scale study of reader interactions with images on Wikipedia

Tiziano Piccardi, Daniele Rama

Wikipedia is the largest source of free encyclopedic knowledge and one of the most visited sites on the Web. To increase reader understanding of the article, Wikipedia editors add images within the text of the article's body. However, despite their widespr ...

SPRINGER2022

MoleculARweb: A Web Site for Chemistry and Structural Biology Education through Interactive Augmented Reality out of the Box in Commodity Devices

Matteo Dal Peraro, Luciano Andres Abriata, Lucien Fabrice Krapp, Fabio Jose Cortes Rodriguez

Augmented/virtual realities (ARs/VRs) promise to revolutionize STEM education. However, most easy-to-use tools are limited to static visualizations, which limits the approachable content, whereas more interactive and dynamic alternatives require costly har ...

AMER CHEMICAL SOC2021

Toward High-Throughput Cryogenic IR Fingerprinting of Mobility-Separated Glycan Isomers

Thomas Rizzo, Ahmed Ben Faleh, Stephan Warnke

Infrared (IR) spectroscopy is a powerful tool used to infer detailed structural information on molecules, often in conjunction with quantum-chemical calculations. When applied to cryogenically cooled ions, IR spectra provide unique fingerprints that can be ...

2021

Unravelling the structures of sodiated beta-cyclodextrin and its fragments

Thomas Rizzo, Robert Paul Pellegrinelli, Eduardo Carrascosa Casado, Ali H Abikhodr

We present cryogenic infrared spectra of sodiated beta-cyclodextrin beta-CD + Na, a common cyclic oligosaccharide, and its main dissociation products upon collision-induced dissociation (CID). We characterize the parent ions using high-resolution ion ...

2021

Building blocks for commodity augmented reality-based molecular visualization and modeling in web browsers

Luciano Andres Abriata

For years, immersive interfaces using virtual and augmented reality (AR) for molecular visualization and modeling have promised a revolution in the way how we teach, learn, communicate and work in chemistry, structural biology and related areas. However, m ...

2020

The Jazz Harmony Treebank

Martin Alois Rohrmeier, Christoph Finkensiep, Daniel Harasim, Petter Harald Ericson

Grammatical models which represent the hierarchical structure of chord sequences have proven very useful in recent analyses of Jazz harmony. A critical resource for building and evaluating such models is a ground-truth database of syntax trees that encode ...

ISMIR2020

Yacora on the Web: Online collisional radiative models for plasmas containing H, H-2 or He

Maurizio Giacomin

Yacora on the Web (www.yacora.de ) is a web application providing access to collisional radiative models based on the flexible solver Yacora. The main application range is plasma diagnostics in low-pressure plasmas. Available online are three collisional r ...

2020

Near-infrared reversible photoswitching of an isolated azobenzene-stilbene dye

Eduardo Carrascosa Casado, Gabriel Da Silva

Photoswitching of a charged azobenzene-stilbene dye is investigated through laser excitation in a tandem ion mobility mass spectrometer. Action spectra associated with E -> Z and Z -> E photoisomerisation of the stilbene group exhibit bands at 685 and 440 ...

Elsevier2020

Combining ultra-high resolution ion-mobility spectrometry with cryogenic IR spectroscopy for the study of biomolecular ions

Thomas Rizzo, Ahmed Ben Faleh, Robert Paul Pellegrinelli, Natalia Yalovenko, Stephan Warnke

Double-resonance spectroscopic schemes in combination with cryogenic ion traps are the go-to techniques when isomer-specific high-resolution spectra are required for analysis of molecular ions. Their limitation lies in the requirement for well-resolved, is ...

2019

Development and performance evaluation of a high mass resolution time of flight laser ablation ionisation mass spectrometer

Reto Wiesendanger

This thesis contributes to the field of analytical chemistry of solid samples by introducing a new instrument with unprecedented performance characteristics and analytical capabilities. The instrument is based on the laser ablation and ionisation time-of-f ...

EPFL2019