(ipynb OR jupyter) AND github - PMC

Aurélien Naldi, Céline Hernandez, Nicolas Levy, Gautier Stoll, Pedro T. Monteiro, Claudine Chaouiya, Tomáš Helikar, Andrei Zinovyev, Laurence Calzone, Sarah Cohen-Boulakia, Denis Thieffry, Loïc Paulevé

Front Physiol. 2018; 9: 680. Published online 2018 Jun 19. doi: 10.3389/fphys.2018.00680

PMCID:: PMC6018415

Abstract Article PDF–1.5M

Select item 66563926.

xml2jupyter: Mapping parameters between XML and Jupyter widgets

Randy Heiland, Daniel Mishler, Tyler Zhang, Eric Bower, Paul Macklin

J Open Source Softw. Author manuscript; available in PMC 2019 Jul 24.

Published in final edited form as: J Open Source Softw. 2019; 4(39): 10.21105/joss.01408. Published online 2019 Jul 1. doi: 10.21105/joss.01408

PMCID:: PMC6656392

Abstract Article PDF–535K

Select item 87920727.

Spectral parameterization for studying neurodevelopment: How and why

Brendan Ostlund, Thomas Donoghue, Berenice Anaya, Kelley E. Gunther, Sarah L. Karalunas, Bradley Voytek, Koraly E. Pérez-Edgar

Dev Cogn Neurosci. 2022 Apr; 54: 101073. Published online 2022 Jan 15. doi: 10.1016/j.dcn.2022.101073

PMCID:: PMC8792072

Abstract Article PDF–5.7M

Select item 81043058.

A PyMOL snippet library for Jupyter to boost researcher productivity

Blaine H. M. Mooers

Comput Sci Eng. Author manuscript; available in PMC 2022 Mar 1.

Published in final edited form as: Comput Sci Eng. 2021 Mar-Apr; 23(2): 47–53. Published online 2021 Feb 16. doi: 10.1109/mcse.2021.3059536

PMCID:: PMC8104305

Abstract Article PDF–1.6M

Select item 110092659.

An open source knowledge graph ecosystem for the life sciences

Tiffany J. Callahan, Ignacio J. Tripodi, Adrianne L. Stefanski, Luca Cappelletti, Sanya B. Taneja, Jordan M. Wyrwa, Elena Casiraghi, Nicolas A. Matentzoglu, Justin Reese, Jonathan C. Silverstein, Charles Tapley Hoyt, Richard D. Boyce, Scott A. Malec, Deepak R. Unni, Marcin P. Joachimiak, Peter N. Robinson, Christopher J. Mungall, Emanuele Cavalleri, Tommaso Fontana, Giorgio Valentini, Marco Mesiti, Lucas A. Gillenwater, Brook Santangelo, Nicole A. Vasilevsky, Robert Hoehndorf, Tellen D. Bennett, Patrick B. Ryan, George Hripcsak, Michael G. Kahn, Michael Bada, William A. Baumgartner, Jr, Lawrence E. Hunter

Sci Data. 2024; 11: 363. Published online 2024 Apr 11. doi: 10.1038/s41597-024-03171-w

PMCID:: PMC11009265

Abstract Article PDF–3.0M

Select item 1043076710.

Open-Source Machine Learning in Computational Chemistry

Alexander Hagg, Karl N. Kirschner

J Chem Inf Model. 2023 Aug 14; 63(15): 4505–4532. Published online 2023 Jul 19. doi: 10.1021/acs.jcim.3c00643

PMCID:: PMC10430767

Abstract Article PDF–3.0M

Select item 1091277811.

Regulation of developmental gatekeeping and cell fate transition by the calpain protease DEK1 in Physcomitrium patens

Viktor Demko, Tatiana Belova, Maxim Messerer, Torgeir R. Hvidsten, Pierre-François Perroud, Ako Eugene Ako, Wenche Johansen, Klaus F. X. Mayer, Odd-Arne Olsen, Daniel Lang

Commun Biol. 2024; 7: 261. Published online 2024 Mar 4. doi: 10.1038/s42003-024-05933-z

PMCID:: PMC10912778

Abstract Article PDF–8.8M

Select item 764393712.

Using interactive digital notebooks for bioscience and informatics education

Alan Davies, Frances Hooley, Peter Causey-Freeman, Iliada Eleftheriou, Georgina Moulton

PLoS Comput Biol. 2020 Nov; 16(11): e1008326. Published online 2020 Nov 5. doi: 10.1371/journal.pcbi.1008326

PMCID:: PMC7643937

Abstract Article PDF–2.7M

Select item 836311213.

New Extensibility and Scripting Tools in the ImageJ Ecosystem

Niklas A. Gahm, Curtis T. Rueden, Edward L. Evans, III, Gabriel Selzer, Mark C. Hiner, Jenu V. Chacko, Dasong Gao, Nathan M. Sherer, Kevin W. Eliceiri

Curr Protoc. Author manuscript; available in PMC 2022 Aug 1.

Published in final edited form as: Curr Protoc. 2021 Aug; 1(8): e204. doi: 10.1002/cpz1.204

PMCID:: PMC8363112

Abstract Article PDF–1.2M

Select item 934888514.

Gwaihir: Jupyter Notebook graphical user interface for Bragg coherent diffraction imaging

David Simonne, Jérôme Carnis, Clément Atlan, Corentin Chatelier, Vincent Favre-Nicolin, Maxime Dupraz, Steven J. Leake, Edoardo Zatterin, Andrea Resta, Alessandro Coati, Marie-Ingrid Richard

J Appl Crystallogr. 2022 Aug 1; 55(Pt 4): 1045–1054. Published online 2022 Jul 15. doi: 10.1107/S1600576722005854

PMCID:: PMC9348885

Abstract Article PDF–1.2M

Select item 796118215.

Appyters: Turning Jupyter Notebooks into data-driven web apps

Daniel J.B. Clarke, Minji Jeon, Daniel J. Stein, Nicole Moiseyev, Eryk Kropiwnicki, Charles Dai, Zhuorui Xie, Megan L. Wojciechowicz, Skylar Litz, Jason Hom, John Erol Evangelista, Lucas Goldman, Serena Zhang, Christine Yoon, Tahmid Ahamed, Samantha Bhuiyan, Minxuan Cheng, Julie Karam, Kathleen M. Jagodnik, Ingrid Shu, Alexander Lachmann, Sam Ayling, Sherry L. Jenkins, Avi Ma'ayan

Patterns (N Y) 2021 Mar 12; 2(3): 100213. Published online 2021 Mar 4. doi: 10.1016/j.patter.2021.100213

PMCID:: PMC7961182

Abstract Article PDF–1.9M

Select item 650980716.

NanoDJ: a Dockerized Jupyter notebook for interactive Oxford Nanopore MinION sequence manipulation and genome assembly

Héctor Rodríguez-Pérez, Tamara Hernández-Beeftink, José M. Lorenzo-Salazar, José L. Roda-García, Carlos J. Pérez-González, Marcos Colebrook, Carlos Flores

BMC Bioinformatics. 2019; 20: 234. Published online 2019 May 9. doi: 10.1186/s12859-019-2860-z

PMCID:: PMC6509807

Abstract Article PDF–702K

Select item 988708017.

JBrowse Jupyter: a Python interface to JBrowse 2

Teresa De Jesus Martinez, Elliot A Hershberg, Emma Guo, Garrett J Stevens, Colin Diesh, Peter Xie, Caroline Bridge, Scott Cain, Robin Haw, Robert M Buels, Lincoln D Stein, Ian H Holmes

Bioinformatics. 2023 Jan; 39(1): btad032. Published online 2023 Jan 17. doi: 10.1093/bioinformatics/btad032

PMCID:: PMC9887080

Abstract Article PDF–651K

Select item 881309118.

PyRosetta Jupyter Notebooks Teach Biomolecular Structure Prediction and Design

Kathy H. Le, Jared Adolf-Bryfogle, Jason C. Klima, Sergey Lyskov, Jason Labonte, Steven Bertolani, Shourya S. Roy Burman, Andrew Leaver-Fay, Brian Weitzner, Jack Maguire, Ramya Rangan, Matt A. Adrianowycz, Rebecca F. Alford, Aleexsan Adal, Morgan L. Nance, Yuanhan Wu, Jordan Willis, Daniel W. Kulp, Rhiju Das, Roland L. Dunbrack, Jr., William Schief, Brian Kuhlman, Justin B. Siegel, Jeffrey J. Gray

Biophysicist (Rockv) Author manuscript; available in PMC 2022 Apr 14.

Published in final edited form as: Biophysicist (Rockv). 2021 Apr; 2(1): 108–122. Published online 2021 Apr 14. doi: 10.35459/tbp.2019.000147