metabolicengineeringgroupcbma Goto Github PK

anacondablogpost

Pydna code examples for our Anaconda blog post

cunha_et_al_2017

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.

ddel

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

elitech-datareader

Elitech RC-4 data access tool and library.

growthmodels

Collection of code for growth modeling

mecwiki

metabolicengineeringgroupcbma.github.io

This is our group wiki.

old_site

This is our group website https://metabolicengineeringgroupcbma.github.io/

pereira_et_al_2022

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.

pozdniakova_et_al_2023

Supplementary data for Pozdniakova 2023

primerdesignnotebook

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.

pta-gfp

GFP

pydna-examples

Jupyter notebooks and data files that demonstrates how pydna can be used to simulate and document cloning.

pydna_template

This is a template repository for a pydna documentation and simulation project.

silva_et_al_2020

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.

silva_et_al_2022

yeastpathwaykit

Yeast pathway kit promoter and terminator vectors and other related public information. Do not put secret information here.

ypk-xylose-pathways

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.