Learn metabolic modelling and using ScrumPy for modelling.
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Updated
Mar 15, 2022 - HTML
Learn metabolic modelling and using ScrumPy for modelling.
Python Implementation of PROM
Cellular economy models based on global optimization using GAMS
Constraint-based metabolic modelling with sparse IPOPT
Flux response of Pseudomonas putida to increased levels of metabolic burden
SYSBIO repository of ENG4BIO group within Universitat Autònoma de Barcelona (UAB) mainly regarding K. phaffi modelling.
ScyNet: Visualisation of community metabolic models in Cytoscape
Docker image for a full ME model stack.
Software developed and main results obtained in the Master dissertation: A model validation pipeline for healthy tissue genome-scale metabolic models. Dissertation link to be added.
Contains NAD biosynthesis model and python scripts to simulate the steady-state calculations.
Code for Model-based Design of Bistable Cell Factories for Metabolic Engineering
Source code and information for journal article Social dynamics and modeling of chrono-nutrition
Search for and find thermodynamic advantages for product synthesis using metabolic single-species community models
"Maps for when the living gets tough: Maneuvering through a hostile energy landscape" | Mondeel, Thierry D.G.A. Rehman, Samrina Zhang, Yanfei Verma, Malkhey Dürre, Peter Barberis, Matteo Westerhoff, Hans V. | 2016 | IFAC-PapersOnLine |
Searches through every possible set of chemical reaction, enzyme pairs to create metabolite pathways from the input chemical to the output chemical. Used to find the optimal DNA sequences to add to a cell for a given input chemical, output chemical and cell.
A jupyter hub docker app for metabolic modelling using mewpy, troppo, cobra, etfl and cplex.
Automatic fitting of growth models to growth data
A repository for all code related to my masters project
Code for Context-specific metabolic network model for PCOS with insulin resistance
Expression, biological and clinical relevance of the collagen pathway genes in prostate carcinoma
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