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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
Probabilistic programming in Python using PyMC3
Salvatier, John, Wiecki, Thomas V., Fonnesbeck, Christopher
Published in PeerJ. Computer science (06.04.2016)
Published in PeerJ. Computer science (06.04.2016)
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Journal Article
PHENIX: a comprehensive Python-based system for macromolecular structure solution
Adams, Paul D., Afonine, Pavel V., Bunkóczi, Gábor, Chen, Vincent B., Davis, Ian W., Echols, Nathaniel, Headd, Jeffrey J., Hung, Li-Wei, Kapral, Gary J., Grosse-Kunstleve, Ralf W., McCoy, Airlie J., Moriarty, Nigel W., Oeffner, Robert, Read, Randy J., Richardson, David C., Richardson, Jane S., Terwilliger, Thomas C., Zwart, Peter H.
Published in Acta crystallographica. Section D, Biological crystallography. (01.02.2010)
Published in Acta crystallographica. Section D, Biological crystallography. (01.02.2010)
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Journal Article
MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads
Uliano-Silva, Marcela, Ferreira, João Gabriel R. N., Krasheninnikova, Ksenia, Formenti, Giulio, Abueg, Linelle, Torrance, James, Myers, Eugene W., Durbin, Richard, Blaxter, Mark, McCarthy, Shane A.
Published in BMC bioinformatics (18.07.2023)
Published in BMC bioinformatics (18.07.2023)
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Journal Article
PyRates—A Python framework for rate-based neural simulations
Gast, Richard, Rose, Daniel, Salomon, Christoph, Möller, Harald E., Weiskopf, Nikolaus, Knösche, Thomas R.
Published in PloS one (16.12.2019)
Published in PloS one (16.12.2019)
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Journal Article
A modular Python framework for rapid development of advanced control algorithms for energy systems
Eser, Steffen, Storek, Thomas, Wüllhorst, Fabian, Dähling, Stefan, Gall, Jan, Stoffel, Phillip, Müller, Dirk
Published in Applied energy (01.05.2025)
Published in Applied energy (01.05.2025)
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Journal Article
Auto-qPCR; a python-based web app for automated and reproducible analysis of qPCR data
Maussion, Gilles, Thomas, Rhalena A., Demirova, Iveta, Gu, Gracia, Cai, Eddie, Chen, Carol X.-Q., Abdian, Narges, Strauss, Theodore J. P., Kelaï, Sabah, Nauleau-Javaudin, Angela, Beitel, Lenore K., Ramoz, Nicolas, Gorwood, Philip, Durcan, Thomas M.
Published in Scientific reports (29.10.2021)
Published in Scientific reports (29.10.2021)
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Journal Article
CFPy —A Python Package for Pre‐ and Postprocessing of the Conduit Flow Process of MODFLOW
Reimann, Thomas, Rudolph, Max Gustav, Grabow, Leonard, Noffz, Torsten
Published in Ground water (01.11.2023)
Published in Ground water (01.11.2023)
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Journal Article
PyGeNN: A Python Library for GPU-Enhanced Neural Networks
Knight, James C., Komissarov, Anton, Nowotny, Thomas
Published in Frontiers in neuroinformatics (22.04.2021)
Published in Frontiers in neuroinformatics (22.04.2021)
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Journal Article
MCell4 with BioNetGen: A Monte Carlo simulator of rule-based reaction-diffusion systems with Python interface
Husar, Adam, Ordyan, Mariam, Garcia, Guadalupe C., Yancey, Joel G., Saglam, Ali S., Faeder, James R., Bartol, Thomas M., Kennedy, Mary B., Sejnowski, Terrence J.
Published in PLoS computational biology (24.04.2024)
Published in PLoS computational biology (24.04.2024)
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Journal Article
ConKit: a python interface to contact predictions
Simkovic, Felix, Thomas, Jens M H, Rigden, Daniel J
Published in Bioinformatics (Oxford, England) (15.07.2017)
Published in Bioinformatics (Oxford, England) (15.07.2017)
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Journal Article
FlowKit: A Python Toolkit for Integrated Manual and Automated Cytometry Analysis Workflows
White, Scott, Quinn, John, Enzor, Jennifer, Staats, Janet, Mosier, Sarah M., Almarode, James, Denny, Thomas N., Weinhold, Kent J., Ferrari, Guido, Chan, Cliburn
Published in Frontiers in immunology (05.11.2021)
Published in Frontiers in immunology (05.11.2021)
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Journal Article
The atomic simulation environment-a Python library for working with atoms
Hjorth Larsen, Ask, Jørgen Mortensen, Jens, Blomqvist, Jakob, Castelli, Ivano E, Christensen, Rune, Du ak, Marcin, Friis, Jesper, Groves, Michael N, Hammer, Bjørk, Hargus, Cory, Hermes, Eric D, Jennings, Paul C, Bjerre Jensen, Peter, Kermode, James, Kitchin, John R, Leonhard Kolsbjerg, Esben, Kubal, Joseph, Kaasbjerg, Kristen, Lysgaard, Steen, Bergmann Maronsson, Jón, Maxson, Tristan, Olsen, Thomas, Pastewka, Lars, Peterson, Andrew, Rostgaard, Carsten, Schiøtz, Jakob, Schütt, Ole, Strange, Mikkel, Thygesen, Kristian S, Vegge, Tejs, Vilhelmsen, Lasse, Walter, Michael, Zeng, Zhenhua, Jacobsen, Karsten W
Published in Journal of physics. Condensed matter (12.07.2017)
Published in Journal of physics. Condensed matter (12.07.2017)
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Journal Article
GLAMbox: A Python toolbox for investigating the association between gaze allocation and decision behaviour
Molter, Felix, Thomas, Armin W, Heekeren, Hauke R, Mohr, Peter N. C
Published in PloS one (16.12.2019)
Published in PloS one (16.12.2019)
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Journal Article
Author Correction: 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