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BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data
Lachance, Jean-Christophe, Lloyd, Colton J., Monk, Jonathan M., Yang, Laurence, Sastry, Anand V., Seif, Yara, Palsson, Bernhard O., Rodrigue, Sébastien, Feist, Adam M., King, Zachary A., Jacques, Pierre-Étienne
Published in PLoS computational biology (01.04.2019)
Published in PLoS computational biology (01.04.2019)
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Journal Article
GenProgJS: A Baseline System for Test-Based Automated Repair of JavaScript Programs
Csuvik, Viktor, Horvath, Daniel, Lajko, Mark, Vidacs, Laszlo
Published in IEEE transactions on software engineering (01.02.2025)
Published in IEEE transactions on software engineering (01.02.2025)
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Journal Article
An empirical study of automated unit test generation for Python
Lukasczyk, Stephan, Kroiß, Florian, Fraser, Gordon
Published in Empirical software engineering : an international journal (01.03.2023)
Published in Empirical software engineering : an international journal (01.03.2023)
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Journal Article
Efficiently accelerated bioimage analysis with NanoPyx, a Liquid Engine-powered Python framework
Saraiva, Bruno M., Cunha, Inês, Brito, António D., Follain, Gautier, Portela, Raquel, Haase, Robert, Pereira, Pedro M., Jacquemet, Guillaume, Henriques, Ricardo
Published in Nature methods (01.02.2025)
Published in Nature methods (01.02.2025)
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Journal Article
Automation and Genetic Algorithm Optimization for Seismic Modeling and Analysis of Tall RC Buildings
Cabrera, Piero A., Medina, Gianella M., Delgadillo, Rick M.
Published in Buildings (Basel) (01.10.2025)
Published in Buildings (Basel) (01.10.2025)
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Journal Article
Brian2CUDA: Flexible and Efficient Simulation of Spiking Neural Network Models on GPUs
Alevi, Denis, Stimberg, Marcel, Sprekeler, Henning, Obermayer, Klaus, Augustin, Moritz
Published in Frontiers in neuroinformatics (31.10.2022)
Published in Frontiers in neuroinformatics (31.10.2022)
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Journal Article
Integrating Hi-C links with assembly graphs for chromosome-scale assembly
Ghurye, Jay, Rhie, Arang, Walenz, Brian P., Schmitt, Anthony, Selvaraj, Siddarth, Pop, Mihai, Phillippy, Adam M., Koren, Sergey
Published in PLoS computational biology (01.08.2019)
Published in PLoS computational biology (01.08.2019)
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Journal Article
MetaLAFFA: a flexible, end-to-end, distributed computing-compatible metagenomic functional annotation pipeline
Eng, Alexander, Verster, Adrian J., Borenstein, Elhanan
Published in BMC bioinformatics (21.10.2020)
Published in BMC bioinformatics (21.10.2020)
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Journal Article
An Improved Copula‐Based Framework for Efficient Global Sensitivity Analysis
Liu, Hongli, Clark, Martyn P., Gharari, Shervan, Sheikholeslami, Razi, Freer, Jim, Knoben, Wouter J. M., Marsh, Christopher B., Papalexiou, Simon Michael
Published in Water resources research (01.01.2024)
Published in Water resources research (01.01.2024)
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Journal Article
TRAIT2D: a Software for Quantitative Analysis of Single Particle Diffusion Data [version 2; peer review: 2 approved]
Reina, Francesco, Wigg, John M.A, Dmitrieva, Mariia, Vogler, Bela, Lefebvre, Joël, Rittscher, Jens, Eggeling, Christian
Published in F1000 research (2022)
Published in F1000 research (2022)
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Journal Article
Reuse of process-based models: automatic transformation into many programming languages and simulation platforms
Midingoyi, Cyrille Ahmed, Pradal, Christophe, Athanasiadis, Ioannis N, Donatelli, Marcello, Enders, Andreas, Fumagalli, Davide, Garcia, Frédérick, Holzworth, Dean, Hoogenboom, Gerrit, Porter, Cheryl, Raynal, Hélène, Thorburn, Peter, Martre, Pierre
Published in in silico plants (01.01.2020)
Published in in silico plants (01.01.2020)
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Journal Article
SciPy 1.0: fundamental algorithms for scientific computing in Python
Virtanen, Pauli, Gommers, Ralf, Oliphant, Travis E., Haberland, Matt, Reddy, Tyler, Cournapeau, David, Burovski, Evgeni, Peterson, Pearu, Weckesser, Warren, Bright, Jonathan, van der Walt, Stéfan J., Brett, Matthew, Wilson, Joshua, Millman, K. Jarrod, Mayorov, Nikolay, Nelson, Andrew R. J., Jones, Eric, Kern, Robert, Larson, Eric, Carey, C J, Polat, İlhan, Feng, Yu, Moore, Eric W., VanderPlas, Jake, Laxalde, Denis, Perktold, Josef, Cimrman, Robert, Henriksen, Ian, Quintero, E. A., Harris, Charles R., Archibald, Anne M., Ribeiro, Antônio H., Pedregosa, Fabian, van Mulbregt, Paul
Published in Nature methods (01.03.2020)
Published in Nature methods (01.03.2020)
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Journal Article
Python to accelerate embedded SoC design: A case study for systems biology
Logaras, Evangelos, Hazapis, Orsalia G., Manolakos, Elias S.
Published in ACM transactions on embedded computing systems (01.11.2014)
Published in ACM transactions on embedded computing systems (01.11.2014)
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Journal Article