reorder and move resources to one file

src/SUMMARY.md

@@ -1,11 +1,4 @@
-[Welcome](./index.md)
-
-- [How to Document](./documentation/index.md)
-
-  - [For leads](./documentation/lead.md)
-  - [For wiki liaisons](./documentation/liaison.md)
-
-- [Project Description](./description.md)
+[Project Description](./description.md)
 
 - [Attributions](./attributions.md)
 
@@ -56,7 +49,12 @@
 
 # Resources
 
-- [iGEM](./resources/igem.md)
-- [Synthetic Biology](./resources/synbio.md)
-- [Modelling](./resources/modelling.md)
-- [Bioinformatics](./resources/bioinformatics.md)
+- [Project Related Resources](./resources/project-related.md)
+- [General Resources](./resources/igem.md)
+
+# For Internal Subteam Members
+
+- [Getting Started (For internal team members)](./index.md)
+  - [How to Document](./documentation/index.md)
+    - [For leads](./documentation/lead.md)
+    - [For wiki liaisons](./documentation/liaison.md)

src/description.md

@@ -1,31 +1,5 @@
-# Project Description
+# Project Description: Improving DNA Storage with Synthetic Biology
 
-When writing the project description, every member should be table to answer the following questions:
+## To be completed
 
-1. What is the team's vision for the chosen project
-2. What is the project explained in a conceptual manner?
-3. What is the project explained in a detailed manner?
 
-## Project Summary
-Solution: Enhance DNA storage process with improved synthesis and storage semantics 
-
-- Wet Lab: The expression of thermostable TdT with E. Coli, and enzymatic
-- Dry Lab: Emphasis on error correction and parallelization with microfluidics
-- Human Practices: 
-
-## Problem
-Ubiquitous data storage in the form of "the cloud" is becoming an everyday norm, becoming the default method of saving all types of information, ranging from videos to photos and more. But data isn’t really in the cloud - it’s stored in giant buildings containing magnetic and optical media such as hard drives, with some buildings taking up "nearly 200 acres of land apiece" (cite). It is predicted that the world will generate around 180 zettabytes of information by 2025, with 22 zettabytes of data being shipped around between 2018 and 2025, 60% in the form of hard drives (cite). With the exponential increase of information creation and sharing, the scalability and capacity of magnetic and optical media cannot meet the demands of the near future. As of 2015, data centers account for around 2% of global energy usage, with individual data centers using as much energy as an airline; this value only grows (cite).
-
-With advancements in DNA synthesis and sequencing, DNA poses a novel medium for information because it is:
-
-- Dense: you can store all of the world’s information in a coffee cup! 
-- Durable: it can be stored for millions of years in the correct conditions
-- Energy efficient: [TODO]
-
-However, DNA storage still faces bottlenecks in synthesis and sequencing. We hope to enhance synthesis with enzymatic DNA synthesis which has several advantages over chemical synthesis. Terminal deoxynucleotidyl transferase (TdT) elongates single stranded oligonucleotides by randomly adding different nucleotides. Moreover, TdT has a preference for the incorporation of some nucleotides over others, leading to increased rates of sequence-specific errors. TdT works only on single-stranded DNA, due to the enzyme’s structure. Thus, if secondary DNA structures form, synthesis efficiency is reduced. In essence, WT TdT isn’t selective enough by itself to perform accurate DNA Synthesis.
-
-Previous iGEM teams have tackled this issue, with mixed results. The latest team, Aachen iGEM 2021, at most was able to encode and decode 15 nucleotides with 40% accuracy. As such, UBCV iGEM 2024 team is attempting to increase the accuracy of the encoding and decoding of larger sequences by using higher reaction temperatures with thermostable TdT as well as optimizing with alternative reagents the overall protocol in order to reduce the systematic and random errors. Big Biotech companies have gotten around these issues by engineering TdT and creating nucleotide complexes; but these are patented and out of the reach of the public.
-
-Additionally, our team hopes to use software to enhance the accuracy of information stored in DNA with error correcting codes, parallelize the synthesis process with microfluidics, and quantify our wet labs work with protein and math modelling. Finally, we hope our project helps to demystify concepts in computation, storage systems and DNA through educational efforts and user-orientated interviews of our graphical user interface. We hope to use the multidisciplinary nature of synthetic biology to enhance synthesis and retrieval steps of DNA storage.
-
-## What is DNA Storage? 

src/resources/igem.md

@@ -1,8 +1,102 @@
-# iGEM
+# General Resources
+
+<!-- toc -->
+
+## Introduction to Synthetic Biology
+Thanks to Piyush and Kimia for these resources!
+
+Synthetic biology is a field of biology that combines principles of engineering and science to create new biological systems or modify existing ones for specific purposes. This can include the engineering of new enzymes, the creation of living organisms with specific properties or the development of new genetic circuits. The ultimate goal of synthetic biology is to create new functions or applications that are not found in nature.
+
+To begin, familiarize yourself with general biology. In the suggested videos below, I will be focusing on the central dogma of biology (how do we get from DNA to protein), but I **highly recommend** you look into additional resources if you need help!
+
+### CrashCourse: DNA Structure and Replication
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/8kK2zwjRV0M?si=Qka0_Mb54TLiqgW9" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
+
+### CrashCourse: Transcription and Translation
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/itsb2SqR-R0?si=KvhQTRVd8KucgzyG" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
+
+### CrashCourse: What is Biotechnology?
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/Qo9gcZ0r8k8?si=nMA58Wy8U3XXxUa8" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
+
+![Plasmid](../static/resources/plasmid.png)
+
+## CSBERG (Canadian Synthetic Biology Education Research Group):
+
+- [YouTube videos](https://www.youtube.com/playlist?list=PLzvN52ZEpjycAiYGH8gwvmNcba9ckz_US)
+- [Google Drive folder](https://drive.google.com/drive/folders/1t2Sdaso1IImNbQC8IbyVLTqBLy8Ftrtb?usp=sharing)
 
 ## iGEM engineering webinars (thanks to Kimia for these resources)
 
 - [https://technology.igem.org/engineering/webinars](https://technology.igem.org/engineering/webinars)
 - [https://2021.igem.org/Engineering/Webinars](https://2021.igem.org/Engineering/Webinars)
+- [Examples of Successful Past iGEM Dry-Lab Projects](https://2020.igem.org/Teams/Mentorship/Dry_Lab_Impulse)
+
+## Bioinformatics
+(thanks to Chae for these resources)
+
+- [Analyzing RNA-seq data with DESeq2](https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html)
+- [RNA-seq workflow: gene-level exploratory analysis and differential expression](https://bioconductor.org/packages/release/workflows/vignettes/rnaseqGene/inst/doc/rnaseqGene.html)
+
+## Chemical Engineering Modelling
+
+- [OpenChemE modelling GitHub](https://github.com/OpenChemE)
+
+## Math Modelling
+
+- [Mathematical modeling in systems biology](https://www.math.uwaterloo.ca/~bingalls/MMSB/Notes.pdf)
+
+## Enzyme Kinetics
+
+(Thanks to Piyush for these resources)
+
+In this section, you will be learning about Enzymes, and how they may be modelled mathematically. This is similar to the Le Chatelier’s principle from **IB Chemistry 12**, so may be a good idea to brush up on that if you are a little rusty!
+
+### OrganicChemTutor: What is an Enzyme?
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/tCGUsiXIYhw?si=P68jJpaMaZKsylAQ" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
+
+### KhanAcademy: Introduction to Enzyme Kinetics
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/X_YXTWU2maY?si=tKspCTakdMpq4kaV" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
+
+### KhanAcademy: Steady States and Michaelis-Menten Equations
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/7u2MkbsE_dw?si=EbxaE-_RQQV75woU" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
+
+### KhanAcademy: Enzymatic Inhibition
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/ALU24yhKJZw?si=ncx0lXGDp2TEbC3n" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
+
+### KhanAcademy: Cooperativity
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/5xp9lI_fXDo?si=Xakc1uBTg53tbJtg" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
+
+### KhanAcademy: Allosteric Regulation and Feedback Loops
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/UWrJssS76XE?si=l4aa-sDBzaye_wwn" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
+
+### KhanAcademy: Non-Enzymatic Protein Function
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/eVmLvbB6L18?si=nY1tfSBOONdYhm1K" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
+
+### KhanAcademy: Covalent Modifications to Enzymes
+
+<iframe width="560" height="315" src="https://www.youtube.com/embed/yqwnRekNLg4?si=0mR1APFVir6rybZO" title="YouTube video player" frameborder="0" allow="accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share" allowfullscreen></iframe>
+
+## Protein Modelling
 
-[Examples of Successful Past iGEM Dry-Lab Projects](https://2020.igem.org/Teams/Mentorship/Dry_Lab_Impulse)
+- [Solvation free energy of ethanol](https://tutorials.gromacs.org/docs/free-energy-of-solvation.html)
+- [Gromacs Tutorials](http://www.mdtutorials.com/gmx/)
+- [Pyrosetta Tutorials](https://www.pyrosetta.org/documentation/tutorials)
+- [Introduction to QM/MM Simulations](https://www.mpinat.mpg.de/634655/Groenhof_2013_Meth_Mol_Biol.pdf)
+- [Quantum Mechanics/ Molecular Mechanics (QM/MM)](https://dasher.wustl.edu/chem478/lectures/lecture-26.pdf)
+- [Hybrid Quantum-Classical simulations (QM/MM) with CP2K interface](https://www.gromacs.org/topic/qmmm.html)
+- [Machine Learning in QM/MM Molecular Dynamics Simulations of Condensed-Phase Systems](https://pubs.acs.org/doi/10.1021/acs.jctc.0c01112)
+- [MiMiC Hybrid Quantum Mechanical/Molecular Mechanical simulations](https://manual.gromacs.org/current/reference-manual/special/mimic-qmmm.html)
+- [Mixed Quantum-Classical simulation techniques](https://manual.gromacs.org/2021.2/reference-manual/special/qmmm.html)
+- [A user-friendly, Python-based quantum mechanics/Gromacs interface: gmx2qmmm](https://onlinelibrary.wiley.com/doi/abs/10.1002/qua.26486)
+- [Practical: Introduction to quantum mechanics / molecular mechanics (QM/MM) simulations](http://cmb.bio.uni-goettingen.de/pract/p7/)
+- [Introduction to QM/MM](https://www.ebi.ac.uk/training/materials/biomolecular-simulations-materials/introduction-to-qm-mm/introduction-to-qm-mm/)

src/resources/project-related.md

@@ -0,0 +1,23 @@
+# Project Related Resources
+
+This is where leads and other subteam members can add ([or request to](https://github.com/UBC-iGEM/internal-wiki-2023-24/pulls)) notes and resources relating specifically to our project.
+
+<!-- toc -->
+## Moore's Law
+
+## Glacial Storage 
+Check out these [dry lab slides](https://docs.google.com/presentation/d/1nQOVYAYPGF8G0qWAzkASHRrQ8TtsM2maiz3NgsDCdHM/edit?usp=sharing) for some info on Glacial Storage!
+
+## Information Theory
+
+### Why binary?
+
+### Error Correction
+
+## Solid Phase Synthesis
+
+![Step 1](./images/sps/sps1.png)
+![Step 2](./images/sps/sps2.png)
+![Step 3](./images/sps/sps3.png)
+![Step 4](./images/sps/sps4.png)
+