Repositories list

• benchling-resources

  Public
  Benchling resources created at DTU Biosustain.

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jul 31, 2025Jul 31, 2025

• dsp_course_proteomics_intro

  Public
  Introduction to massspectrometry-based proteomics.

  Jupyter Notebook

  •3•1•1•2•Updated Jul 29, 2025Jul 29, 2025

• guidelines

  Public
  Guidelines for employees and collaborators at CFB, with the goal of educating readers and minimizing the likelihood of issues arising with our computational platforms.

  best-practicesguidelines

  0•2•0•0•Updated Jul 28, 2025Jul 28, 2025

• dsp_notes

  Public
  Public notes and hints of the Data Science Platform.

  Python

  •1•1•0•3•Updated Jul 28, 2025Jul 28, 2025

• python_package

  Public template
  Example Python package

  Python

  •

  MIT License

  •1•1•2•2•Updated Jul 23, 2025Jul 23, 2025

• dsp_nf-nanoseq-preprocess

  Public
  nextflow pipeline to parse data from our datalake into a format directly compatible with nf-core/nanoseq

  Nextflow

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Jul 16, 2025Jul 16, 2025

• PioGrowth

  Public
  App for analysis of optical density measurements produced mainly with a PioReactors, see https://pioreactor.com/

  R

  •

  MIT License

  •1•0•0•0•Updated Jul 14, 2025Jul 14, 2025

• shu

  Public
  Multi-dimensional, trans-omics metabolic maps.

  visualizationsystems-biologymetabolism

  Rust

  •

  Apache License 2.0

  •1•48•5•0•Updated Jun 20, 2025Jun 20, 2025

• dsp_metagenomics_training

  Public
  Introduction course to metagenomics data analysis

  HTML

  •

  GNU General Public License v3.0

  •2•2•0•0•Updated Jun 11, 2025Jun 11, 2025

• GRASP

  Public
  GRASP allows the user to build kinetic models of cell metabolism and analyse them.

  HTML

  •

  Other

  •2•3•6•11•Updated Jun 10, 2025Jun 10, 2025

• dsp_transcriptomics_training

  Public
  Introduction course to transcriptomics

  HTML

  •

  GNU General Public License v3.0

  •2•5•0•0•Updated May 31, 2025May 31, 2025

• QurvE

  Public
  Robust and user-friendly analysis of growth curves (developed at DTU biosustain)

  R

  •6•0•0•0•Updated May 21, 2025May 21, 2025

• dsp_actions_tutorial

  Public
  Simple GitHub Actions example for the Data Club on the 30th of April at DTU biosustain and DTU bioengineering

  16•2•0•0•Updated Apr 30, 2025Apr 30, 2025

• pankb

  Public
  The Pangenome Knowledge Base (PanKB) serves as an up-to-date resource for pangenomics research methods and the dissemination of results and currently offers basic pangenome characteristics and advanced pangenome analytics for 8 major biotech bacteria families.

  HTML

  •

  MIT License

  •1•4•0•0•Updated Apr 30, 2025Apr 30, 2025

• pankb_db

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Apr 30, 2025Apr 30, 2025

• pyphylon

  Public
  Fork of pyphylon to be used in BGCFlow

  Python

  •

  MIT License

  •2•0•0•0•Updated Apr 29, 2025Apr 29, 2025

• dsp_nf-assembly-to-gene-calling

  Public
  Nextflow

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Apr 9, 2025Apr 9, 2025

• Azure-Seqera-Integrator

  Public
  0•0•0•0•Updated Mar 7, 2025Mar 7, 2025

• bayesian_statistics_for_computational_biology

  Public archive
  A Bayesian statistics course for computational biologists

  HTML

  •

  Creative Commons Attribution 4.0 International

  •2•4•0•0•Updated Mar 4, 2025Mar 4, 2025

• Growth-coupling-suite

  Public
  A constraint-based metabolic model-based workflow for computing and analyzing microbial strain designs which couple a target reaction to growth

  Python

  •

  MIT License

  •1•4•0•0•Updated Feb 24, 2025Feb 24, 2025

• dsp_docker_training

  Public
  Introduction to Docker

  Python

  •1•0•0•0•Updated Feb 24, 2025Feb 24, 2025

• snakemake-ont-bacterial-variants

  Public
  A Snakemake workflow for the identification of variants in bacterial genomes using nanopore long-read sequencing.

  Python

  •

  MIT License

  •2•0•0•0•Updated Feb 17, 2025Feb 17, 2025

• data-catalog-resources

  Public
  Python

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Jan 29, 2025Jan 29, 2025

• NextflowPipelineOrchestrator

  Public
  Nextflow

  •0•0•0•0•Updated Jan 21, 2025Jan 21, 2025

• salb_imodulons

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Jan 20, 2025Jan 20, 2025

• pankb_data_prep

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Jan 11, 2025Jan 11, 2025

• pseudobatch

  Public
  The Pseudobatch transformation is a method to easy analysis of measurement from a fed-batch fermentation process. After transformation, the data can be analysed as if it was obtained from a batch fermentation process. The Pseudobatch transformation is especially useful for fed-batch processes where samples where drawn from the bioreactor.

  microbiologyfermentationfermentation-process+ 1fed-batch

  Jupyter Notebook

  •

  MIT License

  •0•8•3•0•Updated Jan 10, 2025Jan 10, 2025

• snakemake_UmetaFlow

  Public
  Untargeted metabolomics workflow for large-scale data processing and analysis implemented in Snakemake

  Python

  •

  Apache License 2.0

  •7•27•2•0•Updated Jan 5, 2025Jan 5, 2025

• pankb_llm

  Public
  An LLM-based pangenomics chatbot integrated into the PanKB website.

  mongodbazurechatbot+ 6pangenomicscosmosdbstreamlitllmvectordbgenai

  Python

  •1•0•0•0•Updated Dec 11, 2024Dec 11, 2024

• Alleleome

  Public
  Tools to generate core- and panalleleomes.

  Python

  •

  MIT License

  •0•1•0•0•Updated Dec 5, 2024Dec 5, 2024