Explore projects

This project aims to offer a platform for sharing ideas, resources, tools & techniques, interesting publications, interviews and stories from all our community members. https://grp-bio-it.embl-community.io/blog/

Mahak Bhushan, Francesca Coraggio - Rapti Lab, EMBL Heidelberg; Christian Tischer - Centre for Bioimage Analysis, EMBL Heidelberg; ImageJ Macro, Glia volume measurement

Physicochemical properties and indices for amino-acid sequences (ported from R).

Rust coder/decoder for Nucleotide Archive Format (NAF) files.

Collection of small fiji scripts that are not yet part of larger framework.

R package to read, register and compare point sets from single molecule localization microscopy.

Rendered at: https://grp-bio-it.embl-community.io/template-pages-workbench/

This script implements a machine learning pipeline that integrates the ESM2 transformer-based protein model with a Logistic Regression classifier to predict the detectability of microprotein sequences by Mass Spectrometry. The script preprocesses data, extracts embeddings from sequences, performs feature selection, trains a logistic regression model, and evaluates its performance using multiple metrics.

Source code related to the publication "Visualization of loop extrusion by DNA nanoscale tracing in single human cells" by Beckwith, Ødegård-Fougner et.al. DOI: https://doi.org/10.1101/2021.04.12.439407