We have listed all reconstructed genome-scale metabolic models (GEM Models). They includes Bacteria, Archaea, Eukaryotes, and Mixed Species.
You could also use resources which include different GEM models in various formats (Databases).
First, it is helpful to be familiar with some standards in the field of biological networks and GEM models (Standards).
| Standards | |
| Name | Description |
| SBML
(Homepage) |
The Systems Biology Markup Language (SBML) is a
representation format, based on XML, for communicating
and storing computational models of biological processes.
There is also a library called LibSBML which is a free, open-source programming library to help you read, write, manipulate, translate, and validate SBML files and data streams. |
|
It is also useful to take a look at the
"sbml.org
" web page.
In the "SBML Software Guide" page, one could obtain information about all SBML-compatible software packages (which could deal with SBML file format) for models of metabolism, cell signaling, and more. |
|
| CellML
(Homepage) |
It is another XML based markup language for describing mathematical models. |
| SBGN
(Homepage) |
The Systems Biology Graphical Notation (SBGN) is a standard for graphical representation. |
| MIRIAM
(Homepage) |
Minimum Information Requested In the Annotation of biochemical Models (MIRIAM) aims to add further confidence in quantitative biochemical models, making it easier and more precise to search for particular biochemical models, enabling researchers to identify biological phenomena captured by a biochemical model and, perhaps most importantly, facilitating model re-use and model composition. |
| SBO
(Homepage) |
Systems Biology Ontology (SBO) consists of five controlled vocabularies and two relationships: is-part-of and is-a. Qualifying model participants (say as enzyme, macromolecule, metabolite or small species such as an ion) will make it easier to generate meaning from the model. |
| BioPAX
(Homepage) |
Biological Pathway Exchange (BioPAX) is an XML-based format that will act as a bridge between different pathway databases and data. In relation to modeling software, it may offer a means to embed rich annotation data into an SBML or CellML model. |
| TEDDY
(Homepage) |
Terminology for the Description of Dynamics (TEDDY) provides a rich ontology to describe and quantify the kind of behavior that a computational model is able to exhibit (e.g. the characteristics of a model could describe bifurcation behavior in which the functionality of a model could be described as featuring oscillations or switch behavior). |
| MIASE
(Homepage) |
The Minimum Information About a Simulation Experiment (MIASE) will help to describe the simulation algorithms and the simulation tool used, along with all needed parameter settings. |
| CSML
(Homepage) |
The Cell System Markup Language (CSML) is an XML format for modeling, visualizing and simulating biopathways. It supports to represent several pathway types including metabolic, signaling, and genetic regulatory pathways. This project aims to facilitate the exchange of biopathway data in different formats. Effort has been made for data conversion from other XML formats. In addition, to allow extensible and flexible features of CSML, the Cell System Ontology (CSO) has been developed. |
| SED-ML
(Homepage) |
The Simulation Experiment Description Markup Language (SED-ML) is an XML-based format for encoding simulation experiments. It allows to define a computer-readable format for representing the models of biological processes. It can be used with models encoded in several languages, as far as they are in XML. |
| SBOL
(Homepage) |
The Synthetic Biology Open Language (SBOL) is a language for the description and the exchange of synthetic biological parts, devices and systems. |
| Jamborees
(Homepage) |
A metabolic reconstruction jamboree is a community-driven effort to create a high-quality genome-scale biochemical network reconstruction for a target organism. This jamboree approach is analog to genome annotation jamborees that lead to community driven genome annotation process. |
| More information about standards used to share data in life sciences can be found on the website of the BioSharing initiative. | |
| Databases | ||
| Name | Description | Reference |
| MEMOSys
(Homepage) |
Metabolic Model System is a web based bioinformatics platform for the management, storage, and development of metabolic models. It provides the SBML format which enables analysis in external tools. The web application is based on the Java framework. | PMID:
24532766 |
| BiGG
(Homepage) |
It is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. | PMID:
20426874 & New Paper |
| BioModels
(Homepage) |
This Database serves as a reliable repository of computational models of biological processes. It also includes curated and non-curated models. | PMID:
20587024 |
| CellML
(Homepage) |
The purpose of CellML is to store and exchange computer-based mathematical models. It allows scientists to share models even if they are using different modelling tools. It also enables them to reuse components from one model in another, thus accelerating model development. | PMID:
18658182 |
|
Some other useful references:
Paper: Calibration and analysis of genome-based models for microbial ecology (Link) |
||
| GEM Models | ||
| BACTERIA | ||
| Organism | Model Name | Reference |
| Acinetobacter baumannii | AbyMBEL891 | PMID:
20094653 |
| Acinetobacter baylyi | iAbaylyiV4 | PMID:
18840283 |
| Bacillus subtilis | model_v3 | PMID:
17573341 |
| iBsu1103 | PMID:
19555510 |
|
| Bifidobacterium adolescentis | iBif452 | PMID:
24708835 |
| Buchnera aphidicola | iGT196 | PMID:
19232131 |
| Burkholderia cenocepacia | iKF1028 | PMID:
21609491 |
| Chromohalobacter salexigens | iOA584 | PMID:
21251315 |
| Clostridium acetobutylicum | --- | PMID:
18767192 |
| --- | PMID:
18758767 |
|
| Clostridium butyricum | --- | PMID:
25453441 |
| Clostridium thermocellum | iSR432 | PMID:
20307315 |
| Corynebacterium glutamicum | --- | PMID:
18985611 |
| --- | PMID:
19646286 |
|
| --- | PMID:
26392034 |
|
| Dehalococcoides ethenogenes | iAI549 | PMID:
20811585 |
| Escherichia coli | iJE660 | PMID:
10805808 |
| iJR904 | PMID:
12952533 |
|
| iAF1260 | PMID:
17593909 |
|
| iJO1366 | PMID:
21988831 |
|
| iCA1273 | PMID:
21208457 |
|
| MG1655 | PMID:
24974895 |
|
| Faecalibacterium prausnitzii | iFap484 | PMID:
24708835 |
| Francisella tularensis | iRS605 | PMID:
20731870 |
| Geobacillus LC300 | --- | PMID:
26391740 |
| Geobacter metallireducens | --- | PMID:
19175927 |
| Geobacter sulfurreducens | --- | PMID:
16461711 |
| Haemophilus influenzae | iJE296 | PMID:
10364169 |
| iCS400 | PMID:
10716908 |
|
| Helicobacter pylori | iCS291 | PMID:
12142428 |
| iIT341 | PMID:
16077130 |
|
| Klebsiella pneumoniae | iYL1228 | PMID:
21296962 |
| Lactobacillus casei | --- | PMID:
25365062 |
| --- | PMID:
25452194 |
|
| Lactobacillus plantarum | --- | PMID:
17062565 |
| Lactococcus lactis | --- | PMID:
15982422 |
| Mannheimia succiniciproducens | --- | PMID:
15378067 |
| --- | PMID:
17405177 |
|
| Mycobacterium tuberculosis | iNJ661 | PMID:
17555602 |
| GSMN-TB | PMID:
17521419 |
|
| iNJ661m | PMID:
21092312 |
|
| Mycoplasma genitalium | iPS189 | PMID:
19214212 |
| Neisseria meningitidis | --- | PMID:
17617894 |
| Pectobacterium carotovorum | --- | PMID:
25535697 |
| Phaeodactylum tricornutum | --- | Paper_Link |
| Porphyromonas gingivalis | iVM679 | PMID:
18931137 |
| Pseudoalteromonas haloplanktis | --- | PMID:
24889559 |
| Pseudomonas aeruginosa | iMO1056 | PMID:
18192387 |
| Pseudomonas putida | iNJ746 | PMID:
18793442 |
| iJP815 | PMID:
18974823 |
|
| PpuMBEL1071 | PMID:
20540110 |
|
| Rhizobium etli | iOR363 | PMID:
17922569 |
| Rhodobacter sphaeroides | iRsp1095 | PMID:
21777427 |
| Rhodococcus jostii (RHA1) | iMT1174 | PMID:
26248853 |
| Rhodoferax ferrireducens | --- | PMID:
19772637 |
| Salinispora tropica (CNB-440) | --- | Paper_Link |
| Salmonella typhimurium | iRR1083 | PMID:
19356237 |
| iMA945 | PMID:
19690172 |
|
| STM_v1.0 | PMID:
21244678 |
|
| Shewanella oneidensis | iSO783 | PMID:
20589080 |
| Staphylococcus aureus | iSB619 | PMID:
15752426 |
| iMH551 | PMID:
16155945 |
|
| --- | PMID:
19376871 |
|
| Streptococcus thermophilus | --- | PMID:
19346354 |
| Streptomyces coelicolor | --- | PMID:
15930493 |
| --- | PMID:
20338070 |
|
| Synechocystis sp. PCC6803 | --- | Paper_Link |
| iSyn669 | PMID:
21083885 |
|
| Synechococcus elongatus | iSyf715 | PMID:
25141288 |
| Thermotoga maritima | --- | PMID:
19762644 |
| Vibrio vulnificus | VvuMBEL943 | PMID:
21245845 |
| Yersinia pestis | iAN818m | PMID:
19396373 |
| Zymomonas mobilis | ZmobMBEL601 | PMID:
21092328 |
| iZM363 | PMID:
20967753 |
|
| ARCHAEA | ||
| Organism | Model Name | Reference |
| Halobacterium salinarum | --- | PMID:
18213408 |
| Methanosarcina acetivorans | iVS941 | PMID:
21324125 |
| Methanosarcina barkeri | iAF692 | PMID:
16738551 |
| Natronomonas pharaonis | --- | PMID:
20543878 |
| EUKARYOTES | ||
| Organism | Model Name | Reference |
| Arabidopsis thaliana | AraGEM | PMID:
20044452 |
| iRS1597 | Webpage | |
| Aspergillus nidulans | iHD666 | PMID:
18405346 |
| Aspergillus niger | iMA871 | PMID:
18364712 |
| Aspergillus oryzae | --- | PMID:
18500999 |
| Chlamydomonas reinhardtii | iRC1080 | PMID:
21811229 |
| --- | Paper_Link | |
| Cryptosporidium hominis | iNV213 | PMID:
20491062 |
| Ectocarpus siliculosus | --- | PMID:
25065645 |
| Homo sapiens | Recon 1 | PMID:
17267599 |
| Recon 2 | PMID:
23455439 |
|
| Leishmania major | iAC560 | PMID:
18364711 |
| Mortierella alpina | --- | PMID:
25582171 |
| Mus musculus | --- | PMID:
15903248 |
| --- | PMID:
19425150 |
|
| --- | PMID:
20024077 |
|
| iMM1415 | PMID:
20959003 |
|
| iSS1393 | PMID:
23022739 |
|
| Oryza sativa | --- | Paper_Link |
| --- | PMID:
25506349 |
|
| Pichia pastoris | PpaMBEL1254 | PMID:
20503221 |
| iPP668 | PMID:
20594333 |
|
| --- | Paper_Link | |
| Plasmodium falciparum | iPP668 | PMID:
20807400 |
| --- | PMID:
20823846 |
|
| --- | Paper_Link | |
| Saccharomyces cerevisiae | iFF708 | PMID:
12566402 |
| iND750 | PMID:
15197165 |
|
| iLL672 | PMID:
16204195 |
|
| iIN800 | PMID:
18687109 |
|
|
iMH805/775 (Yeast 1.0) |
PMID:
18846089 |
|
| iMM904 | PMID:
19321003 |
|
| improved_iMM904 | PMID:
21190580 |
|
|
YEASTNET (Yeast 7.11) |
Webpage | |
| Scheffersomyces stipitis | --- | Paper_Link |
| Schizochytrium limacinum SR21 | --- | Paper_Link |
| Yarrowia lipolytica | --- | Paper_Link |
| Zea mays | iRS1563 | PMID:
21755001 |
| --- | PMID:
25806041 |
|
| Mixed Models | ||
| Mixed culture of Leptospirillum ferriphilum and Ferroplasma acidiphilum (Link) | ||
| ToMI-FBA: A genome-scale metabolic flux based algorithm to select optimum hosts and media formulations for expressing pathways of interest (Link) | ||