Publications

Citing NWB

If you are using NWB in your research, please use the following citation to acknowledge its use:

Oliver Rübel, Andrew Tritt, Ryan Ly, Benjamin K. Dichter, Satrajit Ghosh, Lawrence Niu, Pamela Baker, Ivan Soltesz, Lydia Ng, Karel Svoboda, Loren Frank, Kristofer E. Bouchard,  The Neurodata Without Borders ecosystem for neurophysiological data science, Oct. 2022,  eLife 11:e78362. https://doi.org/10.7554/eLife.78362

Online and Social Media
Papers
  • Oliver Rübel, Andrew Tritt, Ryan Ly, Benjamin K. Dichter, Satrajit Ghosh, Lawrence Niu, Pamela Baker, Ivan Soltesz, Lydia Ng, Karel Svoboda, Loren Frank, Kristofer E. Bouchard,  The Neurodata Without Borders ecosystem for neurophysiological data science, Oct. 2022,  eLife 11:e78362. https://doi.org/10.7554/eLife.78362  (bioRxiv preprint: https://doi.org/10.1101/2021.03.13.435173)
  • D. Eke, A. Bernard, J. G. Bjaalie, R. Chavarriaga, T. Hanakawa, A. Hannan, S. Hill, M. E. Martone, A. McMahon, O. Rübel, E. Thiels, and F. Pestilli, “International Data Governance for Neuroscience,” Neuron, Dec. 2021, ISSN 0896-6273,  doi: https://doi.org/10.1016/j.neuron.2021.11.017  (PsyArXiv Preprint: doi: https://doi.org/10.31234/osf.io/esz9b
  • D. Kang, O. Rübel,S. Byna, and S. Blanas, “Predicting and Comparing the Performance of Array Management Libraries,” 2020 IEEE International Parallel and Distributed Processing Symposium (IPDPS), New Orleans, LA, USA, 2020, pp. 906-915, doi: 10.1109/IPDPS47924.2020.00097.
  • A. J. Tritt, O. Rübel, B. Dichter, R. Ly, D. Kang, E. F. Chang, L. M. Frank, K. E. Bouchard, “HDMF: Hierarchical Data Modeling Framework for Modern Science Data Standards,” IEEE International Conference on Big Data (Big Data), Los Angeles, CA, USA, December 2019, pp. 165-179. Online on IEEEXplore
  • Rübel, O., Tritt, A., Dichter, B., Braun, T., Cain, N., Clack, N., Davidson, T. J., Dougherty, M., Fillion-Robin, J.-C., Graddis, N., Grauer, M., Kiggins, J. T., Niu, L., Ozturk, D., Schroeder, W., Soltesz, I., Sommer, F. T., Svoboda, K., Ng, L., Frank, L. M., Bouchard, K. NWB:N 2.0: An Accessible Data Standard for Neurophysiology. January, 2019, doi: https://doi.org/10.1101/523035, (bioRxiv preprint)

NWB 1.0:

  • Teeters, J. L., Godfrey, K., Young, R., Dang, C., Friedsam, C., Wark, B., Asari, H., Peron, S., Li, N., Peyrache, A., Denisov, G., Siegle, J. H., Olsen, S. R., Martin, C., Chun, M., Tripathy, S., Blanche, T. J., Harris, K., Buzsáki, G., Koch, C., Meister M., Svoboda, K., Sommer, F. T. (2015). Neurodata without borders: creating a common data format for neurophysiology. Neuron, 88(4), 629-634. Article in Neuron
Posters
  • Kyu Hyun Lee, Eric Denovellis, Ryan Ly, Jeremy Magland, Jeff Soules, Alison Comrie, Jennifer Guidera, Rhino Nevers, Daniel Gramling, Philip Adenekan, Ji Hyun Bak, Emily Monroe, Andrew Tritt, Oliver Rübel, Thinh Nguyen, Dimitri Yatsenko, Joshua Chu, Caleb Kemere, Samuel Garcia, Alessio Buccino, Emily Aery Jones, Lisa Giocomo, and Loren Frank, “Spyglass: a data analysis framework for reproducible and shareable neuroscience research,” SfN 2022, Nov.16, 2022 (Abstract)
  • Michael Wulf, M.Bosc, Ryan Ly, Matthew Avaylon, S. Starosta, Oliver Rübel, and Adam Kepecs , “A universal language and format to describe behavioral tasks and data,” SfN 2022, Nov. 15, 2022 (Abstract)
  • Matthew Avaylon, Ryan Ly, and Oliver Rübel, “Tools for Linking NWB Neurophysiology Data to Ontologies and Digital Identifiers,” SfN 2022, Nov. 13, 2022 (Abstract)
  • Benjamin Dichter, Cody Baker, Ramon Heberto Mayorquin, Anna Szonja Weigl, Ryan Ly, Andrew Tritt, Matthew Avaylon, and Oliver Rübel “Advancing Standardization of Neurophysiology Data Through Dissemination of NWB,” 8th Annual BRAIN Initiative Meeting, June 2022 (virtual)
  • Michael Wulf, Ryan Ly, Matthew Avaylon, Oliver Rübel, and Adam Kepecs et al., “ Generating a formal set of collaborative standards for sharing behavioral data and task designs to enable reproducibility in neuroscience,” Annual BRAIN Initiative Meeting June 2022 (virtual)
  • K. Gunalan, C. Brozdowski, T. Nguyen, B. Dichter,, O. Rübel, R. Ly, D. Yatsenko, “Automated analysis and sharing of neuroscience data using DataJoint, Neurodata Without Borders, and DANDI,” 8th Annual BRAIN Initiative Meeting, June 2022 (virtual)
  • M. Avaylon, R. Ly, A. Tritt P. Baker, O. Rübel, “Enhancing the NWB neurophysiology data standard to support linking of data to online resources and ontologies,” Neuromatch 4.0 Conference, Dec. 2021 (Virtual)[Video]
  • Ryan Ly, Pamela Baker, Benjamin Dichter, Andrew Tritt, Matthew Avaylon, Satrajit Ghosh, Lydia Ng, Oliver Ruebel, “Enhancements to the NWB Data Standard and Software Ecosystem for Neurophysiology,” SfN, Nov. 2021 (Virtual)(Abstract)
  • B. Dichter, L. Taufer, C. Baker, S. Sharda, M. McCormick, O, Rübel, “NWB Widgets, a Python Library for Interactive Visualizations of NWB Data,” SfN, Nov. 2021 (Virtual)(Abstract)
  • P.M. Baker, R. Ly, M. Avaylon, A. Tritt, P. Ray, T. Gillespie, O. Rübel, L. Ng, “Modeling Patch-seq experiment data using ontologies in NWB,” SfN, Nov. 2021 (Virtual)(Abstract)
  • Pamela Baker, Ryan Ly, Andrew Tritt, Matthew Avaylon, Lydia Ng, and Oliver Rübel, “Enhancing standardization of neurophysiology data through integration of experiment metadata and ontologies with NWB,” 7th Annual BRAIN Initiative Investigators Meeting, June 15-17, 2021 (Virtual) [Video]
  • Benjamin Dichter, Ryan Ly, Andrew Tritt, Lawrence Niu, and Oliver Rübel, “Advancing standardization of neurophysiology data through dissemination of NWB,” 7th Annual BRAIN Initiative Investigators Meeting, June 15-17, 2021 (Virtual)
  • Ryan Ly, Benjamin Dichter, Andrew Tritt, Oliver Ruebel, “Extending the Neurodata Without Borders data standard to handle new data types and use cases ,” INCF Neuroinformatics Assembly 2021 (Virtual) [Abstract]
  • Pamela M. Baker, Ryan Ly, Matthew Avaylon, Andrew Tritt, Oliver Ruebel, and Lydia Ng , “Ontology integration and experimental metadata in NWB: modeling Patch-seq datasets,”  INCF Neuroinformatics Assembly 2021 (Virtual) [Abstract]
  • Benjamin Dichter, Matt McCormick, Luiz Tauffer, Jeremy Magland, Lydia Ng, Oliver Ruebel, Michael Grauer, “NWBWidgets: Interactive Visualization for Neurodata Without Borders Files,” INCF Neuroinformatics Assembly 2021 (Virtual) [Abstract]
  • Donghe Kang, Oliver Rübel, Suren Byna, Spyros Blanas, “Comparison of Array Management Library Performance – A Neuroscience Use Case,” SuperComputing 2019, November, 21, 2019, Denver, CO, USA [Online] at https://sc19.supercomputing.org/presentation/?id=rpost191&sess=sess348
  • O. Rübel, A. J. Tritt, B. Dichter, R. Ly, M. Dougherty, V. Baratham, T. J. Davidson, L. Ng, L. M. Frank, K. E. Bouchard, “Extending the NWB:N neurophysiology data standard: Methods and applications,” Neuroscience 2019, October 23, 2019, Chicago, IL, USA, Poster #706.05
  • B. K. Dichter, M. Dougherty, V. Baratham, K. Nasiotis, A. J. Tritt, O. Rübel, E. F. Chang, K. E. Bouchard, “Neurodata without borders: Neurophysiology as a cross-species standard for electrocorticography,” Neuroscience 2019, October 21, 2019, Chicago, IL, USA, Poster #432.04
  • O. Rübel, A. J. Tritt, R. Ly, K. E. Bouchard, “Creating data standards for modern experimental and observational sciences,” DOE Data Day 2019, September 25, 2019, Livermore, CA, USA
  • B. Dichter, M. Dougherty, V. Baratham, K. Nasiotis, O. Woolnough, M. Feyder, A. J. Tritt, O. Rübel, N. Tandon, E. F. Chang, “Extending Neurodata Without Borders: Neurophysiology for Electrocorticography,” Neuroinformatics 2019, September 1, 2019, Warsaw, Poland
  • O. Rübel, A. Tritt, N. H. Cain, B. Dichter, J.-C. Fillion-Robin, D. Ozturk, L.M. Frank, E.F. Chang, F.T. Sommer, K. Svoboda, M. Grauer, W. Schroeder, L. Ng., K. Bouchard, “NWB:N: Advances towards an ecosystem for standardizing neurophysiology,” Neuroscience 2018, Society for Neuroscience, Nov. 6, 2018, San Diego, CA (Poster) (Online Abstract) (PDF)
  • Oliver Rübel, Andrew Tritt, David Camp, Edward F. Chang, David Donofrio, Loren M. Frank, Fritz T. Sommer, Kritofer Bouchard, “An advanced data software architecture for Neurodata Without Borders (NWB) to enable efficient management, use and sharing of neurophysiology data,” Neuroscience 2017, Society for Neuroscience, Nov. 11, 2017, Washington D.C. (Poster) (Online Abstract) (PDF)
Awards
  • 2019 R&D 100 winner, Software/Services (Article)
R&D 100 Award Palque
  • 2020-04-03  INCF endorses NWB as an “INCF Standard and Best Practice”
    • Endorsement: : https://www.incf.org/sbp/nwb
    • Community Review:  M. Martone, R. Gerkin, R. Moucek, S. Das, W. Goscinski, J. Hellgren-Kotaleski, E. T. W. Ho, D. Kennedy, T. Leergaard, M. Abrams, “Call for community review of Neurodata Without Borders: Neurophysiology (NWB:N) 2.0–a data standard for neurophysiology,” F1000 Research, 09 Oct 2019, DOI https://doi.org/10.7490/f1000research.1117538.1
Talks and Tutorials
  • Ryan Ly, Benjamin Dichter, Andrew Tritt, and Oliver Rübel, Extending the Neurodata Without Borders data standard to handle new data types and use cases, Neuromatch 3.0, October 30, 2020 (Virtual)
  • Pamela Baker and Lydia Ng, Modeling of behavioral tasks for data sharing using state machines, Neuromatch 3.0, October 30, 2020 (Virtual)
  • Oliver Rübel, NWB:N 2.0: An Ecosystem for Neurophysiology Data Standardization, Open Source Brain Workshop, Sept. 10, 2019, Alghero, Sardinia, Italy (Slides)
  • Oliver Rübel, Benjamin Dichter, Andrew Tritt, Michael Grauer, Nathan Clack, Lawrence Niu, Ryan Ly, Thomas Braun, Tom Davidson, Thinh Nguyen, Vyassa Baratham, NWB:N User Days 2019, May 13-14, 2019, HHMI Janelia, Ashburn, VA, USA. (Talks and Tutorials)
  • Oliver Rübel and Benjamin Dichter, NWB:N Tutorial at Cosyne 2019, Mar. 4, 2019, Cascais, Portugal. (Tutoral Materials)
  • Oliver Rübel, Andrew Tritt, Kristofer Bouchard, Nicholas Cain, Benjamin Dichter, Michael Grauer, Jean-Christophe Fillion-Robin, Nathan Clack, Lawrence Niu et al., 5th NWB:N Hackathon, Apr. 26-27, 2018, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. (Slides)
Project Reports
  • Benjamin Dichter, Oliver R ̈ubel, Ryan Ly, Satrajit Ghosh, Jerome Lecoq, Saskia de Vries, Carly Kiselycznyk, Kaitlyn Casimo, and Stephanie Albin, “Report: Neurodata Rehack: Generating new insights from existing neurophysiology data through secondary analysis: October 3-5, 2022” Online Technical Report, January 2023, (PDF) (LaTeX)
  • Oliver Rübel, Benjamin Dichter, Ryan Ly , “Report: 2022 NWB Users Days at HHMI Janelia 13th NWB Hackathon: July 25 – 27, 2022,” Online Technical Report, August 2022, (PDF) (LaTeX)
  • Ryan Ly, Benjamin Dichter, Yaroslav O. Halchenko , Satrajit S. Ghosh, and Oliver Rübel, “Report: 2022 NWB-DANDI Remote Developer Hackathon 12th NWB Hackathon: February 15 – 18, 2022“, Online Technical Report, March 23, 2022 (PDF) (LaTeX)
  • Benjamin Dichter, Ryan Ly, Matthew Avaylon, and Oliver Rübel, “Report: 2021 NWB Users Days at INCF Training Weeks 11th NWB Hackathon: August 25 – 27, 2021,” Online Technical Report, September 2021, (PDF) (LaTeX)
  • Ryan Ly, Benjamin Dichter, Andrew Tritt, Pam Baker, Yaroslav O. Halchenko , Satrajit S. Ghosh, and Oliver Rübel, “Report: 2021 NWB-DANDI Remote Developer Hackathon 10th NWB Hackathon: March 30th – April 1st, 2021“, Online Technical Report, May 27, 2021 (PDF) (LaTeX)
  • Ryan Ly, Oliver Rübel, Benjamin Dichter, Andrew Tritt, Pam Baker eds., “Report: 9th NWB Hackathon Virtual User Days; September 2020,” Online Technical Report, April, 2021 (PDF) (LaTeX)
  • Oliver Rübel, Andrew Tritt, Ryan Ly, Benjamin Dichter, Pamela Baker eds., “Report: 8th NWB Hackathon Virtual User Days; May 2020,” Online Technical Report, June 20, 2020 (PDF) (LaTeX)
  • Oliver Rübel, Andrew Tritt, Ryan Ly, Benjamin Dichter eds., “Report: 6th NWB:N Hackathon at HHMI Janelia: User Days and Developer Hackathon,” Online Technical Report, June, 2019 (PDF)
  • Oliver Rübel, Andrew Tritt, and Kristofer Bouchard eds., Report: 5th NWB:N Hackathon at Lawrence Berkeley National Laboratory, User Training and Engagement, Online Technical Report, May, 17, 2018 (PDF)
Software Process
  • Doruk Ozturk, Michael Grauer, Jean-Christophe Fillion-Robin, Will Schroeder and Sandy McKenzie
    • “How to Improve Software Quality in Open Source Projects: Part I – Overview of Continuous Integration (CI) and Software Process in PyNWB” (blog post part 1)
    • “How to Improve Software Quality in Open Source Projects: Part II – Packaging PyNWB for Multiple Operating Systems and Python Versions” (blog post part 2)
    • “How to Improve Software Quality in Open Source Projects: Part III – Code Coverage, Documentation and Style” (blog post part 3)
Community Publications

The following are publications from the broader NWB community. This list is not comprehensive. If you think a important publication is missing from the list, then please let us know via Slack or email.

  • Marike L. Reimer, Lakshmi Bangalore, Stephen G. Waxmanab, Andrew M. Tanab, “Core principles for the implementation of the neurodata without borders data standard,” Journal of Neuroscience Methods January 15, 2021, https://www.sciencedirect.com/science/article/abs/pii/S0165027020303952.
  • Petr Ježek, Jeffery L. Teeters and Friedrich T. Sommer, “NWB Query Engines: Tools to Search Data Stored in Neurodata Without Borders Format,” Frontiers in Neuroinformatics, September 11, 2020, https://www.frontiersin.org/articles/10.3389/fninf.2020.00027/full.
  • Kael Dai, Juan Hernando, Yazan N. Billeh, Sergey L. Gratiy, Judit Planas, Andrew P. Davison, Salvador Dura-Bernal, Padraig Gleeson, Adrien Devresse, Benjamin K. Dichter, Michael Gevaert, James G. King, Werner A. H. Van Geit, Arseny V. Povolotsky, Eilif Muller, Jean-Denis Courcol, Anton Arkhipov, “The SONATA data format for efficient description of large-scale network models,” PLOS Computational Biology, February 24, 2020, https://doi.org/10.1371/journal.pcbi.1007696 (NDX entry)
  • N. Chandravadia, D. Liang, A. G.P. Schjetnan, A. Carlson, M. Faraut, J.M. Chung, C.M. Reed, B. Dichter, U. Maoz, S. Kalia, T. Valiante, A. N. Mamelak & U. Rutishauser, “A NWB-based Dataset and Processing Pipeline of Human Single-Neuron Activity During a Declarative Memory Task” (PyPI)(Datasets)(GitHub)
  • Niccolò Bonacchi, Gaelle Chapuis, Anne Churchland, Kenneth D. Harris, Max Hunter, Cyrille Rossant, Maho Sasaki, Shan Shen, Nicholas A. Steinmetz, Edgar Y. Walker, Olivier Winter, Miles Wells, “Data architecture for a large-scale neuroscience collaboration,” The International Brain Laboratory, bioRxiv, February 2020, id 827873; doi: https://doi.org/10.1101/827873
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