activity
20132026
most citedOne file to share them all: Using the COMBINE Archive and the OMEX format to share all information about a modeling project

186 citations · 485 across the 8 of their papers we have counts for

collaborators

8 papers

quant-ph2026

Precision quantum simulation of magnon spectra and interactions

Trond I. Andersen, Nikita Astrakhantsev, Jeronimo Martinez +329

Quantum simulation promises to advance materials discovery by accurately simulating complex states of matter, their microscopic excitations, and macroscopic response functions. The…

quant-ph2025

Quantum computation of molecular geometry via many-body nuclear spin echoes

C. Zhang, R. G. Cortiñas, A. H. Karamlou +320

Quantum-information-inspired experiments in nuclear magnetic resonance spectroscopy may yield a pathway towards determining molecular structure and properties that are otherwise ch…

cs.DL2020

Nine Best Practices for Research Software Registries and Repositories: A Concise Guide

Task Force on Best Practices for Software Registries, :, Alain Monteil +30

Scientific software registries and repositories serve various roles in their respective disciplines. These resources improve software discoverability and research transparency, pro…

q-bio.QM2017★ 93 cited

Creation and analysis of biochemical constraint-based models: the COBRA Toolbox v3.0

Laurent Heirendt, Sylvain Arreckx, Thomas Pfau +52

COnstraint-Based Reconstruction and Analysis (COBRA) provides a molecular mechanistic framework for integrative analysis of experimental data and quantitative prediction of physico…

cs.CY2016★ 16 cited

Software search is not a science, even among scientists: A survey of how scientists and engineers find software

Michael Hucka, Matthew J. Graham

Improved software discovery is a prerequisite for greater software reuse: after all, if someone cannot find software for a particular task, they cannot reuse it. Understanding peop…

cs.DL2014★ 186 cited

One file to share them all: Using the COMBINE Archive and the OMEX format to share all information about a modeling project

Frank T. Bergmann, Richard Adams, Stuart Moodie +15

Background: With the ever increasing use of computational models in the biosciences, the need to share models and reproduce the results of published studies efficiently and easily…

q-bio.MN2013★ 5 cited

SBML Qualitative Models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools

Claudine Chaouiya, Duncan Berenguier, Sarah M Keating +21

Background: Qualitative frameworks, especially those based on the logical discrete formalism, are increasingly used to model regulatory and signalling networks. A major advantage o…

q-bio.MN2013★ 185 cited

Large-scale generation of computational models from biochemical pathway maps

Finja Büchel, Nicolas Rodriguez, Neil Swainston +23

Background: Systems biology projects and omics technologies have led to a growing number of biochemical pathway reconstructions. However, mathematical models are still most often c…