研究生院Orléans数字化学信息学课程期间与学生共享的笔记本存储库。.zip

# GSON module "chimie informatique sous python" This course is mostly based on [teachopencadd](https://github.com/volkamerlab/teachopencadd). Huge thanks to them for providing such good learning material. ## Launch notebooks directly in your browser - If you prefer the modern `jupyter lab` interface: [](https://mybinder.org/v2/gh/ICOA-SBC/GSON-cheminformatics/HEAD) - be careful that for the exos using `nbautoeval`, the cell output may return error - for the moment it is **NOT recommended to use above method** - If you prefer the traditional `jupyter notebook` interface: [](https://mybinder.org/v2/gh/ICOA-SBC/GSON-cheminformatics/HEAD?urlpath=/tree/) The materials are exactly the same. The only difference is the appearance. The 1st launch can take around 10 minutes, and it will be faster from 2nd time. It **does not require any setup/installation on your machine** (which is quite easy to use). You just need an Internet connection and a browser. **Remarks:** 1. To save resources, your connection to the `Binder` server will be **automatically cut off** if you have no activity (cell edit/cell execution) for around 10 mins 2. Your changes to the notebooks will **NOT be saved**. So if you close the browser and re-open `Binder`, you lose all what you have done previously... ## Special instructions for promo 2023-2024 If you are using `Windows` on your own PC, before each course, please execute the command `git pull` in your terminal, to get the latest version of material. If you are using the `Linux` session on the PCs of "salle info", here are the commands to follow, from Tuesday to Friday: 1. Open a terminal, copy-paste below command into it, and execute it: ```bash /opt/anaconda3/bin/conda init ``` 2. Normally, the message of the terminal will suggest you to close and re-open the terminal after above command is executed successfully. Simply close and re-open another terminal. You should now see `(base)` on the leftmost of your prompt. (ask the teachers if you still cannot see it) 3. Create the virtual environment for this course from given file, by copy-paste below command into your terminal, and execute it: ```bash conda env create -f https://raw.githubusercontent.com/ICOA-SBC/GSON-cheminformatics/master/environment.yml ``` - This file contains a list of `conda`/`pip` packages that are required for this course. - You are encouraged to check the content of this file, to make sure it does not contain malicious software. - This command will take 3-10 mins, depending on the configuration of your PC, and the Internet connection 4. Once above command finishes with success, you can now clone the repo to your local PC, by copy-paste below command into your terminal, and execute it: ```bash git clone https://github.com/ICOA-SBC/GSON-cheminformatics ``` 5. Activate the virtual environment: ```bash conda activate teachopencadd ``` - You should observe that the `(base)` has become `(teachopencadd)`, meaning that you are now in this new virtual environment. 6. You are ready to go. Simply launch the `notebook` interface with command: ```bash jupyter notebook ``` ## Organisation of session 2023-2024 ### Lundi 15 janvier 2024 13h30-17h30 - Introduction - Slides 1_GSON_intro (30 min) XM & JM - Slides 2_introduction_informatique (45 min) XM - Talktorial Introductif 1 Intro Python, jupyter (1h40) XM ### Mardi 16 janvier 2024 13h30-17h30 - Talktorial Introductif 2 Intro chemoinfo - RDKit (1h40) JM - Data Acquisition (1h30) XM - Talktorial 1 Data acquisition from ChEMBL ### Mercredi 17 janvier 2024 13h30-17h30 - Filtering (1h45-2h) JM - Descriptors and ADME (1h30) - Slides 4_Descripteurs_fingerprints - Talktorial 2 Molecular filtering: ADME/Lipinski criteria - Filtering (40 min) XM - Talktorial 3 Substructure removal : PAINS ### Jeudi 18 janvier 2024 13h30-17h30 - Ligand based Screening (2h30) JM - Slides 5_fingerprint_similarity (30 min) - Talktorial 4 Fingerprints and Molecular Similarity (2h) - Clustering (1h45) XM - Talktorial 5 : Compound clustering ### Vendredi 19 janvier 2024 13h30-17h30 - Machine Learning (1h45) JM - Slides 6_Machine Learning - Talktorial 7 Machine Learning (ROC curve) - Applications in chemoinformatic (45 min) XM & JM - Slides 7_Applications - Exam (60 min) ## History of previous years - 2018: Fabrice, Colin - 2019: Colin, Gautier - 2020: Gautier, Pierre-Yves - 21 students - Integration of TeachOpenCADD and binder - 2021: Gautier, Pierre-Yves - 22 students - Distance learning, via TEAMS - Integration of nbautoeval (Exercises and Quiz) - 2022: Pierre-Yves, Xiaojun - 9 students (7 present, 2 absent) - Introduce ```mamba``` for quicker env resolution - Added short introduction of Linux Commands - 2023: Pierre-Yves, Xiaojun - 5 students (4 present, 1 absent) - Created a pre-course questionnaire to better adapt the course to future students attending the course - 2024: Xiaojun, Jérémy - 17 students (16 inscriptions + 1 volunteer participant) - Cleaned not used packages/channels in `environment.yml` for quicker env resolution - Added `Slide 7_Applications`, to showcase other fields of applications not covered in the course ## Installation Suppose that you are using **Linux** (**MacOS** should work the same way, since it is also **Unix**): 1. Install `miniconda` (or `anaconda` if you prefer) - For installation details, please refer to their [official documentation](https://docs.conda.io/en/latest/miniconda.html). 2. Open a terminal, you should normally see `(base)` before your prompt. (See below FAQ part if you cannot see `(base)`) Create the virtual environment for this course from given file: ```bash conda env create -f https://raw.githubusercontent.com/ICOA-SBC/GSON-cheminformatics/master/environment.yml ``` - This file contains a list of `conda`/`pip` packages that are required for this course. - You are encouraged to check the content of this file, to make sure it does not contain malicious software. 3. Open a terminal, and clone the repo to your local PC: ```bash git clone https://github.com/ICOA-SBC/GSON-cheminformatics ``` 4. Activate the virtual environment: ```bash conda activate teachopencadd ``` - You should observe that the `(base)` has become `(teachopencadd)`, meaning that you are now in this new virtual environment. 5. You are ready to go. Simply launch the `notebook` interface with command: ```bash jupyter notebook ``` ## FAQ ### What if you cannot find `conda` by typing `which conda`, or you do not see `base` before your prompt? Experience 2024: In the computer rooms of COST, `conda` is installed at `/opt/anaconda3`, not under each user's `/home`. Furthermore, it is NOT added to the `$PATH`, making it unfindable by `which conda` command. Even more, the `/home` of each student will be automatically deleted on the 2nd day of the course, after restarting the PC...(by default the PCs are automatically shut down during the night). So it means the students have to repeat the steps of - initiate `conda` - create `conda` virtual environment - clone the course material from Tuesday to Friday, before each course starts (which is annoying!) ### Work in progress, reserved for teachers 1. Open a terminal, and type `echo $PATH` to check the existing PATHS (normally you shoud not be able to find `/opt/anaconda3`). 2. Type `gedit ~/.bashrc`. A text editor interface will automatically appear. 3. Add `export PATH=/opt/anaconda3/bin:$PATH` to the end of the file, then save and close the file. 4. Reload the profile with `source ~/.bashrc` 5. Type the command `which conda`, you should be able to find it at `opt/anaconda3/`. 6. Type the command `conda init bash` to initiate it. 7. Reload the profile with `source ~/.bashrc`. After all these steps, you should now see `(base)` before your prompt. ### Anot