Kinetic Modelling also can be accessed through this Tableau Visualization
├── README.md <- The description of this project.
├── Kinetic-Modelling
│ ├── Kinetic Modeling Equation for LIRA.pdf <- Equation of Kinetic Modelling and constanta
│ ├── Kinetic_Modeling_for_LIRA.ipynb <- Kinetic modelling for LIRA with visualization
│ └── kinetic_modelling_for_tableau.ipynb <- Kinetic modelling for combination setup
│
└── LiRA-Optimization
├── autogluon-nupack.ipynb <- Processing using AutoGluon
├── final.csv <- Gathering parameter result
├── NUPACK Design Parameter Settings for LIRA.pdf <- Guide to setup Design Job
├── pipeline.ipynb <- Gathering Sequence, Parameters, and Linear Regression Multivariate Regression
└── table_data_a10996f7-3a7c-49eb-ba3c-bf682effc883.csv <- Raw data
Some of codes used are run on Google Colaboratory and Kaggle, so some of parts (might include pip install) have been included the installations process or using pre-installed package in cloud-based server. However, NUPACK can't run on cloud-based server such as Colab/Kaggle due to its requirement to be installed on top of Linux-based Environment. Follow these guide to install main library used in this repo:
- NUPACK: https://docs.nupack.org/start/
- AutoGluon: https://auto.gluon.ai/stable/install.html