vault backup: 2024-11-19 09:16:28

This commit is contained in:
Dane Sabo 2024-11-19 09:16:28 -05:00
commit eb913dc2dd
18 changed files with 477 additions and 33 deletions

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@ -1,14 +1,26 @@
{
"items": [
{
"type": "file",
"ctime": 1731951492555,
"path": "0 Managerial Pages/1. Task Dashboard.md"
},
{
"type": "file",
"ctime": 1730397400319,
"path": "0 Managerial Pages/To Do List.md"
"path": "0 Managerial Pages/To Do List.md",
"title": "To Do - General"
},
{
"type": "file",
"ctime": 1730397409494,
"path": "4 Qualifying Exam/1 Managing Stuff/0. QE To Do List.md"
"path": "4 Qualifying Exam/1 Managing Stuff/0. QE To Do List.md",
"title": "To Do - Qualifying Exam"
},
{
"type": "file",
"ctime": 1731951337156,
"path": "300s School/ME 2016 - Nonlinear Dynamical Systems 1/To Do - ME 2016.md"
}
]
}

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@ -35,7 +35,6 @@ where !completed
and due > date(today)
and due < date(today) + dur(2 w)
sort due asc
group by file.folder
```
## On The Horizon
---

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@ -14,7 +14,10 @@
- [x] Find Classes📅 2024-10-21 🛫 2024-10-15 ⏳ 2024-10-15 [completion:: 2024-10-15]
- [x] Fill out NRC Update for Mike📅 2024-10-28 🛫 2024-10-15 ⏳ 2024-10-15 [completion:: 2024-10-15]
- [x] Abstract for NPIC+HMIT paper ⏳ 2024-10-21 📅 2024-10-25 ✅ 2025-10-25
- [ ] What the hell is lobot? 📅 2024-11-07 ⏳ 2024-11-05
- [ ] Pick out classes 📅 2024-11-07 ⏳ 2024-11-05
- [x] What the hell is lobot? ⏳ 2024-11-05 📅 2024-11-07 ✅ 2024-11-18
- [x] Pick out classes ⏳ 2024-11-05 📅 2024-11-07 ✅ 2024-11-18
- [ ] fix up to do lists. 📅 2024-11-18
- [x] Figure out NUCE 2100 grade situation 📅 2024-11-18 ✅ 2024-11-18
- [ ] Find NRC wireless rfp 📅 2024-11-19
# Class Stuff
- [x] Move the sketches from my iPad to the notes for ME 2016 📅 2024-10-02 ✅ 2024-10-02

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@ -0,0 +1,50 @@
---
date: 2024-11-08
tags:
---
# Yesterday | Tomorrow
<< [[1 Daily Notes/2024/11 November/2024-11-07]] | [[1 Daily Notes/2024/11 November/2024-11-11 ]] >>
# This Week's Weekly Note
[[ Weekly Note 2024-11-06]]
# Tasks for today
## Due
```dataview
task
where
due <= date(this.date)
and due
and !completed
and status != "-"
sort due asc
group by file.folder
```
## Scheduled
```dataview
task
where
scheduled
and scheduled <= date(this.date)
and !completed
and status != "-"
sort due asc
group by file.folder
```
## Tasks in Progress
```dataview
task
where
status != "-"
and status = "/"
sort due asc
group by file.folder
```
## Completed
```dataview
task
where
completed
and completion = date(this.date)
sort due asc
group by file.folder
```
# Calendar Tasks

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@ -0,0 +1,50 @@
---
date: 2024-11-11
tags:
---
# Yesterday | Tomorrow
<< [[1 Daily Notes/2024/11 November/2024-11-08]] | [[1 Daily Notes/2024/11 November/2024-11-12 ]] >>
# This Week's Weekly Note
[[ Weekly Note 2024-11-06]]
# Tasks for today
## Due
```dataview
task
where
due <= date(this.date)
and due
and !completed
and status != "-"
sort due asc
group by file.folder
```
## Scheduled
```dataview
task
where
scheduled
and scheduled <= date(this.date)
and !completed
and status != "-"
sort due asc
group by file.folder
```
## Tasks in Progress
```dataview
task
where
status != "-"
and status = "/"
sort due asc
group by file.folder
```
## Completed
```dataview
task
where
completed
and completion = date(this.date)
sort due asc
group by file.folder
```
# Calendar Tasks

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@ -0,0 +1,50 @@
---
date: 2024-11-12
tags:
---
# Yesterday | Tomorrow
<< [[1 Daily Notes/2024/11 November/2024-11-11]] | [[1 Daily Notes/2024/11 November/2024-11-13 ]] >>
# This Week's Weekly Note
[[ Weekly Note 2024-11-06]]
# Tasks for today
## Due
```dataview
task
where
due <= date(this.date)
and due
and !completed
and status != "-"
sort due asc
group by file.folder
```
## Scheduled
```dataview
task
where
scheduled
and scheduled <= date(this.date)
and !completed
and status != "-"
sort due asc
group by file.folder
```
## Tasks in Progress
```dataview
task
where
status != "-"
and status = "/"
sort due asc
group by file.folder
```
## Completed
```dataview
task
where
completed
and completion = date(this.date)
sort due asc
group by file.folder
```
# Calendar Tasks

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@ -0,0 +1,50 @@
---
date: 2024-11-13
tags:
---
# Yesterday | Tomorrow
<< [[1 Daily Notes/2024/11 November/2024-11-12]] | [[1 Daily Notes/2024/11 November/2024-11-14 ]] >>
# This Week's Weekly Note
[[ Weekly Note 2024-11-06]]
# Tasks for today
## Due
```dataview
task
where
due <= date(this.date)
and due
and !completed
and status != "-"
sort due asc
group by file.folder
```
## Scheduled
```dataview
task
where
scheduled
and scheduled <= date(this.date)
and !completed
and status != "-"
sort due asc
group by file.folder
```
## Tasks in Progress
```dataview
task
where
status != "-"
and status = "/"
sort due asc
group by file.folder
```
## Completed
```dataview
task
where
completed
and completion = date(this.date)
sort due asc
group by file.folder
```
# Calendar Tasks

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@ -0,0 +1,50 @@
---
date: 2024-11-14
tags:
---
# Yesterday | Tomorrow
<< [[1 Daily Notes/2024/11 November/2024-11-13]] | [[1 Daily Notes/2024/11 November/2024-11-15 ]] >>
# This Week's Weekly Note
[[ Weekly Note 2024-11-13]]
# Tasks for today
## Due
```dataview
task
where
due <= date(this.date)
and due
and !completed
and status != "-"
sort due asc
group by file.folder
```
## Scheduled
```dataview
task
where
scheduled
and scheduled <= date(this.date)
and !completed
and status != "-"
sort due asc
group by file.folder
```
## Tasks in Progress
```dataview
task
where
status != "-"
and status = "/"
sort due asc
group by file.folder
```
## Completed
```dataview
task
where
completed
and completion = date(this.date)
sort due asc
group by file.folder
```
# Calendar Tasks

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@ -0,0 +1,50 @@
---
date: 2024-11-15
tags:
---
# Yesterday | Tomorrow
<< [[1 Daily Notes/2024/11 November/2024-11-14]] | [[1 Daily Notes/2024/11 November/2024-11-18 ]] >>
# This Week's Weekly Note
[[ Weekly Note 2024-11-13]]
# Tasks for today
## Due
```dataview
task
where
due <= date(this.date)
and due
and !completed
and status != "-"
sort due asc
group by file.folder
```
## Scheduled
```dataview
task
where
scheduled
and scheduled <= date(this.date)
and !completed
and status != "-"
sort due asc
group by file.folder
```
## Tasks in Progress
```dataview
task
where
status != "-"
and status = "/"
sort due asc
group by file.folder
```
## Completed
```dataview
task
where
completed
and completion = date(this.date)
sort due asc
group by file.folder
```
# Calendar Tasks

View File

@ -0,0 +1,50 @@
---
date: 2024-11-18
tags:
---
# Yesterday | Tomorrow
<< [[1 Daily Notes/2024/11 November/2024-11-15]] | [[1 Daily Notes/2024/11 November/2024-11-19 ]] >>
# This Week's Weekly Note
[[ Weekly Note 2024-11-13]]
# Tasks for today
## Due
```dataview
task
where
due <= date(this.date)
and due
and !completed
and status != "-"
sort due asc
group by file.folder
```
## Scheduled
```dataview
task
where
scheduled
and scheduled <= date(this.date)
and !completed
and status != "-"
sort due asc
group by file.folder
```
## Tasks in Progress
```dataview
task
where
status != "-"
and status = "/"
sort due asc
group by file.folder
```
## Completed
```dataview
task
where
completed
and completion = date(this.date)
sort due asc
group by file.folder
```
# Calendar Tasks

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@ -46,6 +46,25 @@
file = {/home/danesabo/Zotero/storage/KZSJSUKD/Abelson et al. - 2022 - Structure and interpretation of computer programs.pdf}
}
@article{abramsonAccurateStructurePrediction2024,
title = {Accurate Structure Prediction of Biomolecular Interactions with {{AlphaFold}} 3},
author = {Abramson, Josh and Adler, Jonas and Dunger, Jack and Evans, Richard and Green, Tim and Pritzel, Alexander and Ronneberger, Olaf and Willmore, Lindsay and Ballard, Andrew J. and Bambrick, Joshua and Bodenstein, Sebastian W. and Evans, David A. and Hung, Chia-Chun and ONeill, Michael and Reiman, David and Tunyasuvunakool, Kathryn and Wu, Zachary and Žemgulytė, Akvilė and Arvaniti, Eirini and Beattie, Charles and Bertolli, Ottavia and Bridgland, Alex and Cherepanov, Alexey and Congreve, Miles and Cowen-Rivers, Alexander I. and Cowie, Andrew and Figurnov, Michael and Fuchs, Fabian B. and Gladman, Hannah and Jain, Rishub and Khan, Yousuf A. and Low, Caroline M. R. and Perlin, Kuba and Potapenko, Anna and Savy, Pascal and Singh, Sukhdeep and Stecula, Adrian and Thillaisundaram, Ashok and Tong, Catherine and Yakneen, Sergei and Zhong, Ellen D. and Zielinski, Michal and Žídek, Augustin and Bapst, Victor and Kohli, Pushmeet and Jaderberg, Max and Hassabis, Demis and Jumper, John M.},
date = {2024-06},
journaltitle = {Nature},
volume = {630},
number = {8016},
pages = {493--500},
publisher = {Nature Publishing Group},
issn = {1476-4687},
doi = {10.1038/s41586-024-07487-w},
url = {https://www.nature.com/articles/s41586-024-07487-w},
urldate = {2024-11-13},
abstract = {The introduction of AlphaFold\,21 has spurred a revolution in modelling the structure of proteins and their interactions, enabling a huge range of applications in protein modelling and design26. Here we describe our AlphaFold\,3 model with a substantially updated diffusion-based architecture that is capable of predicting the joint structure of complexes including proteins, nucleic acids, small molecules, ions and modified residues. The new AlphaFold model demonstrates substantially improved accuracy over many previous specialized tools: far greater accuracy for proteinligand interactions compared with state-of-the-art docking tools, much higher accuracy for proteinnucleic acid interactions compared with nucleic-acid-specific predictors and substantially higher antibodyantigen prediction accuracy compared with AlphaFold-Multimer v.2.37,8. Together, these results show that high-accuracy modelling across biomolecular space is possible within a single unified deep-learning framework.},
langid = {english},
keywords = {Drug discovery,Machine learning,Protein structure predictions,Structural biology},
file = {/home/danesabo/Zotero/storage/Y4BDPS2Y/Abramson et al. - 2024 - Accurate structure prediction of biomolecular interactions with AlphaFold 3.pdf}
}
@online{AbstractJulia,
title = {{{AbstractJulia}}},
url = {https://www.algebraicjulia.org/}
@ -8165,6 +8184,34 @@ Insights from the Social Sciences.pdf}
file = {/home/danesabo/Zotero/storage/8EZ9FFD3/Module 10 Review.pdf 2251 NUCE 2100 SEC1250 FUNDAMENTALS NUCLEAR ENGR.pdf;/home/danesabo/Zotero/storage/BK36WRH6/17486254.html}
}
@online{Module111Pressure,
title = {Module 11.1 - {{Pressure Drop}}.Pdf: 2251 {{NUCE}} 2100 {{SEC1250 FUNDAMENTALS NUCLEAR ENGR}}},
url = {https://canvas.pitt.edu/courses/280885/files/17486318?module_item_id=5008255},
urldate = {2024-11-12},
file = {/home/danesabo/Zotero/storage/XLV9LK8M/Module 11.1 - Pressure Drop.pdf 2251 NUCE 2100 SEC1250 FUNDAMENTALS NUCLEAR ENGR.pdf;/home/danesabo/Zotero/storage/K7YI66P2/17486318.html}
}
@online{Module112Closed,
title = {Module 11.2 - {{Closed Channel Analysis}}.Pdf: 2251 {{NUCE}} 2100 {{SEC1250 FUNDAMENTALS NUCLEAR ENGR}}},
url = {https://canvas.pitt.edu/courses/280885/files/17486320?module_item_id=5008256},
urldate = {2024-11-12},
file = {/home/danesabo/Zotero/storage/777A5FPL/Module 11.2 - Closed Channel Analysis.pdf 2251 NUCE 2100 SEC1250 FUNDAMENTALS NUCLEAR ENGR.pdf;/home/danesabo/Zotero/storage/TKW3SUEL/17486320.html}
}
@online{Module113TwoPhase,
title = {Module 11.3 - {{Two-Phase Flow}} and {{Boiling}}.Pdf: 2251 {{NUCE}} 2100 {{SEC1250 FUNDAMENTALS NUCLEAR ENGR}}},
url = {https://canvas.pitt.edu/courses/280885/files/17486319?module_item_id=5008257},
urldate = {2024-11-12},
file = {/home/danesabo/Zotero/storage/EKZ5TJY3/Module 11.3 - Two-Phase Flow and Boiling.pdf 2251 NUCE 2100 SEC1250 FUNDAMENTALS NUCLEAR ENGR.pdf;/home/danesabo/Zotero/storage/V24U7V5E/17486319.html}
}
@online{Module114Boiling,
title = {Module 11.4 - {{Boiling Crisis}}.Pdf: 2251 {{NUCE}} 2100 {{SEC1250 FUNDAMENTALS NUCLEAR ENGR}}},
url = {https://canvas.pitt.edu/courses/280885/files/17486261?module_item_id=5008258},
urldate = {2024-11-12},
file = {/home/danesabo/Zotero/storage/8GFSZ3NN/Module 11.4 - Boiling Crisis.pdf 2251 NUCE 2100 SEC1250 FUNDAMENTALS NUCLEAR ENGR.pdf;/home/danesabo/Zotero/storage/KNVAQ22T/17486261.html}
}
@online{Module81Fission,
title = {Module 8.1 - {{Fission Heat Generation-1}}.Pdf: 2251 {{NUCE}} 2100 {{SEC1250 FUNDAMENTALS NUCLEAR ENGR}}},
url = {https://canvas.pitt.edu/courses/280885/files/17486316?module_item_id=5008211},
@ -10057,6 +10104,15 @@ Insights from the Social Sciences.pdf}
file = {/home/danesabo/Zotero/storage/EX9JBPKZ/Qualifying Exam.pdf;/home/danesabo/Zotero/storage/9DYSHIPL/66db16e7e208c0cf7aee5549.html}
}
@online{QualifyingExama,
title = {Qualifying {{Exam}}},
url = {https://www.overleaf.com/project/66db16e7e208c0cf7aee5549},
urldate = {2024-11-12},
abstract = {An online LaTeX editor thats easy to use. No installation, real-time collaboration, version control, hundreds of LaTeX templates, and more.},
langid = {english},
file = {/home/danesabo/Zotero/storage/TAJZZXSK/Qualifying Exam.pdf;/home/danesabo/Zotero/storage/WC366ERE/66db16e7e208c0cf7aee5549.html}
}
@article{raikwarSoKUsedCryptography2019,
title = {{{SoK}} of {{Used Cryptography}} in {{Blockchain}}},
author = {Raikwar, Mayank and Gligoroski, Danilo and Kralevska, Katina},

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@ -0,0 +1,21 @@
Lorenz system is dissapative. This means:
- Volume in phase space contracts with flow?
This introduces some questions... How do volumes evolve?
n
Suppose a surface $S(t)$ encloses volume $V(t)$, with normal vectors pointing away from the surface ($\vec{n}$).
A trajectory starts on S. let them evolve for $dt$. With a flux vector $\vec{f}$, we have
- $\vec f \cdot \vec n$ - normal, outward component of velocity
In $dt$ time, $dA$ sweeps out a volume.
Volume: $(\vec f \cdot \vec n dt)dA$
$$V(t+dt) = V(t) + \int_S (\vec f \cdot \vec n dt)dA $$
$$\dot{V} = \int_S (\vec f \cdot \vec n)dA $$
Now we can apply the divergence theorem:
$$\dot{V} = \int_V (\nabla \cdot \vec f )dV $$
If you start with a solid blob of initial conditions, this integral will evaluate down to where things end up. If $\dot V$ is negative, then the system will converge to a stable subspace.
Limiting set will consist of
- fixed points
- limit cycles
- strong attractors
Proving which type something will end up on is much harder. But, repellers will always result in a positive $\dot V$.

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@ -1,11 +1,12 @@
# Progress
- [x] Read paper [completion:: 2024-11-19]
- [x] What are the modeling assumptions? [completion:: 2024-11-19]
- [x] What are the solution approaches? [completion:: 2024-11-19]
- [x] Do other things from class relate? [completion:: 2024-11-19]
- [ ] Rederive equations and solutions from the paper
- [ ] What do they leave out?
- [ ] Make things 'VERY CLEAR'
- [ ] Numerical Solution
- [ ] Recreate figure 3
- [ ] Make a parallel implementation
- [x] Read paper [completion:: 2024-11-18]
- [x] What are the modeling assumptions? [completion:: 2024-11-18]
- [x] What are the solution approaches? [completion:: 2024-11-18]
- [x] Do other things from class relate? [completion:: 2024-11-18]
- [x] Rederive equations and solutions from the paper [completion:: 2024-11-18]
- [x] What do they leave out? [completion:: 2024-11-18]
- [x] Make things 'VERY CLEAR' [completion:: 2024-11-18]
- [x] Numerical Solution [completion:: 2024-11-18]
- [x] Recreate figure 3 [completion:: 2024-11-18]
- [x] Make a parallel implementation [completion:: 2024-11-18]

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@ -0,0 +1,4 @@
# Homework
- [x] Homework 2 🛫 2024-10-02 📅 2024-10-04 ✅ 2024-10-04
- [x] Homework 3 🛫 2024-10-14 📅 2024-10-18 ✅ 2024-10-22
- [ ] Mini Project 2 📅 2024-11-22

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@ -1,3 +0,0 @@
# Homework
- [x] Homework 2 🛫 2024-10-02 📅 2024-10-04 ✅ 2024-10-04
- [x] Homework 3 🛫 2024-10-14 📅 2024-10-18 ✅ 2024-10-22

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@ -6,5 +6,5 @@ endDate: 2024-11-06
completed: 2024-11-06T09:47:22.930-05:00
type: single
---
- [ ] Homework 7 📅 2024-11-05
#Homework
- [x] Homework 7 📅 2024-11-05
#Homework [completion:: 2024-11-18]

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@ -5,5 +5,5 @@ date: 2024-11-12
endDate: 2024-11-13
completed: null
---
- [ ] Homework 8 📅 2024-11-12
- [-] Homework 8 📅 2024-11-12
#Homework

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@ -1,11 +1,11 @@
# Old
- [x] Read email from Dr. Cho with shared documents 📅 2024-09-25 ⏳ 2024-09-25 [completion:: 2024-10-16]
- [x] Find papers on verifying robustness⏳ 2024-10-15 📅 2024-10-16 [completion:: 2024-10-15]
- [ ] Start writing about diffusion model📅 2024-10-15
- [ ] What is the generative diffusion model? How does it work?
- [ ] How can we use this to generate new plants?
- [ ] How are we going to tell if they're in the unstrucutred perturbation disk?
- [ ] Create a one dimensional diffusion generative model 📅 2024-10-22 ⏳ 2024-10-17
- [x] Start writing about diffusion model 📅 2024-10-15 ✅ 2024-11-13
- [x] What is the generative diffusion model? How does it work? ✅ 2024-11-13
- [x] How can we use this to generate new plants? ✅ 2024-11-13
- [x] How are we going to tell if they're in the unstrucutred perturbation disk? ✅ 2024-11-13
- [x] Create a one dimensional diffusion generative model ⏳ 2024-10-17 📅 2024-10-22 ✅ 2024-11-13
- [x] Write about how to generate unstructured perturbations📅 2024-10-15 [completion:: 2024-11-05]
- [x] What is disk uncertainty? ✅ 2024-10-17 [completion:: 2024-11-05]
- [x] Why is this something difficult to sample? [completion:: 2024-11-05]
@ -24,8 +24,8 @@
- Talk about filling the disk of uncertainty
- [x] Finish writing risks and contingencies ✅ 2024-11-11
- [x] Write about fitting a model to the data for checking poles and creating useful models ✅ 2024-11-11
- [ ] Make figures
- [ ] Flowchart for whole prcoess
- [x] Make figures ✅ 2024-11-13
- [x] Flowchart for whole prcoess ✅ 2024-11-13
- This should include:
- original bode plot
- discretizing the plot
@ -38,14 +38,15 @@
- Partially done. Must explain that they are sets of plants
- [x] Write broader impacts ✅ 2024-11-11
- [x] Write Tasks section ✅ 2024-11-11
- [ ] Do a lot of formatting
- [x] Do a lot of formatting ✅ 2024-11-18
- [ ] Create presentation outline📅 2024-11-20
# Milestones
- [x] Goals and Outcomes Finished 🆔 kwyu6a ⏳ 2024-10-02 📅 2024-10-04 ✅ 2024-10-02
- [x] State of the Art Finished 🆔 i9ybdy ⏳ 2024-10-09 📅 2024-10-11 ✅ 2024-11-11
- [*] Research Approach Finished 🆔 ha7il5 ⏳ 2024-10-21 📅 2024-10-23
- [*] Broader Impacts, Metrics of Success, Risks and Contingincies Finished 🆔 6chcdh ⏳ 2024-10-28 📅 2024-11-01
- [*] Written Proposal First Draft Complete 🆔 7spba6 ⛔ i9ybdy,6chcdh,kwyu6a,ha7il5 ⏳ 2024-11-01 📅 2024-11-05
- [*] Written Proposal Submitted ⛔ 7spba6,6chcdh,0j2tb1,55hpqw,kwyu6a ⏳ 2024-11-11 📅 2024-11-13
- [x] Research Approach Finished 🆔 ha7il5 ⏳ 2024-10-21 📅 2024-10-23 ✅ 2024-11-13
- [x] Broader Impacts, Metrics of Success, Risks and Contingincies Finished 🆔 6chcdh ⏳ 2024-10-28 📅 2024-11-01 ✅ 2024-11-13
- [x] Written Proposal First Draft Complete 🆔 7spba6 ⛔ i9ybdy,6chcdh,kwyu6a,ha7il5 ⏳ 2024-11-01 📅 2024-11-05 ✅ 2024-11-13
- [x] Written Proposal Submitted ⛔ 7spba6,6chcdh,0j2tb1,55hpqw,kwyu6a ⏳ 2024-11-11 📅 2024-11-13 ✅ 2024-11-13
- [*] Oral Examination First Draft Complete ⏳ 2024-11-20 📅 2024-11-22
- [*] Oral Examination Final Draft Complete ⏳ 2024-11-25 📅 2024-11-27
- [*] QE Exam Complete! :) 📅 2024-12-03