3DGV Manual

Explore Genomic Data in 3D

documentation version 3.4.0

Introduction

3D Genome Viewer
View and explore 3D genome models from Hi-C data using virtual reality technology. Overview The 3D Virtual Reality Genome Viewer is a virtual reality ge- nome viewer that allows us- ers to view 3D genomic models generated from Hi-C data and overlay their models with their own data.

The goal of 3dgv is to build a fully immersive VR genome browser where the user can seamlessly interact with genomic data and we developed features to realize this goal.

TEAM MEMBERS

  • Supervisors
  • Jérôme Waldispühl
  • Mathieu Blanchette
  • Jacek Majewski
  • Team
  • Chris Drogaris (Lead Developer)
  • Aaron Sossin
  • Zheng Yu Cui
  • Alumni
  • Eric Zhang
  • Antoine Guedon
  • Rajae Faraj

Getting Started #back to top

To start you must download application from our website for your Mac or PC

Download Application

System Requirements #back to top

Your system must meet the following requirements for 2D mode.

PC / Mac

Feature Min Requirement
CPU 1.4ghz equivalent or better
RAM 4 GB or more

Your system must meet the following requirements for VR mode.

HTC Vive

Feature Min Requirement
GPU Nvidia GeForce GTX 970, AMD Radeon R9 290 equivalent or better
CPU Intel i5-4590, AMD FX 8350 equivalent or better
RAM 4 GB or more
Video Output HDMI 1.4, DisplayPort 1.2 or newer
USB Port 1x USB 2.0 or better port
OS Windows 7 SP1, Windows 8.1 or later, Windows 10

Occulus

Feature Min Requirement
Processor Intel i5-4590 / AMD Ryzen 5 1500X or greater
Intel i3-6100 / AMD Ryzen 3 1200, FX4350 or greater
Graphics Card NVIDIA GTX 1060 / AMD Radeon RX 480 or greater
NVIDIA GTX 1050 Ti / AMD Radeon RX 470 or greater
Alternative NVIDIA GTX 970 / AMD Radeon R9 290 or greater
NVIDIA GTX 960 4GB / AMD Radeon R9 290 or greater
Memory 8GB+ RAM
OS Windows 10
USB Ports Rift 3x USB 3.0 ports, plus 1x USB 2.0 port
1x USB 3.0 port, plus 2x USB 2.0 ports
Video Output Compatible HDMI 1.3 video output
Compatible HDMI 1.3 video output

Running Application #back to top

PC

  1. Unzip folder, and open up the 3DVG.exe file
  2. Click on 2D or VR
  3. Note: VR only works with Occulus and HTC Vive

Mac

  1. Unzip folder, and move the 3DVG.app file into the Applications folder
  2. Right click the file and select Open to laumch app
  3. Click on 2D or VR
  4. Note: VR only works with Occulus and HTC Vive
  5. Note: Must run from Applications folder to have correct permissions

Video Overview #back to top

The following are video overviews of using 3DGV to enable model, annotations, genes, using data panels and navigating with user controls. Music by: https://www.bensound.com

Opening Application

This video will show basic user navigation and how to enable / disable a model.

Enable Chromosome

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Enable Annotation

This section will teach you how to import your own database for custom models, annotations and genes.

Enable Genes

This section will teach you how to import your own database for custom models, annotations and genes.

User Controls

This video will show basic user navigation and how to enable / disable a model.

Data Panels

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Database Storage

This section will teach you how to import your own database for custom models, annotations and genes.

Database Models

This video will show basic user navigation and how to enable / disable a model.

Database Annotations

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Database Genes

This section will teach you how to import your own database for custom models, annotations and genes.

Cache Manager

This video will show basic user navigation and how to enable / disable a model.

Screenshot System

This video will show basic screenshot system features in action.

Controls Overview #back to top

The following is a visual overview of the in app controls

2D

  • Direction - A,W,S and D for up, down, left, right
  • Menu - 'M' key to open / close
  • Rotation - Mouse move in direction
  • Space bar - Lock camera

VR

  • Direction - Trigger, point and click to move to direction
  • Menu - Menu button to open / close menu
  • Rotation - Look around in any direction

How to Use 3DGV #back to top

Main Menu - #back to top

2D Launch this if you want to run on your computer monitor
VR Launch this if you want to run on your vr system
Database Manager Clears cache and rebuilds database if you added new database files to the system

Database Manager - #back to top

Clear Cache Annotations Clear, deletes annotation cache files
Reload Annotations Clear, deletes annotation cache files
Clear Cache Genes Clear, deletes gene cache files
Reload Genes Reload gene files
Clear and Reload All Runs through all functions with one click

Main Menu (in app) - #back to top

Open / Close menu: Click the 'M' key or minimize icon on left
Genome Opens the genome selection panel
Panels See which data panels are open
Settings Adjust settings to your preference

Movement (2D) - #back to top

Direction: A,W,S and D for up, down, left, right
Menu: 'M' key to open / close
Rotation: Mouse move in direction
Space bar: Lock camera

Movement (VR) - #back to top

Direction: A,W,S and D for up, down, left, right
Menu: 'M' key to open / close
Rotation: Mouse move in direction

Settings - #back to top

Background color: Background color of atmosphere
Player speed: Speed player moves
Sequence width: Hover sequence selection width
Volume: Adjust volume of music
Scale: Adjust model size
Reset: Set back to default

Models (Chromosome) - #back to top

To activate a model, click on Genome / Species / Genome Set / Model Set / then select Chromosome then click Show. These models are located in the following folder:
/Resources/Genome Database/SPECIES/GENOME_SET/Models/
Note: See Database Section of this document to import custom models.

Annotations - #back to top

To activate a model, click on Genome / Annotations (tab on left) / then select the annotations then click Show. To disable it you click select and click button again. These annotations are located in the following folder:
/Resources/Genome Database/SPECIES/GENOME_SET/Annotations/
Note: See Database Section of this document to import custom annotations.

Genes (enable / disable) - #back to top

To activate genes, click on Genome / Gene / to toggle on and off. These genes are located in the following folder:
/Resources/Genome Database/SPECIES/GENOME_SET/Genes/
Note: See Database Section of this document to import custom genes.

Data panels - #back to top

Once a model is enabled, clicking on any part of the chromosome will spawn a data panel with more detailed info with a table / graph based on the selection and if any genes or annotations are enabled within that area. You can close the panel with an X on the top right.

Screenshot System - #back to top

You can use the screenshot button on the bottom right to snap a picture of your current screen in order to reference for later use. Click dots next to camera to see detailed menu with all of your snapshots saved for future reference.

Database #back to top

Models

The model file must be a csv file with the following format must add the file to this path in your application for them to be imported into the application:
/Resources/Genome Database/SPECIES/GENOME_SET/Models

Vertex # Base pair X Coord Y Coord Z Coord
0 0 -0.1674 0.0632 -0.1717
1 2500 -0.2748 -0.0488 -0.0601
... ... ... ... ...
100 75000 -0.2387 -0.1312 -0.1186
View sample model file

Annotations

The annotation file must be a bed file with the following format must add the file to this path in your application for them to be imported into the application:
/Resources/Genome Database/SPECIES/GENOME_SET/Annotations

Chromosome Start End Label Value
chr1 0 5000 start1 0
chr1 7000 7500 start2 0.5
... ... ... ... ...
chr1 10000 15000 start3 1
View sample annotation file

Genes

The gene file must be a bed file with the following format must add the file to this path in your application for them to be imported into the application:
/Resources/Genome Database/SPECIES/GENOME_SET/Genes

Chromosome Start End Label Filler Direction
chr1 100038094 100083373 MFSD14A . +
chr1 100083545 100133095 SASS6 . -
... ... ... ... ... ...
chr1 100266157 100292769 RTCA . +
View sample annotation file


Full Database Sample

Download sample of full database also located here: /Resources/Genome Database/

Download sample full database

Version History (Changelog) #back to top

See changlog for new features added

Changelog


                                        -----------------------------------------------------------------------------------------
                                        Version 3.4.0 - March 1st, 2020
                                        -----------------------------------------------------------------------------------------

                                        - Added cell type category to file system
                                        - Added screenshot system to capture image during exploring genome
                                        - Better visuals for annotations (layering / transparency) to maximize visibility
                                        - Minimize / maximize button added to bottom left
                                        - Color selection for annotations
                                        - Added mouse species in database
                                        - Min annotation base width, this way you can see annotations from further away
                                        - Merged annotations that are close together to save resources
                                        - Annotations fill around model for better visibility
                                        - Minimize / maximize button added to bottom left

                                        -----------------------------------------------------------------------------------------
                                        Version 3.3.1 - October 31st, 2019
                                        -----------------------------------------------------------------------------------------

                                        - added data panel drag with left click in 2D
                                        - added arrow directional system to be along edges

                                        -----------------------------------------------------------------------------------------
                                        Version 3.3.0 - September 29th, 2019
                                        -----------------------------------------------------------------------------------------
                                       
                                        - updated data panels to have correct data

Copyright and license #back to top

Code released under the TBA License.

For more information about copyright and license check tbalicence.com.