Aakansha Mathur's Journal
PROPOSAL & PRESENTATION
Project 1 Proposal Presentation https://docs.google.com/presentation/d/1FFO-xhXOZZZsvXz6sqjlAK2fRbdfb-brp5pLAnzhbdA/edit?usp=sharing
End Presentation for Project 1 https://docs.google.com/presentation/d/1rpIXAg7icREPVooGV76KQEoolAcZfrFS8Hd4354Oh4Q/edit?usp=sharing
End Presentation for Project 2 https://docs.google.com/presentation/d/1p5T70y868X8hsPaML22HQEV1ffDyG08O4yqNlOGjErs/edit?usp=sharing
CONTRIBUTION 1 [added how to install pip to the page] https://www.vrwiki.cs.brown.edu/vr-modeling-software/python
CONTRIBUTION 2 [UnityMol Overview] https://www.vrwiki.cs.brown.edu/vr-visualization-software/unitymol
CONTRIBUTION 3 [UnityMol Installation] https://www.vrwiki.cs.brown.edu/vr-visualization-software/unitymol/unitymol-installation
CONTRIBUTION 4 [PeppyVR Overview] https://www.vrwiki.cs.brown.edu/vr-visualization-software/peppy
CONTRIBUTION 5 [PeppyVR Installation] https://www.vrwiki.cs.brown.edu/vr-visualization-software/peppy/peppy-installation
CONTRIBUTION 6 [D6VR Overview] https://www.vrwiki.cs.brown.edu/vr-visualization-software/d6-vr
CONTRIBUTION 7 [D6VR Installation] https://www.vrwiki.cs.brown.edu/vr-visualization-software/d6-vr/features-of-d6-vr
CONTRIBUTION 8 [User Experience in VR] https://sites.google.com/view/brown-vr-sw-review-2018/vr-visualization-software/user-experience-in-vr?authuser=1
9 Fixes to the Wiki Page
10 Min Fixes
Remove the editable changes from the wiki. Provide the editable link to the students via Slack or email
Provide images of VR hardware. Also, provide purchase links to students.
Added pip installation to https://www.vrwiki.cs.brown.edu/vr-modeling-software/python
1 Hour Fixes
Create a page that provides more information on 'Getting Started': Have a flow chart for students that will help them get into VR. This will help students who are new or have prior experience in VR.
Change the color contrast of the web pages to make the web page more accessible to visually impaired readers
Provide tutorial on how to install apps for other VR hardware (currently its only there for oculus quest 2)
10 Hour Fixes
Add in more video/demo links in VR development software to help students better understand the softwares
Add more applications of VR other than just Medicine. Take in previous years students projects and added it to applications of VR
Improve the loading time of the wiki. It takes time to load especially if its images.
Total: 150 hours
JANUARY (10 Hours)
1/29/22 - 2 Hours
Reviewed the course homepage and familiarized myself with VR
Went through the previous year's wiki and noted down 9 fixes that could improve the wiki
1/30/22 - 4 Hours
Set up the journal
Documented homework 1 on the journal
Made changes to the https://www.vrwiki.cs.brown.edu/vr-modeling-software/python page
Realized really interested in archeological applications of VR. Started searching for various softwares that I can explore as a part of my project! Some of the softwares are:
AVROD: https://store.steampowered.com/app/1495350/AVROD/: It is a VR platform that digitizes archeological sites for study and exploration. It is compatible with HTC Vive and Oculus Rift
Dig@IT: http://www.catalhoyuk.com/files/digit-immersive-vr-app-archaeology. It's a VR app that allows you to view and explore the archeological sites over the years.
1/31/22 - 4 Hours
Read about biochemistry softwares in VR.
Researched on the different softwares that are available.
Looked into softwares that are available on wiki
FEBRUARY (31 Hours)
2/3/22 - 3 Hours
Set up the Oculus Quest 2
Pharmaceutical Drug Discovery: https://nanome.ai/
Chemical Structure Research: Chimerax VR
2/4/22 - 3 Hours
Project Idea: VR softwares for chemical data visualization
Data Viz: https://atlas.illinois.edu/node/647
Chimerax VR: https://www.cgl.ucsf.edu/chimerax/docs/user/vr.html
VR Chem: A VR Molecular Builder - Read the research paper associated with this
2/5/22 - 3 Hours
Three things I will do in the project:
Evaluate different softwares for chemical data analysis
Use different data sets to visualize in VR and understand the scope of the software
Get user feedback on the software to learn more about user experience with these apps.
One class activity we might do for the project:
Visualize chemical data on the software and conduct general discussion on the visualization
Create software demo videos: create videos on how to use the software and on different visualizations obtained from the software. This will make it easier for students to learn and evaluate different softwares. The videos can be uploaded to Youtube and the links could be added to the software description page.
Evaluation Metric: Have some common evaluation metrics be added to the software description page. The software can be evaluated based upon these metrics and the evaluation can be added to the page.
Software Evaluation Metrics:
Collaboration: Does the software allow for multiple users to collaborate in the same space at the same time? This can open room for discussion about the scientific visualization when groups of people are working together.
OS compatibility: Can the VR software work on Windows, Linux and Mac operating systems? VR software should be accessible to all users with all types of OS on their pc.
How good the visualization is: Is the visualization generated for the data - clear and concise? Does the visualization help in meeting the objective of the research?
2/9/22 - 3 Hours
Project Idea: Visualize chemical data on the software and conduct general discussion on the visualization
2/15/22: Finalize 3-4 softwares for experimentation
2/17/22: Use different chemical data to visualize in VR softwares
2/22/22: Develop the in person activity and test the VR software with another student
3/01/22: Work on the project proposal report
3/03/22: Develop the user feedback survey to do testing of the software
3/08/22: Read more VR papers to get more knowledge about chemical data visualization
3/10/22: Final check of the software, activity and finish report
2/14/22 - 3 Hours
Project Goal: Visualize chemical/molecular data on the software and conduct general discussion on the visualization
I have broken down my plan into steps that will help in achieving the project goal
Step 1: Finalize on VR softwares for the project.
Issues: some VR softwares are not compatible with Oculus Quest.
Step 2: Learn more about the data that works with the VR softwares
Unknown: do not have prior knowledge in biochemistry area. Would most likely need to consult a PHD student in biochemistry
Step 3: Finalize on the in-person class activity
Step 4: Update the wiki with software tutorials
2/16/22 - 2 Hours
Peer Review of my journal