Software

I have written some open-source software, some to scratch an itch, and some as part of my research.

Currently Active Projects

NGLess

NGLess is a domain specific language for Next-Generation Sequencing (NGS) processing, with a focus on metagenomics.

More information: https://ngless.embl.de

License: MIT.

mahotas

mahotas is a computer vision package for Python. It operates on numpy arrays. It is implemented in C++ as it has a strong efficiency focus.

License: MIT.

Jug

Jug is a task based framework for running embarassingly parallel code in Python. You can also think of it as a light-weight python-based map-reduce environment.

License: MIT.

mahotas-imread

Imread serves to read and save image files to and from numpy arrays.

License: MIT.

conduit-algorithms

A series of conduit based algorithms in Haskell.

License: MIT

Diskhash

Disk-based hashtable: https://github.com/luispedro/diskhash

fasta_reader

Uses diskhash to index a FASTA file making it very fast to retrieve a sequence:

https://github.com/luispedro/fasta_reader

Reproducible Research

I have also made some code available for reproducible research of published papers.

Dormant Projects

These are projects that work but which I am not too interested in pursuing right now, but which I might revive in the future.

Pymorph: Python Morphology Toolbox

This is a Python image morphology toolbox which I have adopted (i.e., taken over maintaining). This works, but I am not adding any more functionality.

Includes basic operations such as - erode - dilate - open - tophat opening - watershed - ...

License: BSD.

Hex

Hex is a TeX engine in Haskell. It currently does not do much, but it is progressing. The goal is a full reimplementation.

License: GPL.


Copyright (c) 2009-2023. Luis Pedro Coelho. All rights reserved.