pharmb.io

sciluigi

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

plaid

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

robotlab

Cell painting and imaging with robots

imagedb

Image database for pharmbio microscope images

kubeflow-pipelines

pharmbio-web

The Static (Hugo) website for pharmb.io

squid

big-data_course

Material for the Big Data in life science course

big-data_deeplearning

Big data course, Deep learning repo

CellViewer

CellViewer, a customizable, zoomable widget for fluorescent microscopy images

pharmbio-notebook

Docker containers for interactive notebook environments for rancher cluster

helm-charts

phospholipidosis_project

Data analysis and models for predicting phospholipidosis readouts from cell painting

sc_celldeath

Analysis scripts for single-cell celldeath publication

colopaint3D

Supporting scripts and code for Cell Painting in 3D spheroids

ConformalPrediction_Sofia

Assignment_3a_LeukemiaCells

Easier paths leukemia cells BDLS Assignment 3.a

cage2_automation

cp_pipeline

cppipeline2

version 2 of cppipeline

DeepLearningTutorials

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

lmm-student

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

lmu-student

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

pharmbio_LaTeX_templates

A series of LaTeX templates used by us

pipelinegui

ptp

s3uploader

service that uploads images to s3

sarscov2-phenomics-repurposing

This repository contains code and data associated with the manuscript "Morphological cell profiling for drug repurposing against SARS-CoV-2 infection"

SegMine

Playground for Segmentation and Data-mining

SphereDetect

Implementation of algorithm to automatically detect spheroid base Z plane in multiwell microscopy.