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Fruitfly 1.0
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| > Introduction (please delete after reading): | ||
| [standard-GEM](https://github.com/MetabolicAtlas/standard-GEM) is a template repository that aims to standardize the format of genome-scale metabolic models (GEMs) versioned with git. In addition to encouraging the open-sourcing of GEMs, it facilitates the import of GEMs into databases and online websites. Moreover, it provides the community with a familiar structure that is easy to adopt through this repository itself. The template comes with a set of requirements and recommendations, packaged as to-do items in a hidden Markdown file in this repository `.standard-GEM.md`. After downloading this repository, or using it as a template, those to-do items provide guidance to how adherence to the standard can be obtained. | ||
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| > Instructions for this `README` (please delete after reading): | ||
| This is the `README.md` template provided by [standard-GEM](https://github.com/MetabolicAtlas/standard-GEM) and was crafted to cover most use-cases. | ||
| Feel free to edit this template `README`. Blanks are indicated by `{{ test }}`. One may use a search function to find these `{{`. Here are some examples of blanks used throughout this file: `{{organization or username}}` is the organization name or username for this GitHub repository, eg. `SysBioChalmers`; `{{repository name}}` is the name of this GitHub repository, eg. `yeast-GEM`. | ||
| If you find this template does not fit your needs, we would appreciate if you could report this by creating a new issue on [standard-GEM](https://github.com/MetabolicAtlas/standard-GEM/issues). | ||
| # Fruitfly-GEM: The generic genome-scale metabolic model of _Drosophila melanogaster_ | ||
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| ## {{repository name}}: {{repository description}} | ||
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| [](https://badge.fury.io/gh/sysbiochalmers/yeast-gem) | ||
| [](https://zenodo.org/badge/latestdoi/{{Zenodo ID}}) | ||
| [](https://gitter.im/{{organization or username}}/{{repository name}}) | ||
| [](https://badge.fury.io/gh/sysbiochalmers%2FFruitfly-GEM) | ||
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| #### Description | ||
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| {{ fill in a short description or the paper abstract }} | ||
| This repository contains the latest version of Fruitfly-GEM, a fruit fly genome-scale metabolic model. | ||
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| #### Citation | ||
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| {{ provide the citation once available, for example: | ||
| > Lu, H., Li, F., Sánchez, B.J. et al (2019). A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism. Nat Commun 10, 3586 [doi:10.1038/s41467-019-11581-3](https://doi.org/10.1038/s41467-019-11581-3) | ||
| }} | ||
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| Manuscript under preparation | ||
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| #### Keywords | ||
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| > Keywords are be separated by semicolons. | ||
| > The `Model source` field contains the source(s) of the current model, eg existing GEMs. If possible, use the Markdown format to add the URL with the DOI. The (NCBI) taxonomy ID should be provided in the [format from identifiers.org](https://registry.identifiers.org/registry/taxonomy). For the genome identifier, please provide the ENA/GenBank/RefSeq identifier via *identifiers.org*, or from other sources such as PATRIC or KBase. | ||
| #### Model Keywords | ||
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| **Utilisation:** {{ experimental data reconstruction; multi-omics integrative analysis;, _in silico_ strain design; model template }} | ||
| **Field:** {{ metabolic-network reconstruction }} | ||
| **Type of model:** {{ reconstruction; curated }} | ||
| **Model source:** {{ [YeastMetabolicNetwork](http://doi.org/10.1038/nbt1492) }} | ||
| **Omic source:** {{ genomics; metabolomics }} | ||
| **Taxonomic name:** {{ _Saccharomyces cerevisiae_ }} | ||
| **Taxonomy ID:** {{ [taxonomy:559292](https://identifiers.org/taxonomy:559292) }} | ||
| **Genome ID:** {{ [insdc.gca:GCA_000146045.2](https://identifiers.org/insdc.gca:GCA_000146045.2) }} | ||
| **Metabolic system:** {{ general metabolism }} | ||
| **Utilisation:** multi-omics integrative analysis, predictive simulation | ||
| **Field:** metabolic-network reconstruction | ||
| **Type of Model:** reconstruction, curated | ||
| **Model source:** [Human-GEM](https://doi.org/10.1126/scisignal.aaz1482) | ||
| **Omic source:** genomics; metabolomics | ||
| **Taxonomic name:** _Drosophila melanogaster_ | ||
| **Taxonomy ID:** [7227](https://identifiers.org/taxonomy:7227) | ||
| **Genome ID:** [GCA_000001215.4](https://identifiers.org/insdc.gca:GCA_000001215.4) | ||
| **Metabolic System:** general metabolism | ||
| **Tissue:** | ||
| **Bioreactor:** | ||
| **Cell type:** | ||
| **Cell line:** | ||
| **Strain:** {{ S288C }} | ||
| **Condition:** {{ aerobic; glucose-limited; defined media }} | ||
| **Condition:** generic metabolism | ||
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| ### Installation | ||
| ### Model Overview | ||
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| {{ Be mindful of users who do not have a typical background - provide a clear overview of the required software. Also, there might be different requirements for users and collaborators. }} | ||
| |Taxonomy | Template Model | Reactions | Metabolites| Genes | | ||
| | ------------- |:-------------:|:-------------:|:-------------:|:-----:| | ||
| |_Drosophila melanogaster_ | Human-GEM | 12072 | 8164 | 2048 | | ||
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| ### Usage | ||
| ## Installation | ||
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| {{ Describe how to load and save the model. }} | ||
| ### Required Software | ||
| * A functional MATLAB installation (MATLAB 7.3 and higher). | ||
| * The [RAVEN toolbox](https://github.com/SysBioChalmers/RAVEN). | ||
| * The [COBRA toolbox](https://github.com/opencobra/cobratoolbox) (not necessary for most functionality). | ||
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| ### Contributing | ||
| ### Dependencies - Recommended Software | ||
| * The libSBML MATLAB API (version [5.13.0](https://sourceforge.net/projects/sbml/files/libsbml/5.13.0/stable/MATLAB%20interface/) is recommended). | ||
| * [Gurobi Optimizer](http://www.gurobi.com/registration/download-reg) for any simulations. | ||
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| ### Installation Instructions | ||
| * Clone the [master branch](https://github.com/SysBioChalmers/Fruitfly-GEM/tree/master) of this repository, or [download the latest release](https://github.com/SysBioChalmers/Fruitfly-GEM/releases/latest). | ||
| * Add the directory to your MATLAB path (instructions [here](https://se.mathworks.com/help/matlab/ref/addpath.html?requestedDomain=www.mathworks.com)). | ||
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| Contributions are always welcome! Please read the [contributing guideline](.github/CONTRIBUTING.md) to get started. | ||
| ## Usage | ||
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| #### Loading/saving the model | ||
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| `Fruitfly-GEM.mat` (Recommended if on `master` branch) | ||
| * Load and save using the built-in MATLAB `load()` and `save()` functions. | ||
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| `Fruitfly-GEM.xml` (SBML format) | ||
| * Load using the `importModel.m` function (from [RAVEN Toolbox](https://github.com/SysBioChalmers/RAVEN)) | ||
| * Save using the `exportModel.m` function (from [RAVEN Toolbox](https://github.com/SysBioChalmers/RAVEN)) | ||
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| ## Websites | ||
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| - [Metabolic Atlas](https://metabolicatlas.org/) enables visualization and exploration of Fruitfly-GEM content. | ||
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| ### Contributing | ||
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| ### Contributors | ||
| Contributions are always welcome! Please read the [contributing guidelines](.github/CONTRIBUTING.md) to get started. | ||
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| Code contributors are reported automatically by GitHub under [Contributors](https://github.com/{{organization or username}}/{{repository name}}/graphs/contributors), while other contributions come in as [Issues](https://github.com/{{organization or username}}/{{repository name}}/issues). |
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| # Fruitfly-GEM code | ||
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| - `masterScriptFruitflyGEM.m`: The master script for GEM generation. | ||
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| % | ||
| % FILE NAME: masterScriptFruitflyGEM.m | ||
| % | ||
| % | ||
| % PURPOSE: This script is for reconstruction of the Fruitfly-GEM, by using | ||
| % the Human-GEM as template and taking into account specie-specific | ||
| % pathways/reactions. | ||
| % | ||
| % | ||
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| %% Load Human-GEM as template | ||
| load('Human-GEM.mat'); | ||
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| % convert gene identifiers from Ensembl ids to gene symbols | ||
| [grRules,genes,rxnGeneMat] = translateGrRules(ihuman.grRules,'Name','ENSG'); | ||
| ihuman.grRules = grRules; | ||
| ihuman.genes = genes; | ||
| ihuman.rxnGeneMat = rxnGeneMat; | ||
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| %% Use MA reactions identifiers | ||
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| % load reaction annotaiton files | ||
| rxnAssoc = jsondecode(fileread('humanGEMRxnAssoc.JSON')); | ||
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| %replace reaction identifiers with MA ids if available | ||
| ind = getNonEmptyList(rxnAssoc.rxnMAID); | ||
| ihuman.rxns(ind) = rxnAssoc.rxnMAID(ind); | ||
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| %% Generate Fruitfly-GEM by using Human-GEM as template | ||
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| % get ortholog pairs from human to worm | ||
| fruitflyOrthologPairs = extractAllianceGenomeOrthologs('human2FruitflyOrthologs.json'); | ||
| fruitflyGEM = getModelFromOrthology(ihuman, fruitflyOrthologPairs); | ||
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| %% Incorporate species-specific reactions | ||
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| % get metabolic networks based on the KEGG annoation using RAVEN function | ||
| KEGG_human=getKEGGModelForOrganism('hsa'); | ||
| KEGG_fruitfly=getKEGGModelForOrganism('dme'); | ||
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| % remove reactions shared with human | ||
| FruitflySpecificRxns=setdiff(KEGG_fruitfly.rxns,KEGG_human.rxns); | ||
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| % remove reactions included in Human-GEM | ||
| FruitflySpecificRxns=setdiff(FruitflySpecificRxns,rxnAssoc.rxnKEGGID); | ||
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| % get species-specific network for manual inspection and then | ||
| % organize species-specific pathways into two tsv files: | ||
| fruitflySpecificNetwork=removeReactions(KEGG_fruitfly,... | ||
| setdiff(KEGG_fruitfly.rxns,FruitflySpecificRxns), true, true, true); | ||
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| % "fruitflySpecificMets.tsv" contains species-specific metabolites | ||
| metsToAdd = importTsvFile('fruitflySpecificMets.tsv'); | ||
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| % "fruitflySpecificRxns.tsv" contains species-specific reactions | ||
| rxnsToAdd = importTsvFile('fruitflySpecificRxns.tsv'); | ||
| rxnsToAdd.subSystems = cellfun(@(s) {{s}}, rxnsToAdd.subSystems); | ||
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| % integrate fruitfly-specific metabolic network | ||
| [fruitflyGEM, modelChanges] = addMetabolicNetwork(fruitflyGEM, rxnsToAdd, metsToAdd); | ||
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| %% Gap-filling for biomass formation | ||
| [fruitflyGEM, gapfillNetwork]=gapfill4EssentialTasks(fruitflyGEM,ihuman); | ||
| % Added 39 reactions for gap-filling | ||
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| %% Save the model into mat, yml, and xml | ||
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| fruitflyGEM.id = 'Fruitfly-GEM'; | ||
| save('../model/Fruitfly-GEM.mat', 'fruitflyGEM'); | ||
| writeHumanYaml(fruitflyGEM, '../model/Fruitfly-GEM.mat'); | ||
| exportModel(fruitflyGEM, '../model/Fruitfly-GEM.xml'); | ||
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| # Fruitfly-GEM data | ||
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| This directory contains datasets that were used for the generation and curation of Fruitfly-GEM. The files and their contents are briefly summarized below. | ||
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| - `human2FruitflyOrthologs.json`: The human-fruit fly ortholog pairs downloaded from the [Alliance of Genomes Resources](https://www.alliancegenome.org). | ||
| - `fruitflySpecificMets.tsv` and `fruitflySpecificRxns.tsv`: The curated metabolic network that is not part of human metabolism but specific to fruit fly. | ||
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