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    127 repositories

    • benchling-resources

      Public
      Benchling resources created at DTU Biosustain.
      Python
      •
      GNU General Public License v3.0
      •0•0•0•1•Updated Jan 30, 2025Jan 30, 2025

    • data-catalog-resources

      Public
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jan 29, 2025Jan 29, 2025

    • dsp_notes

      Public
      Public notes and hints of the Data Science Platform.
      Jupyter Notebook
      •1•1•0•2•Updated Jan 28, 2025Jan 28, 2025

    • dsp_Docker_training

      Public
      Docker beginners course initially for Data Club format but to be extended to a longer version soon
      Dockerfile
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jan 22, 2025Jan 22, 2025

    • NextflowPipelineOrchestrator

      Public
      Nextflow
      •0•0•0•0•Updated Jan 21, 2025Jan 21, 2025

    • shu

      Public
      Multi-dimensional, trans-omics metabolic maps.
      visualizationsystems-biologymetabolism
      Rust
      •
      Apache License 2.0
      •1•44•4•0•Updated Jan 20, 2025Jan 20, 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-processfed-batch
      Jupyter Notebook
      •
      MIT License
      •0•7•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
      •8•25•2•0•Updated Jan 5, 2025Jan 5, 2025

    • 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•0•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

    • pankb_llm

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

    • dsp_pandas

      Public
      Organize pandas based functionality across projects.
      Python
      •
      MIT License
      •0•0•0•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

    • 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
      •67•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