Software

A non-exhaustive list of coding and analysis projects

Software Packages

metaSolid

Python package which integrates local/cloud LLMs and semantic embeddings models to generate harmonized meta data fields. Harmonization can results from semantic clustering or against a common target.

Hermetica

Protocol version control. Pulls wet lab protocols from multiple sources and provides strict version control by generating a protocol lock file. Wet lab pipeline using multiple protocols are converted into DAG that are also tracked and version controlled.

esgaliant

Building Synthetic data to anchor large scale foundations models and understand that actual biology of large scale data sets.

Vesalius

Dissecting Tissue Anatomy From Spatial Transcriptomics data and Mapping heterogenous Spatial data.

Bombadillo

Spatial Omics simulator including cell-cell interactions.

Kuresi

Assessing Cancer Competivity through ELO style DEG tournaments.

ChIPanalyser

Bioconductor package to predict Transcription Factor Binding to DNA using a statistical thermodynamic framework and evolutionary optimization.

Analysis

Vesalius Analysis

Analysis repository for Vesalius 2.0.0. (Nature Communications).

SPIX Analysis

Nextflow pipeline with containers (Docker and Apptainer) with all the analysis related to the Super Pixel (SPIX) project.

Development enviroment handled with Nix.

esgaliant-an

Nextflow pipeline with containers (Docker and Apptainer) with all the analysis related to the esgliant project.

Development enviroment handled with Nix.

GAND

Nextflow pipeline with conda environments with all the analysis related to the GAND Neuro-degenerative diseases project.

Conda will replaced with containers at publication time.