Posts by Collection

opensource

MNE Python

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Neuro electrophysiology visualization and analysis in Python!

The Docathon

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A week-long global sprint to improve documentation in the open-source community.

Binder

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A tool to create interactive and sharable code repositories.

publications

Decoding spectrotemporal features of overt and covert speech from the human cortex

Published in Frontiers in Neuroengineering, 2014 (paper link)

Using machine learning and predictive models to study how the brain uses experience to understand noisy speech.

Recommended citation: Martin, S., Brunner, P., Holdgraf, C. R., Heinze, H.-J., Crone, N. E., Rieger, J. W., … Pasley, B. N. (2014). Decoding spectrotemporal features of overt and covert speech from the human cortex. Frontiers in Neuroengineering, 7(May), 14. http://doi.org/10.3389/fneng.2014.00014 https://www.frontiersin.org/articles/10.3389/fneng.2014.00014/full

Rapid tuning shifts in human auditory cortex enhance speech intelligibility

Published in Nature Communications, 2016 (paper link)

Using machine learning and predictive models to study how the brain uses experience to understand noisy speech.

Recommended citation: Holdgraf, C. R., de Heer, W., Pasley, B. N., Rieger, J. W., Crone, N., Lin, J. J., … Theunissen, F. E. (2016). Rapid tuning shifts in human auditory cortex enhance speech intelligibility. Nature Communications, 7(May), 13654. http://doi.org/10.1038/ncomms13654 https://www.nature.com/articles/ncomms13654

Portable learning environments for hands-on computational instruction using container-and cloud-based technology to teach data science.

Published in ACM International Conference Proceeding Series, 2017 (paper link)

This paper covers recent work at UC Berkeley using cloud resources and open-source tools for teaching data analytics.

Recommended citation: Holdgraf, C. R., Culich, A., Rokem, A., Deniz, F., Alegro, M., & Ushizima, D. (2017). Portable learning environments for hands-on computational instruction using container-and cloud-based technology to teach data science. In ACM International Conference Proceeding Series (Vol. Part F1287). https://arxiv.org/pdf/1703.04900.pdf

Encoding and Decoding Models in Cognitive Electrophysiology

Published in Frontiers in Systems Neuroscience, 2017 (paper link)

A practical methods paper for fitting predictive models of the brain.

Recommended citation: Holdgraf, C. R., Rieger, J. W., Micheli, C., Martin, S., Knight, R. T., & Theunissen, F. E. (2017). Encoding and decoding models in cognitive electrophysiology. Frontiers in Systems Neuroscience, 11. http://doi.org/10.3389/fnsys.2017.00061 https://www.frontiersin.org/articles/10.3389/fnsys.2017.00061/full

The Types, Roles, and Practices of Documentation in Data Analytics Open Source Software Libraries

Published in Computer Supported Cooperative Work, 2018 (paper link)

A Collaborative Ethnography of Documentation Work

Recommended citation: Geiger, R. S., Varoquaux, N., Mazel-Cabasse, C., & Holdgraf, C. (2018). The Types, Roles, and Practices of Documentation in Data Analytics Open Source Software Libraries. Computer Supported Cooperative Work (CSCW). Computer Supported Cooperative Work (CSCW). https://doi.org/10.1007/s10606-018-9333-1 https://rdcu.be/QDdA

talks

From your laptop to the cloud

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How open-source technologies such as Kubernetes and JupyterHub are making it possible to move analytics workflows from a single laptop to shared computational resources. This opens up possibilities in research, education, and publication. The talk discusses several of these pieces of technology, and covers many interesting case-studies in how it has been used.

Visualizing the brain with open source tools

Published:

How open-source tools make it possible to visualize the human brain from many different perspectives. I discuss challenges in visualizing something as complicated as the brain, and cover many modern-day open source tools that make this possible, discussing the lessons we’ve learned along the way.

Zero to JupyterHub on Kubernetes

Published:

A day-long tutorial covering the basics of managing cloud resources, Docker, Kubernetes, and deploying/maintaining a JupyterHub using these tools.

teaching