Skip to content

@MetabolicEngineeringGroupCBMA Metabolic Engineering Group at CBMA

Change the repository type filter

All

    Repositories list

    18 repositories

    • YeastPathwayKit

      Public
      Yeast pathway kit promoter and terminator vectors and other related public information. Do not put secret information here.
      vectorpromoterspydnaplasmids
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Nov 8, 2024Nov 8, 2024

    • ypk-xylose-pathways

      Public
      Pereira, F., Azevedo, F., Parachin, N. S., Hahn-Hägerdal, B., Gorwa-Grauslund, M. F., & Johansson, B. (2016). Yeast Pathway Kit: A Method for Metabolic Pathway Assembly with Automatically Simulated Executable Documentation. ACS Synthetic Biology, 5(5), 386–394.
      pydnajupyter-notebooks
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Apr 8, 2024Apr 8, 2024

    • pydna-examples

      Public
      Jupyter notebooks and data files that demonstrates how pydna can be used to simulate and document cloning.
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •0•3•0•0•Updated Mar 5, 2024Mar 5, 2024

    • MetabolicEngineeringGroupCBMA.github.io

      Public
      This is our group wiki.
      0•1•0•0•Updated Jan 30, 2024Jan 30, 2024

    • old_site

      Public
      This is our group website https://metabolicengineeringgroupcbma.github.io/
      0•1•0•0•Updated Jan 27, 2024Jan 27, 2024

    • Pozdniakova_et_al_2023

      Public
      Supplementary data for Pozdniakova 2023
      Jupyter Notebook
      •0•0•0•0•Updated Jun 22, 2023Jun 22, 2023

    • Silva_et_al_2022

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Nov 9, 2022Nov 9, 2022

    • pydna_template

      Public template
      This is a template repository for a pydna documentation and simulation project.
      ipynbreproducibilityjupyter-notebookspydna
      Jupyter Notebook
      •0•1•0•0•Updated Nov 9, 2022Nov 9, 2022

    • Pereira_et_al_2022

      Public
      Pereira, Humberto, Flávio Azevedo, Lucília Domingues, and Björn Johansson. 2022. “Expression of Yarrowia Lipolytica Acetyl-CoA Carboxylase in Saccharomyces Cerevisiae and Its Effect on in-Vivo Accumulation of Malonyl-CoA.” *Computational and Structural Biotechnology Journal* 20 (January 1): 779–787.
      bioinformaticsbiologyacademic-paperbiotechnologypythonnotebookjupyter-notebookjupyter-notebooks
      Jupyter Notebook
      •0•0•0•0•Updated Oct 30, 2022Oct 30, 2022

    • Silva_et_al_2020

      Public
      Silva, Paulo César, Javier A. Ceja-Navarro, Flávio Azevedo, Ulas Karaoz, Eoin L. Brodie, and Björn Johansson. 2021. “A Novel D-Xylose Isomerase from the Gut of the Wood Feeding Beetle Odontotaenius Disjunctus Efficiently Expressed in Saccharomyces Cerevisiae.” *Scientific Reports* 11 (1) (February 26): 4766.
      jupyter-notebook
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Oct 30, 2022Oct 30, 2022

    • PrimerDesignNotebook

      Public
      A Jupyter notebook for primer design and/or testing using Pydna. The primers are meant to be used to express genes using the yeast pathway kit system.
      Jupyter Notebook
      •0•0•0•0•Updated Sep 23, 2022Sep 23, 2022

    • AnacondaBlogPost

      Public
      Pydna code examples for our Anaconda blog post
      Jupyter Notebook
      •0•0•0•0•Updated Feb 27, 2022Feb 27, 2022

    • pTA-GFP

      Public
      GFP
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jan 20, 2022Jan 20, 2022

    • dDEL

      Public
      Silva, P. C., Domingues, L., Collins, T., Oliveira, R., & Johansson, B. (2018). Quantitative assessment of DNA damage in the industrial ethanol production strain Saccharomyces cerevisiae PE-2. FEMS Yeast Research. https://doi.org/10.1093/femsyr/foy101
      jupyter-notebooks
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Dec 19, 2021Dec 19, 2021

    • elitech-datareader

      Public
      Elitech RC-4 data access tool and library.
      Python
      •
      MIT License
      •18•0•0•0•Updated Sep 30, 2021Sep 30, 2021

    • Cunha_et_al_2017

      Public
      Costa, C. E., Romaní, A., Cunha, J. T., Johansson, B., & Domingues, L. (2017). Integrated approach for selecting efficient Saccharomyces cerevisiae for industrial lignocellulosic fermentations: Importance of yeast chassis linked to process conditions. Bioresource Technology, 227, 24–34.
      jupyter-notebookspydnasaccharomyces-cerevisiae
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •0•1•0•0•Updated Sep 25, 2021Sep 25, 2021

    • growthmodels

      Public
      Collection of code for growth modeling
      Jupyter Notebook
      •0•0•0•0•Updated Jan 3, 2020Jan 3, 2020

    • MecWiki

      Public
      wikidpadmecpluginswikiwikidpad-wiki
      0•0•0•0•Updated Nov 12, 2019Nov 12, 2019