- 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.
Data Champions Databinge:
- Time: 12:30pm each Friday
- Location: Online using Zoom
With Support from the Digital Alliance we have expanded Databinge as an online meeting to tackle coding and new approaches to data analysis while promoting sound Research Data Management Practice which supports our collaborations and Open Science Practices. The team, spanning the Centre for Brain Health, BCCHRI, ICORD and UVic, will be online via slack and zoom to discuss points of interest in detail and provide focused help. Contact a tutor (see bios here) via email for slack invites and zoom addresses. We recommend labs prep OSF projects in order to share data and code. Info on using OSF can be found here.
Databinge Recommendations on Exploratory Data Analysis and Visualization
At Databinge on Aug 26, 2022 we had a group discussion on best practices for Exploratory Data Analysis and Visualization. What follows below is a summary of the key points. Taken together these practices will:
- Save you time and frustration in conducting your current and future research projects and completing your program.
- Support (computational) reproducibility.
- Support the review process when it is time to publish results.
- Support the adoption of Open Science.
Initial Data Quality Control: Think about where you are in the data processing and analysis pipeline. This spans acquisition to raw data to processed data and all subsequently derived measures. What is the raw data that you have obtained? It might differ from project to project.
- Do initial quality control checks as close to the acquisition of the raw data as possible. Investing time and effort at this stage will mean fewer downstream doubts and follow-up experiments and an overall stronger conclusions later. You will be confident that the rest of your analysis pipeline will have the best possible input.
- Read through several literature sources and work through tutorials that use the quality control measures that you are thinking of applying to your data. You might decide that different sections from different pipelines suit your data and project the best; it’s always good to have a well-rounded understanding of the possible steps that you could apply (but don’t necessarily have to).
Sanity Checks and checkpoints: Try to establish steps in your pipeline where you can look for signatures indicating that the previous steps worked as intended. This could be accomplished by:
- Examining one subject in depth in a multi-subject study
- Having positive and negative controls
- By using a high-quality open data set as input in addition to your own data
Record your steps and your code: Using your method of choice (e.g. code versioning on GitHub, ImageJ macro recorder, Slack channels, note taking software, or your lab book) ensure that you know the steps you took to arrive at your visualizations. Exploring necessitates trying different ways to reach the best possible visualization, most of which will go nowhere, in a short time. It is easy to lose track and it can be frustrating to not be able to reproduce something potentially exciting. Be as comprehensive in the annotation of your steps as possible – someone with zero knowledge of your data or script should be able to at least get an idea of the steps you have taken (even if they don’t understand all of the theoretical underpinning).
Tools: The tools of choice depend on what data you are working with and, like the choice of programming languages, are often driven by what your research community routinely uses. Options include Jupyter notebooks, R Markdown, MATLAB scripts, ImageJ macros, Napari, Open Science Framework and many more. Certain software packages only work in specific programming languages. Databinge is a great forum to discuss the pros and cons of tools with people actively using them.
Community Advice on Data Presentation: Think about how you would like to show the data in presentations, papers and your thesis early on: the earlier, the better. It is tempting to plot a lot of data when exploring but often simpler plots are needed to succinctly convey your message to others. Get other researchers to look at your plots to see if you are conveying what you intend. Additionally, do not underestimate the power of the visual impact of your data. Spend a little time coordinating a colour palette that ties-in the overall experience of your poster or presentation. Often, it is helpful to have someone who is not deeply familiar with your work look at your visualizations as they will not have made the same assumptions as you or someone more familiar may have. This could be a lab member or through a forum like Databinge.
A programmatic approach: In tandem with feedback on your data presentation, work on a programmatic approach (e.g. macros, shiny apps, versioned Jupyter notebooks) to streamline the process of creating your visualizations. This will save lots of time and ensure you treat each piece of data the same. Strive for code that fails elegantly (e.g. warns you when the data input is not as expected).
9-June-2023 Regular Databinge
2-June-2023 CAN Meeting Recap
Group discussion of the 16th Canadian Neuroscience meeting held the previous week in Montreal.
26-May-2023 Special Guest James Mackay
James Mackay discussed his experiments in HD mice that he is interested in modelling computationally, possibly with the virtual brain
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
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. View the slides, code, and workshop recording here.
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. View the slides here.
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.
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.
20-October-2020 TDT Fiber Photometry Workshop
Fiber photometry is a calcium imaging method for detecting neural activity.
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.
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
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
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.
6-December-2019 Pydynamo (Slides Included)
An open-source Python application for analyzing the dynamic morphometrics of neuronal arbors over time
Postponed due to TransLink Strike.
22-November-2019 Version Control With Git (Slides Included)
The basics of version control with git using GitKraken.
15-November-2019 Allen Institute Showcase Symposium Discussion (Slides Included)
Discussion about the Allen Institute Showcase Symposium held Nov. 11-12, 2019
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.
1-November-2019 Sfn Recap (Slides Included)
Presentations by Society for Neuroscience (SfN) 2019 attendees:
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.
4-October-2019 Multiplexed Fluorescent In Situ Hybridization Assays
Postponed due to Climate Strike.
20-September-2019 Voltage Imaging (Slides Included)
Voltage imaging and report on the 2019 Frontiers in Neurophotonics Summer School.
13-September-2019 Cshl Statistical Methods For Functional Genomics (Slides Included)
Report on the CSHL Statistical Methods for Functional Genomics course.
6-September-2019 Jupyterhub (Slides Included)
Introduction to the new JupyterHub on the DMCBH computer cluster.
31-May-2019 Neurophotonics Raspberry Pi Preview (Slides Included)
Hands-on workshop with pis. To be presented at Neurophotonics Summer School in QC.
26-Apr-2019 Optical Sensors For Metabolism (Slides Included)
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.
29-Mar-2019 Jess & The Simple Western Platform: Why You Should (Almost) Never Have To Perform A Traditional Western Blot Ever Again
22-Mar-2019 Designing And Using Advanced Multiphoton Imaging Systems In Neuroscience (Slides Included)
15-Mar-2019 Comprehensive Imaging (Slides Included)
Functional imaging of an entire neuron.
8-Mar-2019 Serial-Scanning Laser For High-Throughput Optogenetic Stimulation (Slides Included)
Opto for automatic experiments.
1-Mar-2019 Chips For Sub-Cellular Ca2+ Analysis (Slides Included)
Code for analyzing astrocyte calcium signals among other things.
8-Feb-2019 Berkeley Advanced Imaging Methods Workshop (Slides Included)
30-November-2018 Fiber Photometry (Slides Included)
Learn about the Raymond lab’s new fiber photometry rig.
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.
26-October-2018 Slap Microscope (Slides Included)
Come learn about a new approach for fast 2p imaging.
19-October-2018 Sql Database (Slides Included)
Come learn how to organize your data.
12-October-2018 Neural Networks (Slides Included)
Come join the discussion on artificial neural networks.
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.
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.
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.
08-June-2018 Raspberry Pi Tutorial (Slides Included)
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.
09-Mar-2018 Mclust Spike Sorting (Slides Included)
Tetrode sorting using Mclust to improve sorting over single cells significantly as well as over stereotrodes.
02-Mar-2018 Minion Sequencing
MinION, the only portable real-time device for DNA and RNA sequencing
23-Feb-2018 Video Rate Flim
Fluorescence lifetime imaging microscopy at video-rate speeds.
16-Feb-2018 Crispr (Slides Included)
An overview of how CRISPR functions, its role and the possibilities that it opens.
02-Feb-2018 Gibson Cloning (Slides Included)
Joining fragments of DNA.
17-Nov-2017 Sfn Tech Pitch
$50 Starbucks gift card to best SFN tech pitch (other than Deisseroth or Boyden labs since we all know how great they are), $25 for the second place. 5 minutes max, no slides only talking and whiteboard, at least 5 pitches lined up for a contest to occur.
03-Nov-2017 Dreadds (Slides Included)
Designer Receptors Exclusively Activated by Designer Drugs.
20-Oct-2017 Illustrator/Inkscape (Slides Included)
Using software such as Inkscape and Illustrator to create vector graphics for figures.
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.
02-Jun-2017 Summer Workshop On The Dynamic Brain (Slides Included)
An in-depth overview of the Summer Workshop on the Dynamic Brain
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
26-May-2017 The Shell (Slides Included)
The Unix Shell
19-May-2017 Linux Survival Guide (Slides Included)
A guide on using Linux.
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.
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?
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.
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.
31-Mar-2017 Rstudio (Slides Included)
RStudio is a free and open-source IDE for R, a programming language for statistical computing and graphics.
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.
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.
10-Mar-2017 Aavs (Slides Included)
03-Mar-2017 Computer Vision (Slides Included)
Crash course on Computer Vision.
24-Feb-2017 Light Sheet Microscopy
Light Sheet Microscopy.
17-Feb-2017 Gcamp (Slides Included)
Imaging brain activity with Calcium Imaging.
10-Feb-2017 Mouse Genetics (Slides Included)
Everything you wanted to know on mouse genetics.
03-Feb-2017 Machine Learning (Slides Included)
Machine Learning with MatLab.
27-Jan-2017 Flim (Slides Included)
Fluorescence lifetime imaging microscopy.
20-Jan-2017 Spike Sorting
Deconvolution. Sharpening images.
02-Dec-2016 Lab View
Developing with Lab View.
25-Nov-2016 Raspberry Pi (Slides Included)
Basics on Raspberry Pis and their Cameras.
04-Nov-2016 Imagej Macros (Slides Included)
Simple ways to automate your image analysis using the indispensable ImageJ.
28-Oct-2016 3d Models With Solidworks (Slides Included)
Learn the basics of 3D modelling in Solidworks.
21-Nov-2016 App Development In Python (Slides Included)
Tips and tricks to building a scientific app using PyCharm.
14-Nov-2016 Mendeley And Ref Management (Slides Included)
How-to guide to manage papers and references with Mendeley.
07-Oct-2016 Git And Github (Slides Included)
Learn git for software version control.
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.