Repositories list

• jaxkineticmodel

  Public
  Building, simulating, and training systems biology models using JAX/Diffrax

  systems-biologydynamical-systemskinetic-modeling+ 1neural-odes

  Jupyter Notebook

  •

  Apache License 2.0

  •1•8•0•0•Updated Nov 24, 2025Nov 24, 2025

• ml-assisted-p-coumaric-acid-optimization

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Nov 18, 2025Nov 18, 2025

• drought-microbiome-analysis

  Public
  A collection of processed datasets and a QIIME2-based pipeline to analyze microbiome data from plant roots and soil

  Python

  •0•0•0•0•Updated Oct 29, 2025Oct 29, 2025

• VB2_network_analysis

  Public
  Comparative analysis of microbial association networks in response to Vitamin B2 (VB2) supplementation.

  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Oct 17, 2025Oct 17, 2025

• tudelft-report-thesis-template

  Public template
  A LaTeX report/thesis template that aims to simplify and improve the (Xe)LaTeX template provided by the TU Delft. Ready-to-go with its rewritten class file and redesigned cover page.

  TeX

  •22•0•0•0•Updated Oct 7, 2025Oct 7, 2025

• Comparative-Microbial-Network-Analysis

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Sep 18, 2025Sep 18, 2025

• simulated-dbtl

  Public
  Jupyter Notebook

  •

  MIT License

  •1•3•0•0•Updated Mar 14, 2025Mar 14, 2025

• safpred

  Public
  Synteny-aware gene function prediction for bacteria using protein embeddings

  Python

  •2•5•1•0•Updated Jan 8, 2025Jan 8, 2025

• SAFPredDB

  Public
  Bacterial synteny database

  Python

  •1•0•0•0•Updated Nov 22, 2024Nov 22, 2024

• multi_meta_omics

  Public
  Reprodubility scripts for an ML pipeline for meta-omics data prediction

  Python

  •0•0•0•0•Updated Nov 5, 2024Nov 5, 2024

• poultry_cecum_response

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Oct 22, 2024Oct 22, 2024

• abaumannii-pangenome

  Public
  Python

  •0•0•0•0•Updated Feb 1, 2024Feb 1, 2024

• RP2023_kirbeyi

  Public
  Research Project 2023-2024 Q2 - Kirbeyi

  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •1•1•0•0•Updated Jan 28, 2024Jan 28, 2024

• RP2023_Jarosz

  Public
  Jupyter Notebook

  •

  BSD 3-Clause "New" or "Revised" License

  •1•0•0•0•Updated Jan 28, 2024Jan 28, 2024

• RP2023_Alwani

  Public
  Contains the PPCA, VAE and CVAE model used for the research project. Aside from this there are separate folders for research documents and the dataset related to the project.

  Jupyter Notebook

  •

  MIT License

  •1•0•0•0•Updated Jan 28, 2024Jan 28, 2024

• SHIP

  Public
  Python

  •

  GNU General Public License v3.0

  •1•6•2•0•Updated Jan 18, 2024Jan 18, 2024

• quanttb

  Public
  QuantTB is a SNP based method to identify and quantify individual strains present in tuberculosis whole genome sequencing datasets.

  Python

  •

  GNU General Public License v3.0

  •5•7•0•3•Updated Jul 6, 2023Jul 6, 2023

• javaml

  Public
  Java Machine Learning Library

  Java

  •20•62•3•1•Updated Jul 3, 2023Jul 3, 2023

• long-read-assembly-benchmark

  Public
  Python

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Jan 27, 2023Jan 27, 2023

• hat

  Public
  Haplotype Assembly Tool

  Python

  •

  GNU General Public License v3.0

  •2•8•0•0•Updated Jul 11, 2022Jul 11, 2022

• GraphClean

  Public
  Assembly graph cleaning through machine learning improves de novo long-read assembly

  Python

  •2•0•0•1•Updated Jun 21, 2022Jun 21, 2022

• vlpb-assembly-workshop

  Public
  1•0•0•0•Updated Jun 8, 2022Jun 8, 2022

• abeellab.github.io

  Public
  HTML

  •0•0•0•0•Updated Mar 30, 2022Mar 30, 2022

• ctag

  Public
  Graph genome browser

  Java

  •

  GNU General Public License v3.0

  •1•1•0•0•Updated Mar 10, 2022Mar 10, 2022

• cs4255

  Public
  Course material for the Algorithms for sequence-based bioinformatics course (CS4255) at TU Delft

  1•2•0•0•Updated Nov 5, 2020Nov 5, 2020

• ptolemy

  Public
  Scala

  •

  GNU General Public License v3.0

  •2•10•5•0•Updated Jul 23, 2020Jul 23, 2020

• atk

  Public
  Abeel Toolkit is set of utility classes that are used in our other projects.

  Java

  •

  Other

  •1•1•0•0•Updated Jun 13, 2020Jun 13, 2020

• redwood2

  Public
  1•0•0•0•Updated Jun 12, 2020Jun 12, 2020

• graphlift

  Public
  1•0•0•0•Updated Apr 2, 2020Apr 2, 2020

• parrot

  Public
  Universal genotyping for Mycobacterium tuberculosis strains from WGS

  Scala

  •

  GNU General Public License v2.0

  •0•0•0•0•Updated Oct 11, 2019Oct 11, 2019