Students will learn analysis and computational tools by exploring open datasets from the Allen Institute. These data also form the basis for the course projects that students will develop over the second week of the course. Every year we select a few recent datasets from the Allen Institute to showcase including large scale physiology, behavior, and anatomy. These are likely to include recordings of neural activity collected using 2-photon calcium imaging or dense electrophysiology using Neuropixels probes, such as the Allen Brain Observatory datasets. These datasets, focused on the mouse visual cortex, contain recordings from large populations of neurons across many brain regions, both in passive and active behavioral conditions. Connectomic electron microscopy (EM) data from the MiCRONS program, or similar Allen Institute EM or high resolution light sheet data, will also be used to explore neuronal morphology, ultrastructure, and connectivity.

Python Boot Camp

The Python boot camp is held in Seattle all day on Saturday and the morning on Sunday, before all workshop participants depart for Friday Harbor, WA. Students who wish to get a start on the Python boot camp can work through the boot camp material and resources from previous years, complete introduction to Python exercises by Code Academy or Google, or see documentation from Python.

Code repositories

Code repositories from past workshops reflect materials and projects included in the workshop curriculum.

• 2022 repository

• 2021 repository

• 2019 repository

• 2018 repository

• 2017 repository

Summer Workshop on the Dynamic Brain Schedule

Please note that students are required to attend the full two weeks of the course, including the middle weekend.

Python Bootcamp | University of Washington 

• Saturday before workshop – 9am – 5pm 
• Sunday before workshop – 9am -12pm

Travel to workshop | Anacortes

• Bus to Anacortes

• Ferry from Anacortes to Friday Harbor

Week 1 | Friday Harbor

• Morning Lectures

• Afternoon dataset explorations

• Meal breaks and social activities throughout

Week 2 | Friday Harbor

• Morning Lectures
• Afternoon work time
• Meal breaks and social activities throughout

Facilities

Seattle, WA – University of Washington and Allen Institute

The Python boot camp is held Saturday all day and Sunday morning before the full workshop group departs for Friday Harbor on Sunday afternoon. On Saturday, students will visit the University of Washington. Breakfast and lunch will be provided. Optional welcome dinner for all SWDB participants.

Accommodations are available at the University of Washington on Friday and Saturday night for students participating in the boot camp, and on Saturday night for students not participating in the boot camp.

Research and technical skills impact

• The Summer Workshop on the Dynamic Brain taught me Python and expanded the range of my computational skills. I probably wouldn’t be a data scientist right now if it weren’t for the workshop. (Participant, 2016)

• Attending the Summer Workshop on the Dynamic Brain gave me my first introduction to Python, which is now my primary coding language. It taught me about open science and the magnitude of possibility with datasets such as those provided by the Allen Institute. I’m now using all of these skills. (Participant, 2014)

• It was an enriching first experience to collaborate with scientists working on different disciplines for a computational neuroscience project. Our project… included three neurophysiologists, a computer scientist, and a statistician (myself). I believe such a practice helps build the ability to accommodate different perspectives to build something greater… I learned about different topics in neuroscience and experimentation, and about Allen Institute datasets, which bettered my understanding of the field. (Participant, 2018)

Career development and collaboration

• I really learned the value of open and reproducible science. I have implemented a policy of open science and data sharing in my lab – including making all data and code available. (Participant, 2017)

• The sheer access to talent and resources is hard to match. I owe a lot of what I do now to the Summer Workshop on the Dynamic Brain, particularly with serving as a strong introduction to modern computational neuroscience and giving me the much needed courage to pursue a doctorate degree in a much more computational lab than in my Master’s. (Federico Bolanos, 2017)

• How to work efficiently in groups. You meet complete strangers and at the end of 2 weeks have had to formulate, work on, and present a project together. That’s a pretty unique skill. (Stephanie Seeman, 2015)

• I think this workshop was one of the handful of factors that made me want to understand what questions were important for neuroscience, not just for neuro-theory. After this experience, I spent several years in an experimental lab for my postdoc, and my career trajectory totally changed as a result. (Participant, 2014)

Professional networks and community

• I found my postdoctoral mentor at Summer Workshop on the Dynamic Brain! I also have longstanding friends/collaborators from the course. (Participant, 2014)

• I found my current post-doc through a connection I made at the course. I’ve also stayed in touch with a few of the students and we continue to support each other in various ways, e.g. going through the job market process. I’ve also continued to interact with a few of the faculty on teaching computational neuroscience. (Madineh Sedigh-Sarvestani, 2016)

• It functioned as a great in depth overview of currently highly active research fields within neuroscience, beyond the ones I knew about off the top of my head. This was great for understanding what work I might want to pursue next in my career. (Emily Gelfand, 2019)