Publications related to Software repository

OPTIMADE, an API for exchanging materials data

Nicola Marzari, Giovanni Pizzi, Martin Uhrin, Boris Kozinsky, Christoph Leopold Talirz, Snehal Pramod Kumbhar, Andrius Merkys, Casper Welzel Andersen, Gian-Marco Rignanese, Matthias Scheffler

The Open Databases Integration for Materials Design (OPTIMADE) consortium has designed a universal application programming interface (API) to make materials databases accessible and interoperable. We outline the first stable release of the specification, v ...

NATURE PORTFOLIO2021

DUBS: A Framework for Developing Directory of Useful Benchmarking Sets for Virtual Screening

Guillaume André Jean Fraux

Benchmarking is a crucial step in evaluating virtual screening methods for drug discovery. One major issue that arises among benchmarking data sets is a lack of a standardized format for representing the protein and ligand structures used to benchmark the ...

2020

Rapid identification and interpretation of gene‐environment associations using the new R.SamBada landscape genomics pipeline

Stéphane Joost, Oliver Michele Selmoni, Estelle Rochat, Sylvie Stucki, Kevin Leempoel, Elia Vajana, Solange Catherine Gaillard

Samβada is a genome‐environment association (GEA) software, designed to search for signatures of local adaptation. However, pre‐ and post‐processing of data can be labour‐intensive, preventing wider uptake of the method. We have now developed R.SamBada, an ...

2019

Reinforcing Civil Engineering Curricula With Courses Including Project-Based Software Applications

Gerard Guell Bartrina

Civil engineering (CE) is one of the broadest engineering fields, if not the most, and requires undergraduate students to be exposed to a variety of topics; each can be easily recognized as a major in its own. Establishing a successful curriculum is a majo ...

IATED-INT ASSOC TECHNOLOGY EDUCATION & DEVELOPMENT2018

Pyroomacoustics: A Python Package For Audio Room Simulation And Array Processing Algorithms

Eric Bezzam, Ivan Dokmanic, Robin Scheibler

We present pyroomacoustics, a software package aimed at the rapid development and testing of audio array processing algorithms. The content of the package can be divided into three main components: an intuitive Python object-oriented interface to quickly c ...

IEEE2018

CHAINIAC: Proactive Software-Update Transparency via Collectively Signed Skipchains and Verified Builds

Bryan Alexander Ford, Linus Gasser, Eleftherios Kokoris Kogias, Philipp Svetolik Jovanovic, Nicolas Gailly, Kirill Nikitin, Ismail Khoffi

Software-update mechanisms are critical to the security of modern systems, but their typically centralized design presents a lucrative and frequently attacked target. In this work, we propose CHAINIAC, a decentralized software-update framework that elimina ...

USENIX Association2017

An Efficient Manipulation Package for Biconditional Binary Decision Diagrams

Giovanni De Micheli, Pierre-Emmanuel Julien Marc Gaillardon, Luca Gaetano Amarù

Biconditional Binary Decision Diagrams (BBDDs) are a novel class of binary decision diagrams where the branching condition, and its associated logic expansion, is biconditional on two variables. Reduced and ordered BBDDs are remarkably compact and unique f ...

IEEE2014

A multi criteria group decision making approach for collaborative software selection problem

Naoufel Cheikhrouhou

Today, operational managers are experiencing difficulties in selecting the software that best suits their increasing number of requirements. These decision makers need to clarify what their needs are, what these packages offer and which software packages b ...

Ios Press2014

Biomechanical ToolKit: Open-source framework to visualize and process biomechanical data

Arnaud Barré, Stéphane Armand

C3D file format is widely used in the biomechanical field by companies and laboratories to store motion capture systems data. However, few software packages can visualize and modify the integrality of the data in the C3D file. Our objective was to develop ...

Elsevier2014

Design of a bed load and driftwood filtering dam, analysis of the phenomena and hydraulic design

Giovanni De Cesare

Flood protection often calls on to the realization of retention works for bed load as well as wood and debris flow. Certain relatively recent arrangements did not perform according to their intended function, what shows the complexity of the design and the ...

CRC Press/Balkema2014

A 2D/3D image analysis system to track fluorescently labeled structures in rod-shaped cells: application to measure spindle pole asymmetry during mitosis

Michaël Unser, Daniel Sage, Viesturs Simanis, Daniel Andreas Schmitter, Anastasia Chasapi, Ioannis Xenarios

Background: The yeast Schizosaccharomyces pombe is frequently used as a model for studying the cell cycle. The cells are rod-shaped and divide by medial fission. The process of cell division, or cytokinesis, is controlled by a network of signaling proteins ...

Biomed Central Ltd2013

Analysing Friedel averages and differences

Philip Pattison

Various practical applications of the average (A) and difference (D) of Friedel opposites are described. Techniques based on the resonant-scattering contribution to Friedel differences are applied to see whether a crystal is centrosymmetric or not, and to ...

International Union of Crystallography2012

Enabling Sophisticated Analysis of x86 Binaries with RevGen

George Candea, Vitaly Chipounov

Current state-of-the-art static analysis tools for binary software operate on ad-hoc intermediate representations (IR) of the machine code. Therefore, even though IRs facilitate program analysis by abstracting away the source language, it is hard to reuse ...

2011

Improved Computation of Propagation Losses in Waveguide Structures Using Perturbation of Boundary Conditions

Michael Mattes

In this letter, a method for the improved consideration of propagation losses in metallic waveguide structures is presented. The method relies on the perturbation of the boundary conditions on the metallic walls of the waveguides. Following this advanced t ...

Institution of Engineering and Technology2011

The Microbe browser for comparative genomics

Jacques Rougemont, Alexandre Gattiker, Marco Pagni, Ioannis Xenarios

The Microbe browser is a web server providing comparative microbial genomics data. It offers comprehensive, integrated data from GenBank, RefSeq, UniProt, InterPro, Gene Ontology and the Orthologs Matrix Project (OMA) database, displayed along with gene pr ...

Oxford University Press2009

Incremental Global Parameter Estimation in Dynamical Systems

Benoît Chachuat

Estimating the parameters of a dynamical system based on measurements is an important task in industrial and scientific practice. Since a model's quality is directly linked to its parameter values, obtaining globally rather than locally optimal values is e ...

American Chemical Society2009

Synchronous versus asynchronous modeling of gene regulatory networks

Giovanni De Micheli, Abhishek Garg, Ioannis Xenarios

In silico modeling of gene regulatory networks has gained some momentum recently due to increased interest in analyzing the dynamics of biological systems. This has been further facilitated by the increasing availability of experimental data on gene–gene, ...

2008

A software package to manipulate space dependencies and geometry in magnetic confinement fusion

Jean-Marc Moret

Improvement in the performance of magnetic confinement devices for nuclear fusion relies on the optimization of the geometry of the plasma: either the two-dimensional (2D) cross-section shape in tokamaks with toroidal symmetry or the 3D magnetic configurat ...

2005