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 (jledue@mail.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
Regular Databinge (First Databinge of 2025!)
NRSC510 Student Project Final Presentations
Students in NRSC 510 unveiled their final coding projects, reflecting on the obstacles they faced, the lessons they learned, and the milestones they achieved over the course of the Fall 2024 semester. Their innovative work encompassed diverse areas, such as implementing data analysis strategies, leveraging machine learning tools, and designing interactive systems for managing experimental data.
Regular Databinge
Regular Databinge (Last Databinge of 2024!)
NRSC510 Student Update Presentations
Students of the NRSC 510 course presented updates regarding their coding projects for the course.
Regular Databinge + NRSC510
Regular Databinge + NRSC510
Regular Databinge + NRSC510
Regular Databinge + NRSC510
Regular Databinge + NRSC510
Regular Databinge + NRSC510
Regular Databinge + NRSC510
Regular Databinge + NRSC510
Regular Databinge + NRSC510
Regular Databinge + NRSC510
Regular Databinge + NRSC510
Regular Databinge + NRSC510
Regular Databinge
Regular Databinge
Regular Databinge
Regular Databinge
Regular Databinge
Regular Databinge
Special Guest Daniel Ramandi
Special Guest graduate student Daniel Ramandi shared highlights from the FENS Forum 2024.
Special Guest Vivian Zhu
Special Guest graduate student Vivian Zhu gave a presentation QuPath, an open software project for bioimage analysis.
Regular Databinge
Special Guest Dr. Eric Denovellis
Dr. Eric Denovellis from the Frank Lab at UCSF consulted on the application of his state space replay classification package to the International Brain Laboratory dataset.
Regular Databinge
Regular Databinge
Regular Databinge
Regular Databinge
Regular Databinge
Regular Databinge
Regular Databinge
Regular Databinge
Code Sharing Discussion
Neurodata Tutor Adrian released his HUB-DT software that simultaneously tracks electrophysiology data and behavioural data. He also presented a study using HUB-DT to look at Parkinson’s patients’ hand movements.
Code Sharing Discussion
NINC Data Analysis Supporter Federico Bolaños presented his initial 2-photon microscopy image restoration using Deep Interpolation. Neurodata tutors suggested data caching/pickling techniques to reduce data processing time.
Regular Databinge
Special Guest Parsa Delavari
Special Guest graduate student Parsa Delavari presented his project on building a computational model of functional connectivity with comparisons to NeuPRINT.
Easter Long Weekend (No Databinge)
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.
Regular Databinge
Special Guest Dr. Kyu Hyun Lee
Dr. Lee from the Frank lab at the University of California San Francisco presented Spyglass, a program used at the Frank Lab to organize and share collected data in the Neurodata Without Borders standard.
Regular Databinge
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.
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.
View the presentation slides here.
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.
Regular Databinge
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.
Regular Databinge
Regular Databinge (Last Databinge of 2023!)
NRSC 510 Student Presentations
Students of the NRSC 510 course (“Topics in Neurodata”) presented updates regarding their coding projects for the course.
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.
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 forParkinson’s Disease, introducing generative and discriminative computational models.
Regular Databinge
Regular Databinge
Regular Databinge
Regular Databinge
Regular Databinge
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.
Special Guest Parsa Delavari
Parsa Delavari presented his ongoing computational neuroscience project at the Tim Murphy lab.
Regular Databinge
Regular Databinge
Regular Databinge
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.
Regular Databinge
Regular Databinge
Regular Databinge
Recap of UBC Psychiatry Research Day
Group members of the Murphy Lab discussed their favourite posters and presentations from UBC Psychiatry Research Day 2023.
Regular Databinge
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.
Canada Day Holiday Weekend (No Databinge)
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.
Regular Databinge
Regular Databinge
Special Guest James Mackay
Group discussion of the 16th Canadian Neuroscience meeting held the previous week in Montreal.
Good Friday Holiday (No Databinge)
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.
Regular Databinge
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.
Report on the Nemonic Multiphoton Course
Nicholas Michelson, Pankaj Gupta, and Tony Fong from the Murphy Lab reported on the Nemonic Multiphoton Course.
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.
Magic Mirror Project
Maryam Mirian and Jalil Alizadeh presented their work on the Magic Mirror Project.
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
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!
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.
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.
Project Eyetracker Analysis Update
Fiza Arshad provided an update on her eyetracker analysis project at Databinge.
Getting the Most Out Of Your Computer
Group discussion on how to get the most out of your computer.
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.
Regular Databinge
Project Pedaling Presentation (Last Databinge of 2022!)
Presentation on #project-pedaling-parkinson by Zahra Alizadeh, Maryam Mirian, and Matt Sacheli.
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.
Remembrance Day (No Databinge)
Recap of Society for Neuroscience
Members of the Murphy Lab gave recaps of their favourite posters from SFN 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/
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.
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).
Thanksgiving Holiday (No Databinge)
Special Guest Rochelin Dalangin
Rochelin Dalangin presented on the Canadian Vectorology and Optogenetics Foundry https://neurophotonics.ca/canadian-optogenetics-vectorology-foundry
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.
Special Guest Hannah Reid
Neurotutor Hannah Reid presented on the ImageJ macro she had been developing for quantifying microglia.
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.
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.
National Truth and Reconciliation Day (No Databinge)
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).
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.
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).
Themed Discussion: Exploratory Data Analysis and Data Visualization
Group discussion on approaches to exploratory data analysis and data visualization.
Canada Day Holiday (No Databinge)
Themed Discussion: Packages for Exploring Big Data
Group discussion on packages for exploring big data.
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.
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.
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
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
Data Champions Databinge Showcase
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.
Themed Discussion: Choice of Coding Languages for Beginners
Group discussion on choice of coding languages for beginners.
Regular Databinge
Themed Discussion: Human Neuroimaging, EEG, and Brain Stimulation
Group discussion on human neuroimaging, EEG, and brain stimulation.
Themed Discussion: Machine Learning, Computer Vision, Data Analysis
Group discussion on machine learning, computer vision, and data analysis.
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.
Regular Databinge
Regular Databinge
Good Friday Holiday (No Databinge)
Diesel2p Ultrawide FOV Scope Building
Dale showed the diesel2p ultrawide field of view 2-photon scope being built.
Med Student FLEX Project
Presentation on the med student FLEX project.
Regular Databinge
Regular Databinge
Regular Databinge
Regular Databinge
Regular Databinge
Special Guest Mehwish Anwer
Mehwish Anwer, a postdoc in the Wellington Lab, shared progress and challenges for tissue clearing analysis.
Regular Databinge
Regular Databinge
Regular Databinge (Return of Databinge for 2022!)
Special Guest Angus Campbell
Angus Campbell presented a paper on using all open public datasets.
Regular Databinge
Regular Databinge
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.
Regular Databinge (Last Databinge of 2021!)
Regular Databinge
Regular Databinge
Regular Databinge
Regular Databinge
Regular Databinge
Regular Databinge
Regular Databinge
Regular Databinge
Regular Databinge
Regular Databinge
Regular Databinge
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
Calcium Imaging Data Processing Pipeline
Sam and Majid from the University of Lethbridge will join Databingeon 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
Regular Databinge
Regular Databinge
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 studyand disseminationof 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 developthe concept foran app,software tool, or programthat will aid the mission of the BC Brain Wellness Program.
For more information on the event, click here
To view project submissions, click here
Regular Databinge
Regular Databinge
iDISCO
A tool/procedure for rapid immunolabeling and volume imaging of biological samples
More information can be found here
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.
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.
Special Guest Edward Yan
Edward Yan from the Murphy lab will be presenting his work on Neuropixel probes and high-density recording.
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.
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
TDT Fiber Photometry Workshop
Fiber photometry is a calcium imaging method for detecting neural activity.
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.
Mathworks
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.
Brain Functional Organization, Connectivity And Behaviour
Meeting Report.
Predicting Task Outcomes From Mesoscale Brain Activity
Learn about modeling to predict task outcomes in Murphy lab automated imaging.
Expansion Microscopy Update (Slides Included)
Update on current protocols and imaging results using expansion microscopy at UBC
Slide Presentation
No Databinge Scheduled (Ubc Winter Break)
Time to hit the books (or slopes).
Dual-Modality Microfluidic-Based Calcium Imaging Setup In C. Elegans
Learn about a new rig being constructed in the Rankin lab.
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
Pydynamo (Slides Included)
An open-source Python application for analyzing the dynamic morphometrics of neuronal arbors over time
Slide Presentation
Sfn Recap (Slides Included)
Presentations by Society for Neuroscience (SfN) 2019 attendees:
3-photon
Interneuron diversity
Flexible electrodes
New neurotransmitter sensors
DeepLabCut and MotionMapper
DeepLabCut and MotionMapper
Hailan Hu lecture and PFC/ACC in social interaction
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
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
Version Control With Git (Slides Included)
The basics of version control with git using GitKraken.
Slide Presentation
Postponed
Postponed due to TransLink Strike.
Multiplexed Fluorescent In Situ Hybridization Assays
Bioimage Informatics 2019 (Slides Included)
Report on BioImage Informatics 2019.
Slide Presentation
Notes
No Presentation Scheduled (Sfn)
No presentation due to Society for Neuroscience (SfN) 2019.
No Presentation Scheduled (Sfn)
No presentation due to Society for Neuroscience (SfN) 2019.
Jupyterhub (Slides Included)
Introduction to the new JupyterHub on the DMCBH computer cluster.
Slide Presentation
Cshl Statistical Methods For Functional Genomics (Slides Included)
Report on the CSHL Statistical Methods for Functional Genomics course.
Slide Presentation
Voltage Imaging (Slides Included)
Voltage imaging and report on the 2019 Frontiers in Neurophotonics Summer School.
Slide Presentation
Postponed
Postponed due to Climate Strike.
Neurophotonics Raspberry Pi Preview (Slides Included)
Hands-on workshop with pis. To be presented at Neurophotonics Summer School in QC.
Slide Presentation
Jupyter & Binder (Slides Included)
Introduction to Python tools, Jupyter Notebook and Binder.
Slide Presentation
Mesoscale Calcium Imaging Analysis
calcium imaging analysis with Matlab.
Chips For Sub-Cellular Ca2+ Analysis (Slides Included)
Code for analyzing astrocyte calcium signals among other things.
Slide Presentation
Serial-Scanning Laser For High-Throughput Optogenetic Stimulation (Slides Included)
Opto for automatic experiments.
Slide Presentation
Comprehensive Imaging (Slides Included)
Functional imaging of an entire neuron.
Slide Presentation
Designing And Using Advanced Multiphoton Imaging Systems In Neuroscience (Slides Included)
Meeting Report.
Slide Presentation
Jess & The Simple Western Platform: Why You Should (Almost) Never Have To Perform A Traditional Western Blot Ever Again
Meeting Report.
Deeplabcut (Slides Included)
Come learn about a new machine learning approach for movement tracking.
Slide Presentation
Post Sfn Discussion
Share what amazed you most at SfN 2018.
Fiber Photometry (Slides Included)
Learn about the Raymond lab’s new fiber photometry rig.
Slide Presentation
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
Neural Networks (Slides Included)
Come join the discussion on artificial neural networks.
Slide Presentation
Slap Microscope (Slides Included)
Come learn about a new approach for fast 2p imaging.
Slide Presentation
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
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
Raspberry Pi Tutorial (Slides Included)
A presentation of general input-output control with a raspberry pi for experimental setups. https://github.com/jamieboyd/neurophoto2018
Slide Presentation
Minion Sequencing
MinION, the only portable real-time device for DNA and RNA sequencing
Not Available
Mclust Spike Sorting (Slides Included)
Tetrode sorting using Mclust to improve sorting over single cells significantly as well as over stereotrodes.
Slide Presentation
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
Crispr (Slides Included)
An overview of how CRISPR functions, its role and the possibilities that it opens.
Slide Presentation
Dreadds (Slides Included)
Designer Receptors Exclusively Activated by Designer Drugs.
Slide Presentation
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
Illustrator/Inkscape (Slides Included)
Using software such as Inkscape and Illustrator to create vector graphics for figures.
Slide Presentation
Summer Workshop On The Dynamic Brain (Slides Included)
An in-depth overview of the Summer Workshop on the Dynamic Brain
Slide Presentation
Hpc (Slides Included)
Short tutorial on how to use linux/unix tools to run code on the centre’s new computer cluster
Slide Presentation
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
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
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
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
Computer Vision (Slides Included)
Crash course on Computer Vision.
ZIP with demo files and slide presentation
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
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
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
Machine Learning (Slides Included)
Machine Learning with MatLab.
ZIP with demo files and slide presentation
Mouse Genetics (Slides Included)
Everything you wanted to know on mouse genetics.
Slide Presentation
Imagej Macros (Slides Included)
Simple ways to automate your image analysis using the indispensable ImageJ.
Slide Presentatioin
Mendeley And Ref Management (Slides Included)
How-to guide to manage papers and references with Mendeley.
Slide Presentation
App Development In Python (Slides Included)
Tips and tricks to building a scientific app using PyCharm.
Slide Presentation
Raspberry Pi (Slides Included)
Basics on Raspberry Pis and their Cameras.
ZIP with demo files and slide presentation
3d Models With Solidworks (Slides Included)
Learn the basics of 3D modelling in Solidworks.
Slide Presentation
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.
Animations And Illustrations
A discussion of different software (notably inkscape and blender) used to create animations for science communication.