Repositories list

• big-data_course

  Public
  Material for the Big Data in life science course

  TeX

  •3•2•0•0•Updated May 5, 2025May 5, 2025

• pharmbio-web

  Public
  The Static (Hugo) website for pharmb.io

  JavaScript

  •8•3•0•4•Updated May 2, 2025May 2, 2025

• imagedb

  Public
  Image database for pharmbio microscope images

  JavaScript

  •1•5•9•3•Updated Apr 28, 2025Apr 28, 2025

• pharmbio-notebook

  Public
  Docker containers for interactive notebook environments for rancher cluster

  Dockerfile

  •1•2•0•1•Updated Apr 15, 2025Apr 15, 2025

• big-data_deeplearning

  Public
  Big data course, Deep learning repo

  Jupyter Notebook

  •0•2•0•0•Updated Apr 15, 2025Apr 15, 2025

• helm-charts

  Public
  Mustache

  •0•1•1•0•Updated Apr 9, 2025Apr 9, 2025

• robotlab

  Public
  Cell painting and imaging with robots

  Python

  •

  MIT License

  •1•12•4•0•Updated Apr 8, 2025Apr 8, 2025

• squid

  Public
  C

  •39•3•6•0•Updated Mar 21, 2025Mar 21, 2025

• DeepLearningTutorials

  Public
  Deep Learning Notebooks adapted for some of our courses by David Holmberg - including PB_SEQ, ULLA, Ai4DD etc

  Jupyter Notebook

  •1•0•0•0•Updated Mar 13, 2025Mar 13, 2025

• cppipeline2

  Public
  version 2 of cppipeline

  Python

  •0•0•0•0•Updated Mar 3, 2025Mar 3, 2025

• pipelinegui

  Public
  JavaScript

  •0•0•1•0•Updated Feb 26, 2025Feb 26, 2025

• cp_pipeline

  Public
  Python

  •0•0•0•0•Updated Feb 26, 2025Feb 26, 2025

• plaid

  Public
  PLAID (Plate Layouts using Artificial Intelligence Design) is a flexible constraint-programming model representing the Plate Layout Design problem.

  artificial-intelligenceconstraint-programmingplaid+ 3experimental-designmicroplate-designmultiplate-layout-design

  Jupyter Notebook

  •4•17•0•2•Updated Feb 5, 2025Feb 5, 2025

• colopaint3D

  Public
  Supporting scripts and code for Cell Painting in 3D spheroids

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Feb 4, 2025Feb 4, 2025

• lmu-student

  Public
  Deep Learning Notebooks adapted for some of our courses by David Holmberg - including PB_SEQ, ULLA, Ai4DD etc

  Jupyter Notebook

  •0•0•0•0•Updated Feb 3, 2025Feb 3, 2025

• lmm-student

  Public
  Deep Learning Notebooks adapted for some of our courses by David Holmberg - including PB_SEQ, ULLA, Ai4DD etc

  Jupyter Notebook

  •0•0•0•0•Updated Feb 3, 2025Feb 3, 2025

• sc_celldeath

  Public
  Analysis scripts for single-cell celldeath publication

  Jupyter Notebook

  •0•1•0•0•Updated Jan 23, 2025Jan 23, 2025

• ConformalPrediction_Sofia

  Public
  0•0•0•0•Updated Dec 21, 2024Dec 21, 2024

• ptp

  Public
  JavaScript

  •1•0•2•0•Updated Dec 19, 2024Dec 19, 2024

• sciluigi

  Public
  A light-weight wrapper library around Spotify's Luigi workflow library to make writing scientific workflows more fluent, flexible and modular

  workflowworkflow-enginescientific-workflows+ 1luigi

  Python

  •

  MIT License

  •56•336•21•3•Updated Dec 10, 2024Dec 10, 2024

• kubeflow-pipelines

  Public
  Python

  •1•3•0•1•Updated Aug 2, 2024Aug 2, 2024

• Assignment_3a_LeukemiaCells

  Public
  Easier paths leukemia cells BDLS Assignment 3.a

  0•0•0•0•Updated Jun 10, 2024Jun 10, 2024

• SegMine

  Public
  Playground for Segmentation and Data-mining

  MIT License

  •1•0•0•0•Updated May 8, 2024May 8, 2024

• rstudio-docker

  Public
  Dockerfile for rstudio server with python support

  Dockerfile

  •0•0•0•0•Updated May 1, 2024May 1, 2024

• nw-cp

  Public
  A master thesis on using Graph Neural Networks and Network Analysis approach in morphological profiling of chemical perturbated cells

  HTML

  •

  MIT License

  •0•1•0•0•Updated Apr 4, 2024Apr 4, 2024

• conformal-eval

  Public
  Refactored version of the Plot_utils library, for generating a single installable distribution

  Python

  •

  MIT License

  •2•2•0•0•Updated Apr 3, 2024Apr 3, 2024

• SC_analysis_Benjamin

  Public
  Main analysis scripts of sc master thesis

  Jupyter Notebook

  •0•0•0•0•Updated Mar 29, 2024Mar 29, 2024

• DeepProfiler_Benjamin

  Public
  DeepProfiler analysis scripts for RH30, Specs3k datasets

  Jupyter Notebook

  •0•0•0•0•Updated Mar 23, 2024Mar 23, 2024

• cplogd-v2.0

  Public
  cpLodD version 2.0 - using ChEMBL v33

  Jupyter Notebook

  •0•2•0•0•Updated Feb 5, 2024Feb 5, 2024

• plot_utils

  Public
  Repo that groups utility functions for e.g. plotting of Conformal prediction metrics

  Jupyter Notebook

  •2•16•0•0•Updated Feb 2, 2024Feb 2, 2024