Ecosyste.ms: Awesome

An open API service indexing awesome lists of open source software.

Awesome Lists | Featured Topics | Projects

https://github.com/sysbiochalmers/cellfactory-ecyeastgem

Code and data for in silico strain design for enhanced production of +100 typical bio-products with yeast as a cell-factory. Predictions are based on the ecYeastGEM model avaiable at ecModels.
https://github.com/sysbiochalmers/cellfactory-ecyeastgem

cell-factory constraint-based-modeling enzyme-constraints yeast

Last synced: about 1 month ago
JSON representation

Code and data for in silico strain design for enhanced production of +100 typical bio-products with yeast as a cell-factory. Predictions are based on the ecYeastGEM model avaiable at ecModels.

Host: GitHub
URL: https://github.com/sysbiochalmers/cellfactory-ecyeastgem
Owner: SysBioChalmers
License: cc-by-4.0
Created: 2019-01-29T09:40:47.000Z (almost 6 years ago)
Default Branch: dev
Last Pushed: 2024-11-15T08:15:55.000Z (about 2 months ago)
Last Synced: 2024-11-15T09:25:06.857Z (about 2 months ago)
Topics: cell-factory, constraint-based-modeling, enzyme-constraints, yeast
Language: MATLAB
Homepage:
Size: 138 MB
Stars: 0
Watchers: 2
Forks: 2
Open Issues: 7
Metadata Files:
- Readme: README.md
- License: LICENSE.md

Awesome Lists containing this project

README

        # Yeast Cell Factory: Large-scale *in silico* strain design for enhanced production of +100 chemicals in *S. cerevisiae*

* Brief Model Description:

This repository contains the data and scripts necessary for _in silico_ strain design for enhanced production of +100 chemicals using an enzyme-constrained model of *S. cerevisiae's* metabolism.

* KeyWords:

**Category:** Constraint-based methods; **Utilisation:** predictive simulation, _in silico_ strain design; **Field:** cell factory _in silico_ design; Metabolic engineering **Model Source:** [yeast-GEM](https://github.com/SysBioChalmers/yeast-GEM),[ecYeastGEM](https://github.com/SysBioChalmers/ecModels); **Taxonomy:** _Saccharomyces cerevisiae_; **Metabolic System:** General Metabolism; enzyme constraints.

* Last update: 2021-04-21

## Product list:

* Note:

The predicted gene targets for the following bioproducts can be found in https://github.com/SysBioChalmers/CellFactory-ecYeastGEM/tree/dev/results/production_targets. For each bioproduct, the gene targets could be divided into three levels- L1, L2, and L3 based on the filtration steps in ecFactory (https://github.com/SysBioChalmers/ecFactory).”

| Name | Formula | KEGG ID | CHEBI ID | Group | class | Gene target |

|:-------:|:--------------:|:---------:|:----------:|:-----:|:-----:|:-----:|

| (R,R)-2,3-butanediol  | C4H10O2 | C03044 | 16982 | native | alcohol | Link |

| 2-phenylethanol  | C8H10O | C05853 | 49000 | native | alcohol | Link |

| glycerol  | C3H8O3 | C00116 | 17754 | native | alcohol | Link |

| isoamylol  | C5H12O | C07328 | 15837 | native | alcohol | Link |

| isobutanol  | C4H10O | C14710 | 46645 | native | alcohol | Link |

| choline  | C5H14NO | C00114 | 15354 | native | alkaloid | Link |

| hypoxanthine  | C5H4N4O | C00262 | 17368 | native | alkaloid | Link |

| xanthine  | C5H4N4O2 | C00385 | 17712 | native | alkaloid | Link |

| glutathione  | C10H17N3O6S | C00051 | 16856 | native | amino acid | Link |

| L-alanine  | C3H7NO2 | C00041 | 16977 | native | amino acid | Link |

| L-arginine  | C6H14N4O2 | C00062 | 16467 | native | amino acid | Link |

| L-asparagine  | C4H8N2O3 | C00152 | 17196 | native | amino acid | Link |

| L-aspartate  | C4H7NO4 | C00049 | 17053 | native | amino acid | Link |

| L-citrulline  | C6H13N3O3 | C00327 | 16349 | native | amino acid | Link |

| L-cysteine  | C3H7NO2S | C00097 | 17561 | native | amino acid | Link |

| L-glutamate  | C5H8NO4 | C00025 | 29985 | native | amino acid | Link |

| L-glutamine  | C5H10N2O3 | C00064 | 18050 | native | amino acid | Link |

| L-glycine  | C2H5NO2 | C00037 | 15428 | native | amino acid | Link |

| L-histidine  | C6H9N3O2 | C00135 | 15971 | native | amino acid | Link |

| L-homoserine  | C4H9NO3 | C00263 | 15699 | native | amino acid | Link |

| L-isoleucine  | C6H13NO2 | C00407 | 17191 | native | amino acid | Link |

| L-leucine  | C6H13NO2 | C00123 | 15603 | native | amino acid | Link |

| L-lysine  | C6H15N2O2 | C00047 | 32551 | native | amino acid | Link |

| L-methionine  | C5H11NO2S | C00073 | 16643 | native | amino acid | Link |

| L-phenylalanine  | C9H11NO2 | C00079 | 17295 | native | amino acid | Link |

| L-proline  | C5H9NO2 | C00148 | 17203 | native | amino acid | Link |

| L-serine  | C3H7NO3 | C00065 | 17115 | native | amino acid | Link |

| L-threonine  | C4H9NO3 | C00188 | 16857 | native | amino acid | Link |

| L-tryptophan  | C11H12N2O2 | C00078 | 16828 | native | amino acid | Link |

| L-tyrosine  | C9H11NO3 | C00082 | 17895 | native | amino acid | Link |

| L-valine  | C5H11NO2 | C00183 | 16414 | native | amino acid | Link |

| ornithine  | C5H13N2O2 | C01602 | 46912 | native | amino acid | Link |

| putrescine  | C4H14N2 | C00134 | 326268 | native | bioamine | Link |

| spermine  | C10H30N4 | C00750 | 45725 | native | bioamine | Link |

| Free fatty acids | nan | nan | nan | native | fatty acids and lipids | Link |

| laurate  | C12H23O2 | C02679 | 18262 | native | fatty acids and lipids | Link |

| oleate  | C18H34O2 | C00712 | 16196 | native | fatty acids and lipids | Link |

| palmitoleate  | C16H29O2 | C08362 | 32372 | native | fatty acids and lipids | Link |

| succinate  | C4H4O4 | C00042 | 30031 | native | fatty acids and lipids | Link |

| triacylglycerol  | C6H5O6R3 | C00422 | 17855 | native | fatty acids and lipids | Link |

| guanine  | C5H5N5O | C00242 | 16235 | native | nucleic acid | Link |

| thymidine  | C10H14N2O5 | C00214 | 17748 | native | nucleic acid | Link |

| (S)-lactate  | C3H6O3 | C00186 | 16651 | native | organic acid | Link |

| (S)-malate  | C4H6O5 | C00149 | 15589 | native | organic acid | Link |

| 2-oxoglutarate  | C5H6O5 | C00026 | 16810 | native | organic acid | Link |

| acetate  | C2H4O2 | C00033 | 15366 | native | organic acid | Link |

| citrate  | C6H8O7 | C00158 | 16947 | native | organic acid | Link |

| fumarate  | C4H4O4 | C00122 | 18012 | native | organic acid | Link |

| glycolate  | C2H4O3 | C00160 | 17497 | native | organic acid | Link |

| hexanoate  | C6H12O2 | C01585 | 17120 | native | organic acid | Link |

| pyruvate  | C3H3O3 | C00022 | 15361 | native | organic acid | Link |

| acetaldehyde  | C2H4O | C00084 | 15343 | native | other | Link |

| urea  | CH4N2O | C00086 | 16199 | native | other | Link |

| ergosterol  | C28H44O | C01694  | 16933 | native | other | Link |

| L-phenylacetylcarbinol  | C9H10O2 | nan | nan | heterologous | alcohol | Link |

| n-butanol  | C4H10O | C06142 | 28885 | heterologous | alcohol | Link |

| (S)-Reticuline  | C19H23NO4 | C02105 | 16718 | heterologous | alkaloid | Link |

| psilocybin  | C12H17N2O4P | C07576 | 8614 | heterologous | alkaloid | Link |

| Nicotianamine  | C12H21N3O6 | C05324 | 17721 | heterologous | amino acid | Link |

| 4-hydroxymandelic  | C8H8O4 | C11527 | 16388 | heterologous | aromatic | Link |

| cinnamate  | C9H8O2 | C00423 | 15669  | heterologous | aromatic | Link |

| mandelic  | C8H8O3 | C01984 | 17756 | heterologous | aromatic | Link |

| p-coumaric acid  | C9H8O3 | C00811 | 32374 | heterologous | aromatic | Link |

| rosmarinate  | C18H16O8 | C01850 | 50371 | heterologous | aromatic | Link |

| Salidroside  | C14H20O7 | C06046 | 9009 | heterologous | aromatic | Link |

| Tyrosol  | C8H10O2 | C06044 | 1879 | heterologous | aromatic | Link |

| vanillinbetaglucoside | nan | nan | nan | heterologous | aromatic | Link |

| ARA  | C20H32O2 | C00219  | 15843 | heterologous | fatty acids and lipids | Link |

| DHA  | C22H32O2 | C06429 | 28125 | heterologous | fatty acids and lipids | Link |

| EPA  | C20H30O2 | C06428 | 28364 | heterologous | fatty acids and lipids | Link |

| docosanol  | C22H46O | D03884 | 31000 | heterologous | alcohol | Link |

| catechin  | C15H14O6 | C06562 | 15600 | heterologous | flavonoid | Link |

| genistein  | C15H10O5 | C06563 | 28088 | heterologous | flavonoid | Link |

| kaempferol  | C15H10O6 | C05903 | 28499 | heterologous | flavonoid | Link |

| naringenin  | C15H12O5 | C00509 | 17846 | heterologous | flavonoid | Link |

| quercetin  | C15H10O7 | C00389 | 16243 | heterologous | flavonoid | Link |

| astaxanthin  | C40H52O4 | C08580 | 40968 | heterologous | terpene | Link |

| betaxanthin  | C18H18N2O7 | C08565 | 8341 | heterologous | terpene | Link |

| _-carotene  | C40H56 | C02094 | 17579 | heterologous | terpene | Link |

| artemisinic acid  | C15H22O2 | C20309 | 63749 | heterologous | terpene | Link |

| 3-hydroxypropanoate  | C3H6O3 | C01013 | 16510 | heterologous | organic acid | Link |

| 3-hydroxypropanoate  | C3H6O3 | C01013 | 16510 | heterologous | organic acid | Link |

| Adipic acid  | C6H10O4 | D08839  | 30832 | heterologous | organic acid | Link |

| cis,cis-muconate  | C6H6O4 | C02480 | 16508 | heterologous | organic acid | Link |

| Itaconic acid  | C5H6O4 | C00490 | 17240 | heterologous | organic acid | Link |

| Ethylene  | C2H4 | C06547 | 18153 | heterologous | other | Link |

| 1,3,5-trihydroxyxanthone  | C13H8O5 | C10094 | 514 | heterologous | other | Link |

| glucagon  | C153H225N43O49S | C01501 | 5391 | heterologous | protein | Link |

| Human Serum Albumin | nan | nan | nan | heterologous | protein | Link |

| hemoglobin  | nan | C01708  | 5656 | heterologous | protein | Link |

| lactase  | nan | EC 3.2.1.23 | nan | heterologous | protein | Link |

| _-Amylase  | - | EC 3.2.1.1 | - | heterologous | protein | Link |

| resveratrol  | C14H12O3 | C03582 | 27881 | heterologous | other | Link |

| alpha-Farnesene  | C15H24 | C09665 | 10280 | heterologous | terpene | Link |

| amorphadiene  | C15H24 | C16028 | 52026 | heterologous | terpene | Link |

| Geraniol  | C10H18O | C01500 | 17447 | heterologous | terpene | Link |

| Limonene  | C10H16 | C06078 | 15384 | heterologous | terpene | Link |

| linalool  | C10H18O | C03985 | 17580 | heterologous | terpene | Link |

| lupeol  | C30H50O | C08628 | 6570 | heterologous | terpene | Link |

| Oleanolic acid  | C30H48O3 | C17148 | 37659 | heterologous | terpene | Link |

| patchoulol  | C15H26O | C19755 | 7940 | heterologous | terpene | Link |

| protopanaxadiol  | C30H52O3 | C20715  | 75950 | heterologous | terpene | Link |

| Santalene  | C15H24 | C19736 | nan | heterologous | terpene | Link |

| _-Amyrin  | C30H50O | C08616 | 10352 | heterologous | terpene | Link |

| _-ionone  | C13H20O | C12287 | 32325 | heterologous | terpene | Link |

## Installation

### Required Software:

* A functional Matlab installation (MATLAB 7.3 or higher).

* The [RAVEN toolbox](https://github.com/SysBioChalmers/RAVEN)

* A [git wrapper](https://github.com/manur/MATLAB-git) added to the search path.

### Dependencies - Recommended Software:

* For Matlab, the [libSBML MATLAB API](https://sourceforge.net/projects/sbml/files/libsbml/MATLAB%20Interface/) (version 5.17.0 is recommended).

* [Gurobi Optimizer](http://www.gurobi.com/registration/download-reg) for any simulations.

### Installation Instructions

* For users: Clone it from [`master`](https://github.com/SysBioChalmers/CellFactory-yeast-GEM) in the Github repo, or just download [the latest release](https://github.com/SysBioChalmers/CellFactory-yeast-GEM/releases).

* For contributors: Fork it to your Github account, and create a new branch from [`devel`](https://github.com/SysBioChalmers/CellFactory-yeast-GEM/tree/devel).

## Contributing

Contributions are always welcome! Please read the [contributions guideline](https://github.com/SysBioChalmers/CellFactory-yeast-GEM/blob/master/.github/CONTRIBUTING.md) to get started.

  

## Contributors

* [Hongzhong Lu](https://www.sysbio.se/people/hongzhong-lu) ([@hongzhonglu](https://github.com/hongzhonglu)), Chalmers University of Technology, Gothenburg Sweden

* [Ivan Domenzain](https://github.com/IVANDOMENZAIN) ([@IVANDOMENZAIN](https://github.com/IVANDOMENZAIN)), Chalmers University of Technology, Gothenburg Sweden

* [Yao Lu](hhttps://www.sysbio.se/people/yao-lu), Chalmers University of Technology, Gothenburg Sweden