Aakansha Mathur's Journal

Project 1 Proposal https://docs.google.com/document/d/1gVQu1Ew6SJE0JaGRD1UTQEhRWwyNNQZmigEEWl0eCD8/edit?usp=sharing 

Project 1 Proposal Presentation https://docs.google.com/presentation/d/1FFO-xhXOZZZsvXz6sqjlAK2fRbdfb-brp5pLAnzhbdA/edit?usp=sharing 

Project 1 Update https://docs.google.com/presentation/d/17J0gWdg_z78ocUV3WyZR-MKSIc_TETjmmOENjD3EZHU/edit?usp=sharing 

In-class Activity https://www.vrwiki.cs.brown.edu/course-home-page/journals/aakansha-mathurs-journal/aakanshas-in-class-activity 

End Presentation for Project 1 https://docs.google.com/presentation/d/1rpIXAg7icREPVooGV76KQEoolAcZfrFS8Hd4354Oh4Q/edit?usp=sharing 

Project 2 Proposal https://docs.google.com/document/d/1RA0ULcc0EAhLsqr1wIZdvudTXxi85SxA7qcQ0m3ZfbU/edit?usp=sharing 

Project 2 Presentation https://docs.google.com/presentation/d/16_rpaPE9NxIQXnO327FnVpOpwkbdb39gnGccMMINSOs/edit?usp=sharing 

Project 2 Update https://docs.google.com/presentation/d/1-xB-f8FlbvJXcXDFoIlnPXpnJLJfhAFIqNhq_SVvuMw/edit?usp=sharing 

End Presentation for Project 2 https://docs.google.com/presentation/d/1p5T70y868X8hsPaML22HQEV1ffDyG08O4yqNlOGjErs/edit?usp=sharing 

Poster https://drive.google.com/file/d/1bMEx55rJH8hcGr10LCbx5eDVLbFoFZwh/view?usp=sharing 

In-class Activity https://www.vrwiki.cs.brown.edu/course-home-page/journals/aakansha-mathurs-journal/aakanshas-second-in-class-activity 

Flash Talk https://docs.google.com/presentation/d/12dIFjR_oppQrvscS_ZgLGs7XG6-Bu9JUSYkqAmBNPhI/edit?usp=sharing 

1/29/22 - 2 Hours

• Joined slack

• 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

2/3/22 - 3 Hours

• Set up the Oculus Quest 2

• Project Ideas:

  • Pharmaceutical Drug Discovery: https://nanome.ai/

  • Chemical Structure Research: Chimerax VR

2/4/22 - 3 Hours

• Project Idea: VR softwares for chemical data visualization

  • Potential Softwares:

    • Data Viz: https://atlas.illinois.edu/node/647

    • Nanome: https://nanome.ai/

    • 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

• Potential Deliverables:

  • 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

  • Milestones:

    • 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

• Project Plan:

  • 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

• Project Evaluation

  • The questions are:

    • The proposed project clearly identifies deliverable additions to our VR Software Wiki - 5 (Strongly agree)

    • The proposed project involves collaboration in VR - 4 (Agree)

    • The proposed project involves large scientific data visualization along the lines of the "Scientific Data" wiki page and identifies the specific data type and software that it will use - 5 (Strongly Agree)

    • The proposed project has a realistic schedule with explicit and measurable milestones at least each week and mostly every class - 5 (Strongly Agree)

    • The proposed project includes an in-class activity - 5 (Strongly Agree)

    • The proposed project has resources available with sufficient documentation - 5 (Strongly Agree)

• Prepared a presentation with project description

2/16/22 - 2 Hours

• Peer Review of my journal 

• Journal activities are explicitly and clearly related to course deliverables

  • 5 - Yes. I have logged all work done for VR class. The activities are close to my project and the course deliverables.

• Deliverables are described and attributed in wiki

  • 3 -  Deliverables are described in the wiki. The deliverables and milestones can be made more explicit

• report states total amount of time

  • 5 - Yes

• total time is appropriate

  • 5 - Yes

• Key for each criterion:

  • 5 == exceeds expectations

  • 4 == meets expectations

  • 3 == mostly solid with some gaps

  • 2 == shows some progress

  • 1 == some attempt

  • 0 == not found

2/23/22 - 5 Hours

• Downloaded Volume Renderer for the in-class activity

• Looked into softwares for visualization

  • ProteinVR - https://durrantlab.pitt.edu/pvr 

    • Web application that allows you to visualize the protein structures in VR mode

    • However, the software is not compatible with Oculus Quest 2

  • UnityMol - http://www.baaden.ibpc.fr/umol/ 

    • A VR application to visualize molecular data

• Read research paper to learn more about VR softwares and their application in biochemistry

2/25/22 - 3 Hours

• Downloaded UnityMol via SourceForgeNet: https://sourceforge.net/projects/unitymol/files/

• Acquainted myself with the software and downloaded RNA data

• Explored different features of the application

2/27/22 - 3 Hours

• Created presentation for the class on Tuesday

• Downloaded required softwares for Beatrice's activity

• Researched for more VR softwares for chemical data visualization

2/28/22 - 3 Hours

• Updated journal with logs of all work and the evaluations

• Prepared powerpoint for presentation

• Prepared for Beatrice's in-class activity

3/2/22 - 4 Hours

• Prepared for Amanda's in class activity

• Found PeppyVR for building chemical structures. 

• Installed PeppyVR and understood its functionality 

3/7/22 - 4 Hours

• Prepared for Lucia's in class activity

• Finalized on UnityMol and PeppyVR for in-class activity. These two softwares can be done independently 

• Downloaded Nanome and completed its tutorial to understand how Nanome works

3/8/22 - 5 Hours

• Prepared for Tongyu's in-class activity

• Read and gained understanding about protein structures in biochemistry

3/9/22 - 4 Hours

• Prepared for Mandy's in class activity

• Explored Nanome collaborative features for in-class activity

3/13/22 - 5 Hours

• Prepared for Maia's in class activity

• Consulted with a student in biology to learn more about protein structures, amino acides and peptide bonds

3/14/22 - 4 Hours

• Prepared for Shashidhar's in class activity

• Prepared documentation for in-class activity. 

• Created Google form for in-class activity

3/16/22 - 5 Hours

• Created tutorials for UnityMol and PeppyVR to be added to the wiki

• Prepared project 1 final presentation 

3/21/22 - 5 Hours

• Read the seven scenarios paper

• Added the tutorials to the wiki

• Prepared a draft for project 2

3/23/22 - 4 Hours

• Created project 2 presentation slides for class

• Evaluating Project 2 Plan:

  • The proposed project clearly identifies deliverable additions to our VR Software Wiki: 4

  • The proposed project involves collaboration in VR: 3

  • The proposed project involves large scientific data visualization along the lines of the "Scientific Data" wiki page and identifies the specific data type and software that it will use: 5

  • The proposed project has a realistic schedule with explicit and measurable milestones at least each week and mostly every class: 4

  • The proposed project includes an in-class activity: 5

  • The proposed project has resources available with sufficient documentation: 5

• 3/23/22 - 5 Hours

  • Prepared final documentation for in-class activity

  • Reviewed UnityMol, PeppyVR for independent aspect of the activity

  • Redid the Nanome tutorial as a final check

  • Tested the collaborative aspect of Nanome once again

  • Reread some basic concepts of proteins 

4/4/22 - 4 Hours

• Updated the journal

• Revised final project plan

  • Selected collaborative analysis to evaluate user experience in data visualization software

  • Updated the milestone to be as follows:

    • 4/7: Read papers on evaluating collaborative aspect of softwares

    • 4/14: Finalize softwares for the project and begin drafting the wiki contributions

    • 4/21: Finalize and conduct the in-class activity

    • 4/28: Wrap up documentation for project 2

4/6/22 - 4 Hours

• Read more on user interface in VR. Reread seven scenarios paper to gather better insights on UIX

• Chose collaborative mode in VR to study user interface

• Researched into softwares for collaborative data visualization

4/11/22 - 4 Hours

• Surveyed different VR softwares for data visualization and collaboration:

  • Data Visualization (Requested Demos)

    • 3Data (https://3data.io)

    • BadVR (https://badvr.com)

    • D6VR (https://d6vr.io)

    • Immersion Analytics (https://www.immersionanalytics.com)  

  • Collaborative Virtual Simulation

    • Engage

    • Spatial

    • WondaVR

    • Glue

4/13/22 - 4 Hours

• Downloaded and tested Engage for data visualization and collaboration

• Finalized the evaluation metrics for evaluating different VR softwares:

  • Text Readability 

  • Viewing Distance

  • Simulator Sickness

  • Brightness Changes

  • Comfortable Interactions

  • Navigation

  • Speed at which user understands the software

  • Duration of user’s physical work

  • Head Tracking

  • Aesthetics 

  • Collaboration

• Received replies from different VR software companies and initiated communication with them

4/18/22 - 4 Hours

• Communicated with D6VR and BadVR for software demos.

• Researched into more softwares for data visualization

• Prepared slides for project 2 updates

4/20/22 - 4 Hours

• Prepared for Amanda and Mandy's in class activities

• Researched into DataViz VR software for data visualization.

• Downloaded beta version of DataViz VR and tested it for data visualization

• Researched on datasets that could be used for visualization 

4/25/22 - 4 Hours

• Prepared for Sayan, Jacobi and Tongyu's in class activities

• Communicated with D6VR and schedule meeting for software demo

• Got access to D6VR software and performed the necessary installation for meeting on Wednesday

4/27/22 - 4 Hours

• Prepared for Shashidhar and Lucia's in-class activities.

• Prepared documentation and survey for my in-class activity

• Met with D6VR and learnt about software

• Got leader account access and uploaded resources to visualize in the software

5/2/2022 - 4 Hours

• Prepared for Beatrice, Robert and Maia's in-class activities

• Downloaded Amanda dataset and loaded it into D6VR software

• Realized that the entire dataset crashes the D6VR app. Hence, loaded a subset of the dataset

5/4/2022 - 4 Hours

• Prepared for Paul, Alastair, Jennifer and Nick's in-class activities

• Downloaded Virtualitics and revisited the data visualization for Amanda's dataset 

• Evaluated Immersion Analytics, D6VR and Virtualitics based upon the evaluation metrics

5/9/2022 - 5 Hours

• Prepared slides for final presentation 

• Prepared flashtalk slides

5/11/2022 - 4 Hours

• Created different subsets of Amanda's dataset and tested D6VR

• Drafted D6VR overview, installation

• Drafted User Experience in VR page

5/17/2022 - 5 Hours

• Created poster for demo day

• Updated the drafts for wiki contributions

5/17/2022 - 5 Hours

• Updated poster and wiki contributions drafts

• Published the wiki contributions