Databinge

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.

Upcoming databinges

7-December-2018 Automated Cage Behavioral Assessment in Mice

                Cameron Woodard will present on the task he has created for assessing motor control in Mice using an automated, home-cage based setup.

Automated Cage System







 

 

 

 

Past Databinges

30-November-2018 Fiber Photometry Using TDT and Doric Components

                Ellen Koch from Lynn Raymond's lab will tell us about their new setup for fiber photometry in rodents, (and possibly about their early experiments with Huntington's mice).

TDT fiber Photometry

slides







 

 

 

 

9-November-2018 Deep Lab Cut

                Brandon Forys will present on the Deep Lab Cut algorithm for tracking animal motion and his work adapting it to relate mouse behavior to meso-scale brain activity.

DeepLabCut







 

 

 

 

26-October-2018 SLAPMi

                Patrick Coleman from Kurt Haas's lab will present about SLAPMI, a new microscope design by former lab member Kaspar Podgorski.

SLAPMi?







 

 

 

 

19-October-2018 Databases with SQL

                David Bierbrauer (again!) from Tim Murphy’s lab will tell us about building databases using SQL for storing experimental Metadata associated with primary data sets. This approach will allow you to: Keep track of all your research data; Rapidly search and group data along any metadata grouping that makes sense (i.e. all male subjects, all female subjects, All Male Subjects on the third trial, etc); Export and import data from the database easily using Python; and build online databases with convenient Javascript integration.

Slides

SQL







 

 

 

 

12-October-2018 Artificial Neural Networks

                David Bierbrauer from Tim Murphy's lab will tell us about the basics behind artificial neural networks for general machine learning approaches and convolutional neural networks for image processing.

Slides

ANNs







 

 

 

 

5-October-2018 Canadian Neurophotonics Platform

                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

                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

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

Slide Presentation Available here

 

More Info






 

 

 

 

08-June-2018 Raspberry Pi Tutorial

                A presentation of general input output control with a raspberry pi for experimental setups. https://github.com/jamieboyd/neurophoto2018

Slide Presentation







 

 

16-Mar-2018 Janelia Meeting Report Frontiers in Microscopy Technologies

                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

                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

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

Slide Presentation







 

 

02-Feb-2018 Gibson Cloning

                Joining fragments of DNA.

Slide Presentation







 

 

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 white board, at least 5 pitches lined up for contest to occur.

Not Available







 

 

03-Nov-2017 DREADDs

                Designer Receptors Exclusively Activated by Designer Drugs.

Slide Presentation







 

 

20-Oct-2017 Illustrator/Inkscape

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

Slide Presentation







 

 

13-Oct-2017 Blender

               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

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

Slide Presentation







 

 

09-Jun-2017 HPC

               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

               The Unix Shell

Lesson







 

 

19-May-2017 Linux Survival Guide

               A guide on using Linux.

Slide Presentation







 

 

12-May-2017 Bayesian Stats

               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

               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.

                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.

               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

                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

               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

                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

               Adeno-Associated Virus!

Slide Presentation







 

 

03-Mar-2017 Computer Vision

               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

               Imaging brain activity with Calcium Imaging.

Slide Presentation







 

 

10-Feb-2017 Mouse Genetics

               Everything you wanted to know on mouse genetics..

Slide Presentation







 

 

03-Feb-2017 Machine Learning

               Machine Learning with MatLab.

ZIP with demo files and slide presentation









 

 

27-Jan-2017 FLIM

               Fluorescence lifetime imaging microscopy.







 

 

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

               Basics on Raspberry Pis and their Cameras.

ZIP with demo files and slide presentation







 

 

04-Nov-2016 ImageJ Macros

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

Slide Presentatioin







 

 

28-Oct-2016 3D Models with Solidworks

                Learn the basics of 3D modelling in Solidworks.

Slide Presentation







 

 

21-Nov-2016 App Development in Python

                Tips and tricks to building a scientific app using PyCharm.

Slide Presentation







 

 

14-Nov-2016 Mendeley and Ref Management

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

Slide Presentation







 

 

07-Oct-2016 Git and Github

                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.

Not Available







 

 

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.

Check the calendar for upcoming meetings!