Steffen Klamt's Lab at the Max Planck Institute Magdeburg

All

17 repositories

straindesign
Public
StrainDesign is a python package for the computational design of metabolic networks and based on COBRApy
bioinformatics systems-biology computational-biology milp mcs cobrapy strain-engineering strain-design optknock optcouple
Python
•
Apache License 2.0
•7•39•10•0•Updated Sep 27, 2024Sep 27, 2024
GDP-Fucose_OptMet2023_Paper
Public
Contains all relevant data of the 2023 GDP-Fucose paper.
model-based-optimization kinetic-modeling cell-free-production enzyme-cascade nucleotide-sugar gdp-fucose parameter-uncertainty
Component Pascal
•
Apache License 2.0
•0•3•0•0•Updated Jun 28, 2024Jun 28, 2024
OptMSP
Public
Jupyter Notebook
•
Apache License 2.0
•0•2•0•0•Updated Jan 17, 2024Jan 17, 2024
autopacmen
Public
Retrieves kcat data and adds protein allocation constraints to stoichiometric metabolic models according to the sMOMENT method
bioinformatics systems-biology computational-biology metabolic-models
HTML
•
Apache License 2.0
•7•12•6•0•Updated Jul 11, 2023Jul 11, 2023
TCOSA
Public
Thermodynamic Cofactor Swapping Analysis
Python
•
Apache License 2.0
•0•1•0•0•Updated Jul 7, 2023Jul 7, 2023
CNApy
Public
The Klamt lab is the main developer of CNApy, an integrated environment for metabolic network analysis which you can find here: https://github.com/cnapy-org/CNApy
Apache License 2.0
•0•1•0•0•Updated Jul 15, 2022Jul 15, 2022
astheriscPackage
Public
Search for and find thermodynamic advantages for product synthesis using metabolic single-species community models
bioinformatics systems-biology computational-biology thermodynamics metabolic-models metabolic-network
MATLAB
•
Apache License 2.0
•0•0•0•0•Updated Jun 1, 2022Jun 1, 2022
CNAhelpers
Public
A bunch of functions that come in handy when working with CNA
MATLAB
•
Apache License 2.0
•1•1•0•0•Updated Dec 3, 2021Dec 3, 2021
Models_E.coli_High_ATP_Demand
Public
Kinetic and stoichiometric model for the simulation of enforced ATPwasting in E.coli
Component Pascal
•
Apache License 2.0
•0•3•0•0•Updated Nov 23, 2021Nov 23, 2021
Kinetic-models-of-E.-coli
Public
Kinetic model of E. coli's central metabolism under anaerobic conditions. These models are part of a submitted manuscript of Boecker et al.
0•3•0•0•Updated Oct 8, 2021Oct 8, 2021
MCS_growth-coupling
Public
Scripts to compute MCS for different growth coupling degrees
MATLAB
•
GNU General Public License v3.0
•0•0•0•0•Updated Jul 27, 2021Jul 27, 2021
CommModelPy
Public
Create stoichiometric metabolic network models of single-species or multi-species communities
bioinformatics systems-biology computational-biology metabolic-models metabolic-network
Python
•
Apache License 2.0
•0•3•0•0•Updated Jul 20, 2021Jul 20, 2021
MCS_extended
Public
MATLAB
•0•0•0•0•Updated Jul 30, 2020Jul 30, 2020
FLB_NB_benchmarks
Public
Functions and data for running the benchmarks
MATLAB
•0•0•0•0•Updated Jun 9, 2020Jun 9, 2020
characterize_and_rank_MCS
Public
Characterizing and Ranking Computed Metabolic Engineering Strategies, Schneider P and Klamt S (2019), Bioinformatics, 25: 3063-3072
MATLAB
•0•0•0•0•Updated Mar 4, 2020Mar 4, 2020
MEMO
Public
Models and scripts for the MEMO paper
MATLAB
•
MIT License
•0•1•0•0•Updated Jan 14, 2020Jan 14, 2020
Anleitung
Public
Anleitung zur Benutzung unserer GitHub-Organisation
0•2•0•0•Updated Nov 28, 2019Nov 28, 2019