5 Minutes of Fame
In the Czodrowski lab (www.czodrowskilab.org) group meeting, we started a session “5 Minutes of Fame”. Here, we update each other about any sort of (scientific/technological) news that might be of interest to the group.
Content
SAR table in Jupyter notebook
Date: 2023-03-10
Author: Julien Hazemann
Description: Structure-Activity Relationship (SAR) of a tetrahydroisoquinoline series antagonist of the OX1 and OX2 orexin receptors.
Jupyter Graffiti: an interactive screencast for jupyter notebook
Date: 2022-12-16
Author: Michel Lim
Description: functions and usage of Jupyter Graffiti.
What’s new in Python 3.11: My favorite additions
Date: 2022-12-09
Author: Aishvarya Tandon
Description: This notebook shows 3 new features/updates in Python 3.11.
Cohen’s kappa
Date: 2022_11_20
Author: Alexander Mielke
Description: Short presentation on the Cohen’s kappa score and weighted versions.
Cell Cropping with Otsu’s Method
Date: 2022_11_24
Author: Son Ha
Description: Pythonic way of cropping cells from microscopy images using Otsu’s method.
AIDD School Feedback
Date: 2022_11_11
Author: Son Ha
Description: Recap of AIDD School, a series of talks organised by AIDD, an EU program which Son is a part of.
gitbook
Date: 2022_11_04
Author: Paul Czodrowski
Description: gitbook
RDKit Feedback
Date: 2022_10_28
Author: Marcel Baltruschat, Aishvarya Tandon, Helge Vatheuer, Son Ha
Description: Highlights of 2022 RDKit UGM.
Clustering of Mpro fragment hits with SOM
Date: 2022-10-27
Author: Julien Hazemann
Description: Clustering of SARS-COV-2 Mpro Fragment Hits with a Self-Organizing Map.
Write (and read) configs with TOML
Date: 2022-10-07
Author: Aishvarya Tandon
Description: Quick introduction to TOML with hands-on tutorial. You will also learn how convenient it is to prepare and read log or config files made by TOML.
IPython Widgets and Voilà
Date: 2022-09-16
Author: Marcel Baltruschat
Description: This notebook shows how you can build interactive widgets in Jupyter notebooks and use Voilà to create a standalone web application out of it.
Writefull
Date: 2022-09-09
Author: Anna Riede
Description: Academic Writing requires more than a spell check. Check out “Writefull” (https://www.writefull.com/) to improve your scientific papers / lab reports / …
GitHubCopilot meets RDKit
Date: 2022-08-12
Author: Helge Vatheuer
Description: Simple tasks of rdkit performed with the Copilot plugin inside VSCode – live demo is actually more impressive than the notebook.
Gradio
Date: 2022-08-05
Author: Son Ha
Description: Quick and convenient way to set up a web interface for you machine learning model.
Quantum Mechanics
Date: 2022-07-22
Author: Paul Czodrowski
Description: Quantum mechanics and analytical chemistry courses ported to Jupyter notebooks. One more thing: Blog entry by Derek Lowe
Tikzplotlib
Date: 2022-06-24
Author: Luca Kröll
Description: Short introduction to TikZ package in LaTeX and tikzplotlib tool for Python. Fascilitates making graphs and figures for LaTeX documents.
Decision Tree Classifier
Date: 2022-06-10
Author: Katharina Alker
Description: This notebook describes how to apply a DecisionTreeClassifier with the implemented algorithm of scikit-learn, which can be found on https://scikit-learn.org/stable/modules/tree.html. Including overtraining plot and visualisation of the important features using the example of morgan fingerprints.
(How to) Use Cohen’s kappa for your binary classification models!
Date: 2022-05-06
Author: Aishvarya Tandon
Description: This notebook introduces you to Cohen’s kappa and how to incorporate it with your binary classification model workflow. It’s use with k-fold cross-validation and Optuna hyperparameter optimization is also discussed.
Streamlit
Date: 2022-04-29
Author: Helge Vatheuer
OpenAI and Phrasebank
Date: 2022-04-08
Author: Son Ha
Description: 1) OpenAI Gym is a collection of Reinforcement Learning environment for you to train your RL algorithm. 2) Academic Phrasebank is a collection of academic sounding phrases you can use for your report/paper.
Track Optuna Hyperparameter Tuning with MLflow
Date: 2022-03-18
Author: Marcel Baltruschat
Description: This notebook shows how you can do hyperparameter tuning with Optuna and track the results with MLflow. It includes examples for automatic logging together with scikit-learn as well as manual logging with PyTorch.
molplotly
Date: 2022-03-11
Author: Prof. Dr. Paul Czodrowski
CReM – chemically reasonable mutations
Date: 2022-02-25
Author: Julien Hazemann
OpenMM PyMol
Date: 2022-02-18
Author: Frederik Götz
Bunte Tüte
Date: 2022-02-10
Author: Helge Vatheuer
Quick intro to Optuna
Date: 2022-02-04
Author: Aishvarya Tandon
Description: This notebook introduces you to Optuna and provides cheminformatics examples for its usage.
GNN Interpretability
Date: 2022-01-28
Author: Marcel Baltruschat
Description: This notebook explores PyTorch Captum and GNNExplainer integrated in PyTorch Geometric to make Graph Neural Networks interpretable and more understandable. As an example, a GNN classification model for dividing compounds in two classes according to their mutagenic effect on a bacterium is examined.
Graph Classification with Graph Neural Networks
Date: 2022-01-21
Author: Son Ha
Description: This Notebook goes through how to construct a simple Graph Neural Network with PyTorch Geometric.
Dynamut Omicron Mpro with P132H mutation
Date: 2021-12-17
Author: Julien Hazemann
AiZynthFinder
Date: 2021-12-17
Author: Julien Hazemann
Data Visualisation Catalogue
Date: 2021-11-12
Author: Juliana Gretz
Generating a SARS-CoV Mpro chemical space with Reinvent
Date: 2021-11-05
Author: Julien Hazemann
Regex Cheatsheet
Date: 2021-10-08
Author: Juliana Gretz
Pyro Showcase
Date: 2021-09-24
Author: Son Ha
Description: This notebook showcases some implementation of Pyro, a library built on PyTorch to facilitate your need for deep neural network statistical modeling.
mols2grid
Date: 2021-09-02
Author: Prof. Dr. Paul Czodrowski
Impact of chemical transformations on the hERG inhibition
Date: 2021-08-27
Author: Julien Hazemann
Load and write Pandas Dataframe faster, securely and efficiently with Parquet
Date: 2021-08-20
Author: Aishvarya Tandon
Description: In this notebook, I compare different dataframe saving and reading techniques, with the focus on parquet. I show that using parquet to save and read big dataframes has advantages over other methods.
DeepFrag
Date: 2021-07-23
Author: Helge Vatheuer
Speed Up Cheminformatics
Date: 2021-07-16
Author: Marcel Baltruschat
Description: This notebook shows possibilities to speed up cheminformatics using NVIDIA® RAPIDS and Python Multiprocessing. This example includes exploring chemical space, calculating fingerprints, perform clustering or train machine learning models.
Covid-19 Moonshot
Date: 2021-07-09
Author: Prof. Dr. Paul Czodrowski
What’s new in Python 3.8 and 3.9
Date: 2021-02-04
Author: Marcel Baltruschat
Description: This notebook shows a quick summary of some interesting and useful new features introduced in Python 3.8 and 3.9.