Repositories list

• Growth-coupling-suite

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

  Python

  •

  MIT License

  •1•3•1•0•Updated Dec 23, 2024Dec 23, 2024

• 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

  •0•2•0•0•Updated Dec 20, 2024Dec 20, 2024

• benchling-resources

  Public
  Benchling resources created at DTU Biosustain.

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Dec 16, 2024Dec 16, 2024

• pankb_data_prep

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Dec 13, 2024Dec 13, 2024

• pankb_llm

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

  mongodbazurechatbot+ 6pangenomicscosmosdbstreamlitllmvectordbgenai

  Python

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

• pankb_db

  Public
  Python

  •

  MIT License

  •0•0•0•0•Updated Dec 10, 2024Dec 10, 2024

• Alleleome

  Public
  Tools to generate core- and panalleleomes.

  Python

  •

  MIT License

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

• snakemake_UmetaFlow

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

  Python

  •

  Apache License 2.0

  •8•24•2•1•Updated Dec 2, 2024Dec 2, 2024

• dsp_pandas

  Public
  Organize pandas based functionality across projects.

  Python

  •

  MIT License

  •0•0•0•0•Updated Nov 28, 2024Nov 28, 2024

• 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•7•3•0•Updated Nov 28, 2024Nov 28, 2024

• dsp_nextflow_training

  Public
  Hands-on Nextflow training materials and information

  nextflow

  Python

  •

  GNU General Public License v3.0

  •0•2•1•0•Updated Nov 26, 2024Nov 26, 2024

• salb_imodulons

  Public
  Jupyter Notebook

  •

  MIT License

  •0•0•0•0•Updated Nov 25, 2024Nov 25, 2024

• dsp_notes

  Public
  Public notes and hints of the Data Science Platform.

  Jupyter Notebook

  •1•1•0•2•Updated Nov 22, 2024Nov 22, 2024

• dsp_workshop_datavizR

  Public
  Workshop Data Science

  HTML

  •0•1•0•0•Updated Nov 20, 2024Nov 20, 2024

• git-tutorial

  Public
  VS Code on Binder

  Python

  •

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

  •66•3•2•0•Updated Nov 14, 2024Nov 14, 2024

• git-training-table-cool

  Public
  A git training repository for table Cool

  Python

  •

  GNU General Public License v3.0

  •4•0•0•1•Updated Nov 13, 2024Nov 13, 2024

• pyOpenMS_UmetaFlow

  Public
  Untargeted metabolomics workflow for data processing and analysis written in Jupyter notebooks (Python)

  Jupyter Notebook

  •

  Apache License 2.0

  •7•18•1•0•Updated Nov 11, 2024Nov 11, 2024

• dsp_workshop_bash

  Public
  Resources to be used in conjunction with the Bash workshop from the Data Science Platform

  Shell

  •0•1•0•0•Updated Nov 5, 2024Nov 5, 2024

• dsp_nfcore_rnaseq

  Public
  Guide to run nf-core RNA sequencing analysis pipeline in our Azure cloud infrastructure

  0•0•0•0•Updated Oct 30, 2024Oct 30, 2024

• git_training_henry_recording

  Public
  Demo repo for git and GitHub live demo recording

  Python

  •0•0•0•0•Updated Oct 24, 2024Oct 24, 2024

• bgcflow

  Public
  Snakemake workflow for the analysis of biosynthetic gene clusters across large collections of genomes (pangenomes)

  Python

  •

  MIT License

  •9•0•0•0•Updated Oct 16, 2024Oct 16, 2024

• notes_template

  Public template
  Notes template build on Sphinx, Myst parser and a template

  Python

  •

  GNU General Public License v3.0

  •4•0•0•0•Updated Oct 4, 2024Oct 4, 2024

• dsp_notes_template_test

  Public
  Example template testing for course

  Python

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Oct 3, 2024Oct 3, 2024

• simplified_data_science_project_template

  Public template
  A template for data science projects. Simplified, based on datadriven.org's cookiecutter.

  Other

  •0•0•0•0•Updated Sep 20, 2024Sep 20, 2024

• dsp_nfcore_taxprofiler

  Public
  Taxonomica profiling using nf-core/taxprofiler pipeline

  Nextflow

  •

  GNU Affero General Public License v3.0

  •0•0•0•0•Updated Sep 11, 2024Sep 11, 2024

• Maud

  Public
  Enzyme models that take into account kinetics, allostery and thermodynamics

  Python

  •

  GNU General Public License v3.0

  •2•27•22•2•Updated Sep 3, 2024Sep 3, 2024

• ESS-Designs

  Public
  HTML

  •

  MIT License

  •0•0•0•0•Updated Aug 22, 2024Aug 22, 2024

• code-quality-check

  Public
  0•0•0•0•Updated Aug 21, 2024Aug 21, 2024

• shu

  Public
  Multi-dimensional, trans-omics metabolic maps.

  visualizationsystems-biologymetabolism

  Rust

  •

  Apache License 2.0

  •1•44•7•1•Updated Aug 19, 2024Aug 19, 2024

• dsp_nfcore-nanoseq

  Public
  Nanopore demultiplexing, QC and alignment pipeline

  Nextflow

  •

  MIT License

  •82•0•0•0•Updated Aug 13, 2024Aug 13, 2024