Databinge

Time: 12:30pm each Friday
Location: Online using Zoom

Databinge is an online forum for sharing knowledge about computational methods and applications. We provide assistance for data analysis, visualization, and machine learning methods while encouraging open-science practices.

The team of tutors will be online via zoom to discuss points of interest in detail, troubleshoot code, and provide focused project support.

Join us on our Slack workspace to get announcements for upcoming Databinge meetings. Contact a tutor or Jeffrey LeDue (jeffrey.ledue@ubc.ca) via email for Slack invites and zoom addresses.

 

Inclusivity

Databinge is a forum for everyone. We strive to provide a means to help others build their skills and further their projects while we do the same. Creativity is maximized when researchers with diverse strengths work together.

Collaboration

Science is by its nature a community enterprise. Databinge encourages collaboration by working together starting early in the discovery process and using open data and code where possible.

Agility

New techniques, methods and approaches emerge continuously. Databinge strives to be responsive to this and enable adoption through collaborative workshops.

Sound Practice

Databinge strives to help improve practices including data and code management to further open science

Past Databinges:

9-Februrary-2024 Regular Databinge

 

2-Februrary-2024 Special Guest Dr. Eric Denovellis

Dr. Eric Denovellis from the Frank Lab at UCSF presented the neuroscience tools he built, such as the spectral connectivity package, ripple detection package, and state space replay classification package. He also shared his lessons learned from building neuroscience tools in the past, as his tips on good coding practices to ensure quality, efficiency, and longevity in software.

26-January-2024 Introductory Apptainer Presentation

Raina Cao and Hannah Cha gave an introductory presentation on the usage of Conda environments in Apptainer Containers, as well as container implementation on Compute Canada servers. The demo featured a tutorial on downloading an example brain slice image from the AllenSDK API. The presentation slides can be downloaded here.

19-January-2024 Special Guest Dr. Paul Cisek

Dr. Cisek from the University of Montreal gave a presentation on “Rethinking Behaviour in the Light of Evolution.” He introduced his research on phylogenetic refinement and the affordance competition hypothesis. A discussion was held afterwards on how his research impacts the field of neuroscience as a whole.

12-January-2024 Data Processing Workshop Discussion (First Databinge of 2024!)

Tutors and Dynamic Brain Circuits Cluster members held a discussion on possible neuroscience data processing packages to showcase for a data processing workshop before the 2024 CAN Meeting. Software brought up included the Cascade, pynapple, and neuromaps packages.

22-December-2023 Regular Databinge (Last Databinge of 2023!)

 

15-December-2023 Regular Databinge

 

8-December-2023 NRSC 510 Student Project Final Presentations

Students of NRSC 510 presented their final coding project over the course of the Fall 2023 semester, along with their trials, tribulations, and triumphs. The projects ranged from applying data analysis methods and using machine learning applications to creating an interactive database for tracking experiments.

1-December-2023 Regular Databinge

 

24-November-2023 Regular Databinge

 

17-November-2023 NRSC 510 Maryam Mirian Machine Learning Lecture

Maryam Mirian gave a lecture on ongoing work at Dr. Martin McKeown’s lab involving machine learning in Neuroscience for Parkinson’s Disease, introducing generative and discriminative computational models.

10-November-2023 NeuroAI Montreal 2023 Discussion

Parsa Delavari presented interesting topics on the use of AI in neuroscience from the NeuroAI meeting in Montreal. Discussions covered Dr. Paul Cisek’s affordance competition hypothesis and an upcoming machine learning framework for modelling neural activity dynamics across neural recordings.

3-November-2023 NRSC 510 Student Presentations

Students of the NRSC 510 course (“Topics in Neurodata”) presented updates regarding their coding projects for the course.

27-October-2023 Regular Databinge

 

20-October-2023 Regular Databinge

 

13-October-2023 Regular Databinge

 

6-October-2023 Regular Databinge

 

29-September-2023 Regular Databinge

 

22-September-2023 Regular Databinge

 

15-September-2023 Regular Databinge

 

8-September-2023 Special Guest Parsa Delavari

Parsa Delavari presented his ongoing computational neuroscience project at the Tim Murphy lab.

1-September-2023 Allen Institute Summer Workshop Dynamic Brain Course Discussion

Dr. Tim Murphy shared details from his trip to Friday Harbor to present at the Allen Institute Summer Workshop on the Dynamic Brain. The Allen Institute OpenScope project and generative adversarial networks (GANs) for brain imaging were notable topics. Details about the Allen Institute Summer Workshop 2023 can be found here.

25-August-2023 Regular Databinge

 

18-August-2023 Regular Databinge

 

11-August-2023 Special Guest Frederico Bolaños

Frederico Bolaños presented his PhD work on visual coding in mice, which can be read here.

Slides can be viewed here.

4-August-2023 Regular Databinge

 

28-July-2023 Regular Databinge

 

21-July-2023 Regular Databinge

 

14-July-2023 Regular Databinge

 

7-July-2023 NRSC 510 Discussion

Databinge Tutors discussed the current state and participation in the new NRSC 510 course (Topics in Neurodata), a project-driven class with an introduction to coding and an emphasis on working with data. This course will be first taught in Fall 2023.

30-June-2023 Canada Day Holiday Weekend (No Databinge)

 

23-June-2023 Special Guest David Buzorgnia

David Buzorgnia from Thrita Technologies Inc. will give a presentation on the company’s aims in developing a personalized computer model of the human brain. There may be internship opportunities through the Mitacs program for grad students and post doctoral researchers who are interested in working with the company to advance this field. View the presentation slides here.

16-June-2023 Regular Databinge

 

9-June-2023 Recap of UBC Psychiatry Research Day

Group members of the Murphy Lab discussed their favourite posters and presentations from UBC Psychiatry Research Day 2023.

26-May-2023 Special Guest James Mackay

Group discussion of the 16th Canadian Neuroscience meeting held the previous week in Montreal.

19-May-2023 Regular Databinge

 

12-May-2023 Regular Databinge

 

5-May-2023 Special Guest Dongsheng Xiao

Dongsheng Xiao presented his mesoscale generative adversarial network project (MesoGAN) to connect brain activity and behavior– details about the project here.

28-April-2023 Special Guest Ewa Zarnowska

Ewa Zarnowska from Coherent Laser presented her current work involving functional brain studies using multiphoton microscopy and Coherent Corp. Multiphoton Lasers.

21-April-2023 Regular Databinge

 

14-April-2023 Project Pedaling Parkinson

Zahra Alizadeh presented an update on Project Pedaling Parkinson, looking at the effects of cycling on EEG and EMG scans of Parkinson patients. View the presentation slides here.

7-April-2023 Good Friday Holiday (No Databinge)

 

31-March-2023 Special Databinge with UBC ARC

Please join us at 12:00 pm on Friday, March 31 for a special Databinge workshop with UBC ARC and BCCHRI Trainee Omics Group.  Learn how to move your R based research project from your personal computer to High Performance Computing (HPC) cluster e.g. UBC Sockeye. No registration required!

24-March-2023 LLMs for Brain Health 2023 Hackathon

The virtual kick-off for the LLMs for Brain Health 2023 Hackathon took place during Databinge hours. Participants were invited to explore the potential of ChatGPT and other large language models (LLMs) to aid work in brain health.

To view project submissions, click here

17-March-2023 Magic Mirror Project

Maryam Mirian and Jalil Alizadeh presented their work on the Magic Mirror Project.

10-March-2023 Peter Hogg Presentation

Peter Hogg from the Murphy Lab discussed his visit to the Allen Institute and how it is helping with his progress on the SLAP2 microscope that is being built at UBC.

3-March-2023 Report on the Nemonic Multiphoton Course

Nicholas Michelson, Pankaj Gupta, and Tony Fong from the Murphy Lab reported on the Nemonic Multiphoton Course.

24-February-2023 Getting the Most Out Of Your Computer

Group discussion on how to get the most out of your computer.

17-February-2023 Project Eyetracker Analysis Update

Fiza Arshad provided an update on her eyetracker analysis project at Databinge.

10-February-2023 Special Guest Walter Sena

Walter Sena, NeuroCog founder and post doctorate fellow at UBC Psychiatry, shared his ideas for predicting cognitive decline using objective measurements from remote eye-tracking and deep learning.

3-February-2023 Special Guest Pankaj Gupta

Pankaj Gupta from the Murphy Lab shared his experience at the UWashington Centre Neuroscience Center Datathon event with new data from the Allen Institute and updated us on his RNN project.

27-January-2023 Special Databinge with Eugene Barsky (Return of Databinge for 2023!)

Please join us at Databinge on Jan 27th for “Data Deposit Basics” with Eugene Barsky. Eugene is the UBC Library’s Research Data Management Librarian and he will cover file naming, folder structures, README files, metadata, PIDs, Data Management Plans and FAIR principles.

9-December-2022 Project Pedaling Presentation (Last Databinge of 2022!)

Presentation on #project-pedaling-parkinson by Zahra Alizadeh, Maryam Mirian, and Matt Sacheli.

2-December-2022 Regular Databinge

 

25-November-2022 Special Databinge with Jeff Clune

Jeff Clune, from UBC Computer Science, will discussed his lab’s computer vision work. Prof Clune’s talk will focus on his lab’s project in identifying, counting and describing animals in the wild with deep learning. You can read more here: https://pubmed.ncbi.nlm.nih.gov/29871948/

18-November-2022 Recap of Society for Neuroscience

Members of the Murphy Lab gave recaps of their favourite posters from SFN 2022.

11-November-2022 Remembrance Day (No Databinge)

 

4-November-2022 Best Practices in Teaching and Learning of Programming and Data Science

Group Discussion on best practices in teaching and learning of programming and data science.

28-October-2022 Special Guest Rochelin Dalangin

Rochelin Dalangin presented on the Canadian Vectorology and Optogenetics Foundry https://neurophotonics.ca/canadian-optogenetics-vectorology-foundry

21-October-2022 Thanksgiving Holiday (No Databinge)

 

14-October-2022 Special Guest Prof Randy McIntosh

Prof Randy McIntosh (SFU) https://www.sfu.ca/sfunews/stories/2022/01/prominent-neuroscientist-to-advance-brain-research-through-new-s.html discussed how we can get involved with the International Neuroinformatics Coordinating Facility (https://www.incf.org).

7-October-2022 SFARI and NeuroAI Reports

William Casazza presented on SFARI (https://www.sfari.org/event/in-search-of-causality-from-neuropsychiatric-genetics-to-pathophysiology/). Tony Fong and Edward Yan presented on interesting tools that they saw at NeuroAI in Seattle.

30-September-2022 National Truth and Reconciliation Day (No Databinge)

 

23-September-2022 Special Databinge with University of Oregon

Luca Mazzucato, Lia Papadopoulos, Daniel Hulsey from the University of Oregon (Eugene) presented on their BRAIN Initiative funded collaborative project.

16-September-2022 Special Guest Pankaj Gupta

Pankaj Gupta from the Murphy Lab presented his experience as a TA at the “Summer Workshop on the Dynamic Brain” which is offered by UW/Allen Institute each year in Friday Harbor.

9-September-2022 Special Guest Hannah Reid

Neurotutor Hannah Reid presented on the ImageJ macro she had been developing for quantifying microglia.

2-September-2022 Cross-Validated CPCA in Python Presentation

Hosted by Abhijit Chinchani. His lab mate Brian presented on a cross validated CPCA that he had implemented in Python. The Jupyter notebook available on GitHub.

26-August-2022 Themed Discussion: Exploratory Data Analysis and Data Visualization

Group discussion on approaches to exploratory data analysis and data visualization.

19-August-2022 Themed Discussion: Fluorescence Microscopy, Tissue Clearing and Expansion

Group discussion on Fluorescence microscopy, tissue clearing and expansion. Peter Hogg presented on his experiences on his trip to New York (Cold Spring).

12-August-2022 Themed Discussion: Omics, Sequencing Data, and Analysis

Group discussion on Omics and sequencing data and analysis. Nikita Telkar presented on her experience at the RStudio conference she attended and gave a brief recap on the Precision Health Analysis Bootcamp. 

5-August-2022 Themed Discussion: Fluorescence Microscopy, Tissue Clearing, and Expansion

Group discussion on Fluorescence microscopy, tissue clearing and expansion. Mehwish Anwer presented on quantifying cleared brain tissue, including the results she received from LifeCanvas Technologies, and how we might validate and reproduce these numbers with brainquant3d (https://github.com/sunilgandhilab/brainquant3d) and/or SMART (https://sgoldenlab.github.io/SMART/index.html).

29-July-2022 Themed Discussion: Omics, Sequencing Data, and Analysis

Group discussion on Omics and sequencing data and analysis. Jenn Kim presented on her experience at the Cold Spring Harbor Labs course titled “Statistical Analysis for Genome Scale Data”. https://meetings.cshl.edu/courses.aspx?course=C-data&year=22

22-July-2022 Themed Discussion: Fluorescence Microscopy, Tissue Clearing, and Expansion

Group discussion on Fluorescence microscopy, tissue clearing and expansion. Tony Fong shared his experiences at the Neurophotonics Summer School in Quebec City.

15-July-2022 Themed Discussion: Human Neuroimaging, EEG, and Brain Stimulation

Group discussion on human neuroimaging, EEG, and brain stimulation. Abhijit Chinchani presented on what he saw in Glasgow at the human brain mapping conference.

8-July-2022 Themed Discussion: Packages for Exploring Big Data

Group discussion on packages for exploring big data.

1-July-2022 Canada Day Holiday (No Databinge)

 

24-June-2022 Themed Discussion: Choice of Coding Languages for Beginners

Group discussion on choice of coding languages for beginners.

17-June-2022 Themed Discussion: Fluorescence Microscopy, Tissue Clearing, and Expansion

Group discussion on Fluorescence microscopy, tissue clearing and expansion. Mathias Delhaye and Sarah Ebert provided updates on the latest developments of their projects.

10-June-2022 Data Champions Databinge Showcase

 

3-June-2022 Themed Discussion: Planning Experiments, Effect Sizes, and Power Calculations

Group discussion on planning experiments, effect sizes, power calculations. Sarah Wang and Gale Chen, cluster Co-op students, presented what they have learned so far about using Datajoint: https://www.datajoint.org

27-May-2022 Themed Discussion: Omics, Sequencing Data, and Analysis

Group discussion on Omics and sequencing data and analysis. William Casazza and Nikita Telkar presented updates on the differential methylation analysis tutorial they were developing.

20-May-2022 Themed Discussion: Machine Learning, Computer Vision, Data Analysis

Group discussion on machine learning, computer vision, and data analysis.

13-May-2022 Themed Discussion: Human Neuroimaging, EEG, and Brain Stimulation

Group discussion on human neuroimaging, EEG, and brain stimulation.

6-May-2022 Regular Databinge

 

29-April-2022 Med Student FLEX Project

Presentation on the med student FLEX project.

22-April-2022 Diesel2p Ultrawide FOV Scope Building

Dale showed the diesel2p ultrawide field of view 2-photon scope being built.

15-April-2022 Good Friday Holiday (No Databinge)

 

8-April-2022 Regular Databinge

 

1-April-2022 Regular Databinge

 

25-March-2022 Regular Databinge

 

18-March-2022 Regular Databinge

 

11-March-2022 Regular Databinge

 

4-March-2022 Regular Databinge

 

25-February-2022 Regular Databinge

 

18-February-2022 Regular Databinge

 

11-February-2022 Special Guest Mehwish Anwer

Mehwish Anwer, a postdoc in the Wellington Lab, shared progress and challenges for tissue clearing analysis.

4-February-2022 Regular Databinge

 

28-January-2022 Regular Databinge

 

21-January-2022 Special Guest Angus Campbell

Angus Campbell presented a paper on using all open public datasets.

14-January-2022 Regular Databinge (Return of Databinge for 2022!)

 

17-December-2021 Regular Databinge (Last Databinge of 2021!)

 

10-December-2021 Studying Differences in EEG Forecasting for Parkinson’s Fisease Patients vs Healthy Controls Using Dynamic Mode Decomposition

Maryam Mirian and Abhijit Chinchani presented on studying differences in EEG forecasting for Parkinson’s disease patients vs healthy controls using Dynamic Mode Decomposition.

3-December-2021 Regular Databinge

 

26-November-2021 Regular Databinge

 

19-November-2021 Regular Databinge

 

12-November-2021 Regular Databinge

 

5-November-2021 Regular Databinge

 

29-October-2021 Regular Databinge

 

22-October-2021 Regular Databinge

 

15-October-2021 Regular Databinge

 

8-October-2021 Regular Databinge

 

1-October-2021 Regular Databinge

 

24-September-2021 Regular Databinge

 

17-September-2021 Regular Databinge

 

11-September-2021 Calcium Imaging Data Processing Pipeline

Sam and Majid from the University of Lethbridge will join Databinge on Sept 11 to go over the pipeline they are employing to process calcium imaging data from in vivo two-photon microscopy. 

Their pipeline will make use of the Suite2p pipeline created by the Howard Hughes Medical Institute. More information on Suite2p can be found at https://github.com/MouseLand/suite2p

10-September-2021 Regular Databinge

 

3-September-2021 Regular Databinge

 

27-August-2021 Regular Databinge

 

20-August-2021 Regular Databinge

 

13-August-2021 Brain-Tech 2021

This virtual event taking place during Databinge hours brings together students and researchers from diverse fields to brainstorm and prototype novel applications to support brain wellness. These applications may either improve brain wellness directly through the encouragement of healthy lifestyles or indirectly by contributing to the study and dissemination of brain wellness concepts. Researchers and students studying healthcare, neuroscience, computer science, and biomedical engineering are invited to contribute their unique expertise to this event. It is anticipated that winning teams will develop the concept for an app, software tool, or program that will aid the mission of the BC Brain Wellness Program.

For more information on the event, click here

To view project submissions, click here

30-April-2021 Neurodata Without Borders Presentation

Nuerodata Without Borders is a consortium of researchers and foundations that are dedicated to breaking down the obstacles to data sharing in the neuroscience community. Databinge will be hosting a special presentation on Neurodata Without Borders presented by Adrien Peyrache.

For more information on Neurodata Without Borders, please click here.

16-April-2021 iDISCO

A tool/procedure for rapid immunolabeling and volume imaging of biological samples

More information can be found here

19-March-2021 Special Guest Edward Yan

Edward Yan from the Murphy lab will be presenting his work on Neuropixel probes and high-density recording.

4-March-2021 Special Guest Shay Neufeld

Shay is the Data Product Lead at Inscopix where he leads a team in Vancouver, BC focused on building data analysis products and services for the neuroscience community. Prior to joining Inscopix, he worked as a Senior Data Scientist for Livestories (a small public health-focused analytics company in Seattle), as well as a Machine Learning Engineer & Product Consultant for Boston Children’s Hospital Technology & Innovation Development Office. Shay received a Ph.D. in Neuroscience from Harvard in 2017 where his research focused on investigating how neural circuits in the basal ganglia engender reinforcement learning & goal-directed behavior.

19-February-2021 UBC Digital Research Infrastructure Showcase

UBC Advanced Research Computing(ARC), in partnership with Djavad Mowafaghian Centre for Brain Health (DMCBH), will showcase UBC ARC digital research infrastructure: Sockeye and Chinook

More information on UBC ARC can be found here.

29-January-2021 Git and GitHub (Slides Included)

A presentation on Git and GitHub which a set of tools used for version control and project collaboration.

Slide Presentation

20-October-2020 TDT Fiber Photometry Workshop

Fiber photometry is a calcium imaging method for detecting neural activity.

11-September-2021 Calcium Imaging Data Processing Pipeline

Sam and Majid from the University of Lethbridge will join Databinge on Sept 11 to go over the pipeline they are employing to process calcium imaging data from in vivo two-photon microscopy. 

Their pipeline will make use of the Suite2p pipeline created by the Howard Hughes Medical Institute. More information on Suite2p can be found at https://github.com/MouseLand/suite2p

5-June-2020 Mathworks

MathWorks is the leading developer of mathematical computing software for engineers and scientists and is known for developing programs such as MATLAB. Aycan Hacioglu will be attending Databinge to discuss MATLAB resources and possible tutorial topics.

Pre-Curtailment Databinge

  • Time: 4:00-5:30pm each Friday
  • Location: Koerner F103
  • Food: Pizza at 4:30pm

Open to all UBC labs. Databinge is an interactive drop-in meeting for neuroscientists with the goal of furthering training and collaboration. Supported in part by the DMCBH and the Canadian Neurophotonics Platform, our goal is to promote collaboration and emphasize practical know-how via the use of UBC licensed and open-source software and sharing of protocols. Each Friday we will have an open house in which interested labs can have a data show-and-tell, problem-solving session, and/or technique presentation including interactive analysis using the facilities of the NINC. We encourage the use of MATLAB, ImageJ, Python, and LabView as well as cloud-based data storage/software archiving to facilitate sharing amongst labs.

13-March-2020 Predicting Task Outcomes From Mesoscale Brain Activity

Learn about modeling to predict task outcomes in Murphy lab automated imaging.

6-March-2020 Brain Functional Organization, Connectivity And Behaviour

Meeting Report.

28-February-2020 Dual-Modality Microfluidic-Based Calcium Imaging Setup In C. Elegans

Learn about a new rig being constructed in the Rankin lab.

21-February-2020 No Databinge Scheduled (Ubc Winter Break)

Time to hit the books (or slopes).

14-February-2020 Veta: An Open Source Tool For Combining Tms With Behavioural Tasks

Learn about this software

7-February-2020 Expansion Microscopy Update (Slides Included)

Update on current protocols and imaging results using expansion microscopy at UBC

Slide Presentation

31-January-2020 Github, Osf, And The Brain Circuits Cluster (Slides Included)

Review of the Dynamic Brain Circuits cluster resources and overview of activities in 2020.

Slide Presentation

6-December-2019 Pydynamo (Slides Included)

An open-source Python application for analyzing the dynamic morphometrics of neuronal arbors over time

Slide Presentation

29-November-2019 Postponed

Postponed due to TransLink Strike.

22-November-2019 Version Control With Git (Slides Included)

The basics of version control with git using GitKraken.

Slide Presentation

15-November-2019 Allen Institute Showcase Symposium Discussion (Slides Included)

Discussion about the Allen Institute Showcase Symposium held Nov. 11-12, 2019

Presentation 1

Presentation 2

Presentation 3

8-November-2019 Deeplabcut And Beyond (Slides Included)

DeepLabCut: “a software package for animal pose estimation”. A presentation about phase space analysis, motion mapper, and applications in neural encoding.

Slide Presentation

25-October-2019 No Presentation Scheduled (Sfn)

No presentation due to Society for Neuroscience (SfN) 2019.

18-October-2019 No Presentation Scheduled (Sfn)

No presentation due to Society for Neuroscience (SfN) 2019.

11-October-2019 Bioimage Informatics 2019 (Slides Included)

Report on BioImage Informatics 2019.

Slide Presentation

Notes

4-October-2019 Multiplexed Fluorescent In Situ Hybridization Assays

27-September-2019 Postponed

Postponed due to Climate Strike.

20-September-2019 Voltage Imaging (Slides Included)

Voltage imaging and report on the 2019 Frontiers in Neurophotonics Summer School.

Slide Presentation

13-September-2019 Cshl Statistical Methods For Functional Genomics (Slides Included)

Report on the CSHL Statistical Methods for Functional Genomics course.

Slide Presentation

6-September-2019 Jupyterhub (Slides Included)

Introduction to the new JupyterHub on the DMCBH computer cluster.

Slide Presentation

31-May-2019 Neurophotonics Raspberry Pi Preview (Slides Included)

Hands-on workshop with pis. To be presented at Neurophotonics Summer School in QC.

Slide Presentation

26-Apr-2019 Optical Sensors For Metabolism (Slides Included)

2-photon imaging.

Slide Presentation

18-Apr-2019 (Thursday) Mesoscale Calcium Imaging Analysis

calcium imaging analysis with Matlab.

5-Apr-2019 Jupyter & Binder (Slides Included)

Introduction to Python tools, Jupyter Notebook and Binder.

Slide Presentation

29-Mar-2019 Jess & The Simple Western Platform: Why You Should (Almost) Never Have To Perform A Traditional Western Blot Ever Again

Meeting Report.

22-Mar-2019 Designing And Using Advanced Multiphoton Imaging Systems In Neuroscience (Slides Included)

Meeting Report.

Slide Presentation

15-Mar-2019 Comprehensive Imaging (Slides Included)

Functional imaging of an entire neuron.

Slide Presentation

8-Mar-2019 Serial-Scanning Laser For High-Throughput Optogenetic Stimulation (Slides Included)

Opto for automatic experiments.

Slide Presentation

1-Mar-2019 Chips For Sub-Cellular Ca2+ Analysis (Slides Included)

Code for analyzing astrocyte calcium signals among other things.

Slide Presentation

8-Feb-2019 Berkeley Advanced Imaging Methods Workshop (Slides Included)

Meeting report.

Slide Presentation

30-November-2018 Fiber Photometry (Slides Included)

Learn about the Raymond lab’s new fiber photometry rig.

Slide Presentation

16-November-2018 Post Sfn Discussion

Share what amazed you most at SfN 2018.

9-November-2018 Deeplabcut (Slides Included)

Come learn about a new machine learning approach for movement tracking.

Slide Presentation

26-October-2018 Slap Microscope (Slides Included)

Come learn about a new approach for fast 2p imaging.

Slide Presentation

19-October-2018 Sql Database (Slides Included)

Come learn how to organize your data.

Slide Presentation

12-October-2018 Neural Networks (Slides Included)

Come join the discussion on artificial neural networks.

Slide Presentation

5-October-2018 Canadian Neurophotonics Platform (Slides Included)

Ellen Koch will tell us about the current state of neurophotonics and what she learned at the course in Laval last summer.

Slide Presentation

28-September-2018 Advanced Research Computing Resources At UBC (Slides Included)

Representatives from Advanced Research Computing at UBC will be joining us to talk about available High-Performance Computing and data storage resources available to researchers on campus at UBC and through WestGrid and Compute Canada.

Slide Presentation

21-September-2018 Imaging Structure And Function In The Nervous System- Highlights And Emerging Technologies (Slides Included)

Tristan Dellazizzo Toth will tell us about his experience at the Cold Spring Harbor course he took this summer.

Slide Presentation

More Info

16-Mar-2018 Janelia Meeting Report Frontiers In Microscopy Technologies (Slides Included)

Discussing an overview of the Janelia Spring Conference on Frontiers in Microscopy Technologies and Strategies for Bioimaging Centers Network.

Slide Presentation

09-Mar-2018 Mclust Spike Sorting (Slides Included)

Tetrode sorting using Mclust to improve sorting over single cells significantly as well as over stereotrodes.

Slide Presentation

02-Mar-2018 Minion Sequencing

MinION, the only portable real-time device for DNA and RNA sequencing

Not Available

23-Feb-2018 Video Rate Flim

Fluorescence lifetime imaging microscopy at video-rate speeds.

Not Available

16-Feb-2018 Crispr (Slides Included)

An overview of how CRISPR functions, its role and the possibilities that it opens.

Slide Presentation

02-Feb-2018 Gibson Cloning (Slides Included)

Joining fragments of DNA.

Slide Presentation

03-Nov-2017 Dreadds (Slides Included)

Designer Receptors Exclusively Activated by Designer Drugs.

Slide Presentation

20-Oct-2017 Illustrator/Inkscape (Slides Included)

Using software such as Inkscape and Illustrator to create vector graphics for figures.

Slide Presentation

13-Oct-2017 Blender (Slides Included)

A talk on the benefits of rendering for creating figures and basic understanding of algorithms to calculate pixel colour value.

Slide Presentation

02-Jun-2017 Summer Workshop On The Dynamic Brain (Slides Included)

An in-depth overview of the Summer Workshop on the Dynamic Brain

Slide Presentation

09-Jun-2017 Hpc (Slides Included)

Short tutorial on how to use linux/unix tools to run code on the centre’s new computer cluster

Slide Presentation

26-May-2017 The Shell (Slides Included)

The Unix Shell

Lesson

19-May-2017 Linux Survival Guide (Slides Included)

A guide on using Linux.

Slide Presentation

12-May-2017 Bayesian Stats (Slides Included)

A theory in which the evidence about the true state of the world is expressed in terms of “Degrees of Belief” know as Bayesian Probabilities.

Slide Presentation

28-Apr-2017 Stats Primer (Slides Included)

Basic statistical tests like the t test are used by almost all neuroscientists but how do they work and allow us to make inferences from our data? What are the assumptions? What are the differences between commonly used t tests?

ZIP with demo files and slide presentation

21-Apr-2017 Resamapling, Bootstrap, And Permutation Testing Part 2. (Slides Included)

A discussion of resampling techniques to estimate standard error and confidence intervals as well as do hypothesis testing. These methods are very useful for exploring your data and make few assumptions about the underlying distribution.

ZIP with demo files and slide presentation

07-Apr-2017 Resamapling, Bootstrap, And Permutation Testing Part 1. (Slides Included)

A discussion of resampling techniques to estimate standard error and confidence intervals as well as do hypothesis testing. These methods are very useful for exploring your data and make few assumptions about the underlying distribution.

ZIP with demo files and slide presentation

31-Mar-2017 Rstudio (Slides Included)

RStudio is a free and open-source IDE for R, a programming language for statistical computing and graphics.

ZIP with demo files and slide presentation

24-Mar-2017 Data Analysis (Slides Included)

A discussion of key guiding principles for any rigorous and honest data analysis. These principles were fueled by years of analyzing mostly behavioral and electrophysiology data, but should extend to all analyses. Topics include: Why Bayesian analyses are (now) awesome, why Frequentist analyses are useful, why Frequentist statistical philosophy is nonsense, and the critical importance of failure.

Slide Presentation

17-Mar-2017 Graph Theory (Slides Included)

Learn about how graphs can help you understand brain networks and how you can use computers to analyse the produced graphs.

Slide Presentation

10-Mar-2017 Aavs (Slides Included)

Adeno-Associated Virus!

Slide Presentation

03-Mar-2017 Computer Vision (Slides Included)

Crash course on Computer Vision.

ZIP with demo files and slide presentation

24-Feb-2017 Light Sheet Microscopy

Light Sheet Microscopy.

Not Available

17-Feb-2017 Gcamp (Slides Included)

Imaging brain activity with Calcium Imaging.

Slide Presentation

10-Feb-2017 Mouse Genetics (Slides Included)

Everything you wanted to know on mouse genetics.

Slide Presentation

03-Feb-2017 Machine Learning (Slides Included)

Machine Learning with MatLab.

ZIP with demo files and slide presentation

27-Jan-2017 Flim (Slides Included)

Fluorescence lifetime imaging microscopy.

Slide Presentation

20-Jan-2017 Spike Sorting

Sorting Spikes.

Not Available

09-Dec-2016 Deconvolution

Deconvolution. Sharpening images.

Not Available

02-Dec-2016 Lab View

Developing with Lab View.

Not Available

25-Nov-2016 Raspberry Pi (Slides Included)

Basics on Raspberry Pis and their Cameras.

ZIP with demo files and slide presentation

04-Nov-2016 Imagej Macros (Slides Included)

Simple ways to automate your image analysis using the indispensable ImageJ.

Slide Presentatioin

28-Oct-2016 3d Models With Solidworks (Slides Included)

Learn the basics of 3D modelling in Solidworks.

Slide Presentation

21-Nov-2016 App Development In Python (Slides Included)

Tips and tricks to building a scientific app using PyCharm.

Slide Presentation

14-Nov-2016 Mendeley And Ref Management (Slides Included)

How-to guide to manage papers and references with Mendeley.

Slide Presentation

07-Oct-2016 Git And Github (Slides Included)

Learn git for software version control.

Slide Presentation

30-Sep-2016 Animations And Illustrations

A discussion of different software (notably inkscape and blender) used to create animations for science communication.

23-Sep-2016 Intro To Databinge

Open to all UBC labs. Databinge is an interactive drop-in meeting for neuroscientists with the goal of furthering training and collaboration. Supported in part by the DMCBH and the Canadian Neurophotonics Platform, our goal is to promote collaboration, emphasise practical know-how via the use of UBC licensed and open-source software, and sharing of protocols. Each Friday we will have an open house in which interested labs can have a data show-and-tell, problem solving session, and/or technique presentation, including interactive analysis using the facilities of the NINC. We encourage the use of MatLab, ImageJ, Python, and LabView as well as cloud-based data storage/software archiving to facilitate sharing amongst labs. Located at Koerner F103, anyone interested can drop-in and experience Databinge. Presenters offer demo files to aid in the understanding of large topics, and pizza is handed out at 4:30pm every meeting.

9-Februrary-2024 Regular Databinge

 

2-Februrary-2024 Special Guest Dr. Eric Denovellis

Dr. Eric Denovellis from the Frank Lab at UCSF presented the neuroscience tools he built, such as the spectral connectivity package, ripple detection package, and state space replay classification package. He also shared his lessons learned from building neuroscience tools in the past, as his tips on good coding practices to ensure quality, efficiency, and longevity in software.

26-January-2024 Introductory Apptainer Presentation

Raina Cao and Hannah Cha gave an introductory presentation on the usage of Conda environments in Apptainer Containers, as well as container implementation on Compute Canada servers. The demo featured a tutorial on downloading an example brain slice image from the AllenSDK API. The presentation slides can be downloaded here.

19-January-2024 Special Guest Dr. Paul Cisek

Dr. Cisek from the University of Montreal gave a presentation on “Rethinking Behaviour in the Light of Evolution.” He introduced his research on phylogenetic refinement and the affordance competition hypothesis. A discussion was held afterwards on how his research impacts the field of neuroscience as a whole.

12-January-2024 Data Processing Workshop Discussion (First Databinge of 2024!)

Tutors and Dynamic Brain Circuits Cluster members held a discussion on possible neuroscience data processing packages to showcase for a data processing workshop before the 2024 CAN Meeting. Software brought up included the Cascade, pynapple, and neuromaps packages.

22-December-2023 Regular Databinge (Last Databinge of 2023!)

 

15-December-2023 Regular Databinge

 

8-December-2023 NRSC 510 Student Project Final Presentations

Students of NRSC 510 presented their final coding project over the course of the Fall 2023 semester, along with their trials, tribulations, and triumphs. The projects ranged from applying data analysis methods and using machine learning applications to creating an interactive database for tracking experiments.

1-December-2023 Regular Databinge

 

24-November-2023 Regular Databinge

 

17-November-2023 NRSC 510 Maryam Mirian Machine Learning Lecture

Maryam Mirian gave a lecture on ongoing work at Dr. Martin McKeown’s lab involving machine learning in Neuroscience for Parkinson’s Disease, introducing generative and discriminative computational models.

10-November-2023 NeuroAI Montreal 2023 Discussion

Parsa Delavari presented interesting topics on the use of AI in neuroscience from the NeuroAI meeting in Montreal. Discussions covered Dr. Paul Cisek’s affordance competition hypothesis and an upcoming machine learning framework for modelling neural activity dynamics across neural recordings.

3-November-2023 NRSC 510 Student Presentations

Students of the NRSC 510 course (“Topics in Neurodata”) presented updates regarding their coding projects for the course.

27-October-2023 Regular Databinge

 

20-October-2023 Regular Databinge

 

13-October-2023 Regular Databinge

 

6-October-2023 Regular Databinge

 

29-September-2023 Regular Databinge

 

22-September-2023 Regular Databinge

 

15-September-2023 Regular Databinge

 

8-September-2023 Special Guest Parsa Delavari

Parsa Delavari presented his ongoing computational neuroscience project at the Tim Murphy lab.

1-September-2023 Allen Institute Summer Workshop Dynamic Brain Course Discussion

Dr. Tim Murphy shared details from his trip to Friday Harbor to present at the Allen Institute Summer Workshop on the Dynamic Brain. The Allen Institute OpenScope project and generative adversarial networks (GANs) for brain imaging were notable topics. Details about the Allen Institute Summer Workshop 2023 can be found here.

25-August-2023 Regular Databinge

 

18-August-2023 Regular Databinge

 

11-August-2023 Special Guest Frederico Bolaños

Frederico Bolaños presented his PhD work on visual coding in mice, which can be read here.

Slides can be viewed here.

4-August-2023 Regular Databinge

 

28-July-2023 Regular Databinge

 

21-July-2023 Regular Databinge

 

14-July-2023 Regular Databinge

 

7-July-2023 NRSC 510 Discussion

Databinge Tutors discussed the current state and participation in the new NRSC 510 course (Topics in Neurodata), a project-driven class with an introduction to coding and an emphasis on working with data. This course will be first taught in Fall 2023.

30-June-2023 Canada Day Holiday Weekend (No Databinge)

 

23-June-2023 Special Guest David Buzorgnia

David Buzorgnia from Thrita Technologies Inc. will give a presentation on the company’s aims in developing a personalized computer model of the human brain. There may be internship opportunities through the Mitacs program for grad students and post doctoral researchers who are interested in working with the company to advance this field. View the presentation slides here.

16-June-2023 Regular Databinge

 

9-June-2023 Recap of UBC Psychiatry Research Day

Group members of the Murphy Lab discussed their favourite posters and presentations from UBC Psychiatry Research Day 2023.

26-May-2023 Special Guest James Mackay

Group discussion of the 16th Canadian Neuroscience meeting held the previous week in Montreal.

19-May-2023 Regular Databinge

 

12-May-2023 Regular Databinge

 

5-May-2023 Special Guest Dongsheng Xiao

Dongsheng Xiao presented his mesoscale generative adversarial network project (MesoGAN) to connect brain activity and behavior– details about the project here.

28-April-2023 Special Guest Ewa Zarnowska

Ewa Zarnowska from Coherent Laser presented her current work involving functional brain studies using multiphoton microscopy and Coherent Corp. Multiphoton Lasers.

21-April-2023 Regular Databinge

 

14-April-2023 Project Pedaling Parkinson

Zahra Alizadeh presented an update on Project Pedaling Parkinson, looking at the effects of cycling on EEG and EMG scans of Parkinson patients. View the presentation slides here.

7-April-2023 Good Friday Holiday (No Databinge)

 

31-March-2023 Special Databinge with UBC ARC

Please join us at 12:00 pm on Friday, March 31 for a special Databinge workshop with UBC ARC and BCCHRI Trainee Omics Group.  Learn how to move your R based research project from your personal computer to High Performance Computing (HPC) cluster e.g. UBC Sockeye. No registration required!

24-March-2023 LLMs for Brain Health 2023 Hackathon

The virtual kick-off for the LLMs for Brain Health 2023 Hackathon took place during Databinge hours. Participants were invited to explore the potential of ChatGPT and other large language models (LLMs) to aid work in brain health.

To view project submissions, click here

17-March-2023 Magic Mirror Project

Maryam Mirian and Jalil Alizadeh presented their work on the Magic Mirror Project.

10-March-2023 Peter Hogg Presentation

Peter Hogg from the Murphy Lab discussed his visit to the Allen Institute and how it is helping with his progress on the SLAP2 microscope that is being built at UBC.

3-March-2023 Report on the Nemonic Multiphoton Course

Nicholas Michelson, Pankaj Gupta, and Tony Fong from the Murphy Lab reported on the Nemonic Multiphoton Course.

24-February-2023 Getting the Most Out Of Your Computer

Group discussion on how to get the most out of your computer.

17-February-2023 Project Eyetracker Analysis Update

Fiza Arshad provided an update on her eyetracker analysis project at Databinge.

10-February-2023 Special Guest Walter Sena

Walter Sena, NeuroCog founder and post doctorate fellow at UBC Psychiatry, shared his ideas for predicting cognitive decline using objective measurements from remote eye-tracking and deep learning.

3-February-2023 Special Guest Pankaj Gupta

Pankaj Gupta from the Murphy Lab shared his experience at the UWashington Centre Neuroscience Center Datathon event with new data from the Allen Institute and updated us on his RNN project.

27-January-2023 Special Databinge with Eugene Barsky (Return of Databinge for 2023!)

Please join us at Databinge on Jan 27th for “Data Deposit Basics” with Eugene Barsky. Eugene is the UBC Library’s Research Data Management Librarian and he will cover file naming, folder structures, README files, metadata, PIDs, Data Management Plans and FAIR principles.

9-December-2022 Project Pedaling Presentation (Last Databinge of 2022!)

Presentation on #project-pedaling-parkinson by Zahra Alizadeh, Maryam Mirian, and Matt Sacheli.

2-December-2022 Regular Databinge

 

25-November-2022 Special Databinge with Jeff Clune

Jeff Clune, from UBC Computer Science, will discussed his lab’s computer vision work. Prof Clune’s talk will focus on his lab’s project in identifying, counting and describing animals in the wild with deep learning. You can read more here: https://pubmed.ncbi.nlm.nih.gov/29871948/

18-November-2022 Recap of Society for Neuroscience

Members of the Murphy Lab gave recaps of their favourite posters from SFN 2022.

11-November-2022 Remembrance Day (No Databinge)

 

4-November-2022 Best Practices in Teaching and Learning of Programming and Data Science

Group Discussion on best practices in teaching and learning of programming and data science.

28-October-2022 Special Guest Rochelin Dalangin

Rochelin Dalangin presented on the Canadian Vectorology and Optogenetics Foundry https://neurophotonics.ca/canadian-optogenetics-vectorology-foundry

21-October-2022 Thanksgiving Holiday (No Databinge)

 

14-October-2022 Special Guest Prof Randy McIntosh

Prof Randy McIntosh (SFU) https://www.sfu.ca/sfunews/stories/2022/01/prominent-neuroscientist-to-advance-brain-research-through-new-s.html discussed how we can get involved with the International Neuroinformatics Coordinating Facility (https://www.incf.org).

7-October-2022 SFARI and NeuroAI Reports

William Casazza presented on SFARI (https://www.sfari.org/event/in-search-of-causality-from-neuropsychiatric-genetics-to-pathophysiology/). Tony Fong and Edward Yan presented on interesting tools that they saw at NeuroAI in Seattle.

30-September-2022 National Truth and Reconciliation Day (No Databinge)

 

23-September-2022 Special Databinge with University of Oregon

Luca Mazzucato, Lia Papadopoulos, Daniel Hulsey from the University of Oregon (Eugene) presented on their BRAIN Initiative funded collaborative project.

16-September-2022 Special Guest Pankaj Gupta

Pankaj Gupta from the Murphy Lab presented his experience as a TA at the “Summer Workshop on the Dynamic Brain” which is offered by UW/Allen Institute each year in Friday Harbor.

9-September-2022 Special Guest Hannah Reid

Neurotutor Hannah Reid presented on the ImageJ macro she had been developing for quantifying microglia.

2-September-2022 Cross-Validated CPCA in Python Presentation

Hosted by Abhijit Chinchani. His lab mate Brian presented on a cross validated CPCA that he had implemented in Python. The Jupyter notebook available on GitHub.

26-August-2022 Themed Discussion: Exploratory Data Analysis and Data Visualization

Group discussion on approaches to exploratory data analysis and data visualization.

19-August-2022 Themed Discussion: Fluorescence Microscopy, Tissue Clearing and Expansion

Group discussion on Fluorescence microscopy, tissue clearing and expansion. Peter Hogg presented on his experiences on his trip to New York (Cold Spring).

12-August-2022 Themed Discussion: Omics, Sequencing Data, and Analysis

Group discussion on Omics and sequencing data and analysis. Nikita Telkar presented on her experience at the RStudio conference she attended and gave a brief recap on the Precision Health Analysis Bootcamp. 

5-August-2022 Themed Discussion: Fluorescence Microscopy, Tissue Clearing, and Expansion

Group discussion on Fluorescence microscopy, tissue clearing and expansion. Mehwish Anwer presented on quantifying cleared brain tissue, including the results she received from LifeCanvas Technologies, and how we might validate and reproduce these numbers with brainquant3d (https://github.com/sunilgandhilab/brainquant3d) and/or SMART (https://sgoldenlab.github.io/SMART/index.html).

29-July-2022 Themed Discussion: Omics, Sequencing Data, and Analysis

Group discussion on Omics and sequencing data and analysis. Jenn Kim presented on her experience at the Cold Spring Harbor Labs course titled “Statistical Analysis for Genome Scale Data”. https://meetings.cshl.edu/courses.aspx?course=C-data&year=22

22-July-2022 Themed Discussion: Fluorescence Microscopy, Tissue Clearing, and Expansion

Group discussion on Fluorescence microscopy, tissue clearing and expansion. Tony Fong shared his experiences at the Neurophotonics Summer School in Quebec City.

15-July-2022 Themed Discussion: Human Neuroimaging, EEG, and Brain Stimulation

Group discussion on human neuroimaging, EEG, and brain stimulation. Abhijit Chinchani presented on what he saw in Glasgow at the human brain mapping conference.

8-July-2022 Themed Discussion: Packages for Exploring Big Data

Group discussion on packages for exploring big data.

1-July-2022 Canada Day Holiday (No Databinge)

 

24-June-2022 Themed Discussion: Choice of Coding Languages for Beginners

Group discussion on choice of coding languages for beginners.

17-June-2022 Themed Discussion: Fluorescence Microscopy, Tissue Clearing, and Expansion

Group discussion on Fluorescence microscopy, tissue clearing and expansion. Mathias Delhaye and Sarah Ebert provided updates on the latest developments of their projects.

10-June-2022 Data Champions Databinge Showcase

 

3-June-2022 Themed Discussion: Planning Experiments, Effect Sizes, and Power Calculations

Group discussion on planning experiments, effect sizes, power calculations. Sarah Wang and Gale Chen, cluster Co-op students, presented what they have learned so far about using Datajoint: https://www.datajoint.org

27-May-2022 Themed Discussion: Omics, Sequencing Data, and Analysis

Group discussion on Omics and sequencing data and analysis. William Casazza and Nikita Telkar presented updates on the differential methylation analysis tutorial they were developing.

20-May-2022 Themed Discussion: Machine Learning, Computer Vision, Data Analysis

Group discussion on machine learning, computer vision, and data analysis.

13-May-2022 Themed Discussion: Human Neuroimaging, EEG, and Brain Stimulation

Group discussion on human neuroimaging, EEG, and brain stimulation.

6-May-2022 Regular Databinge

 

29-April-2022 Med Student FLEX Project

Presentation on the med student FLEX project.

22-April-2022 Diesel2p Ultrawide FOV Scope Building

Dale showed the diesel2p ultrawide field of view 2-photon scope being built.

15-April-2022 Good Friday Holiday (No Databinge)

 

8-April-2022 Regular Databinge

 

1-April-2022 Regular Databinge

 

25-March-2022 Regular Databinge

 

18-March-2022 Regular Databinge

 

11-March-2022 Regular Databinge

 

4-March-2022 Regular Databinge

 

25-February-2022 Regular Databinge

 

18-February-2022 Regular Databinge

 

11-February-2022 Special Guest Mehwish Anwer

Mehwish Anwer, a postdoc in the Wellington Lab, shared progress and challenges for tissue clearing analysis.

4-February-2022 Regular Databinge

 

28-January-2022 Regular Databinge

 

21-January-2022 Special Guest Angus Campbell

Angus Campbell presented a paper on using all open public datasets.

14-January-2022 Regular Databinge (Return of Databinge for 2022!)

 

17-December-2021 Regular Databinge (Last Databinge of 2021!)

 

10-December-2021 Studying Differences in EEG Forecasting for Parkinson’s Fisease Patients vs Healthy Controls Using Dynamic Mode Decomposition

Maryam Mirian and Abhijit Chinchani presented on studying differences in EEG forecasting for Parkinson’s disease patients vs healthy controls using Dynamic Mode Decomposition.

3-December-2021 Regular Databinge

 

26-November-2021 Regular Databinge

 

19-November-2021 Regular Databinge

 

12-November-2021 Regular Databinge

 

5-November-2021 Regular Databinge

 

29-October-2021 Regular Databinge

 

22-October-2021 Regular Databinge

 

15-October-2021 Regular Databinge

 

8-October-2021 Regular Databinge

 

1-October-2021 Regular Databinge

 

24-September-2021 Regular Databinge

 

17-September-2021 Regular Databinge

 

11-September-2021 Calcium Imaging Data Processing Pipeline

Sam and Majid from the University of Lethbridge will join Databinge on Sept 11 to go over the pipeline they are employing to process calcium imaging data from in vivo two-photon microscopy. 

Their pipeline will make use of the Suite2p pipeline created by the Howard Hughes Medical Institute. More information on Suite2p can be found at https://github.com/MouseLand/suite2p

10-September-2021 Regular Databinge

 

3-September-2021 Regular Databinge

 

27-August-2021 Regular Databinge

 

20-August-2021 Regular Databinge