Table 2.
Software applications for constraint-based modeling and/or genome-scale metabolic reconstruction. In References [141,144], all of these tools are reviewed in more detail.
| Name (and Reference) | Language | Interface | Development | OS |
|---|---|---|---|---|
| COBRA Toolbox [141] | MATLAB COBRA.py, COBRA.jl (Python and Julia) |
Script | Open source | AllM |
| RAVEN [145] | MATLAB | Script | Open source | AllM |
| CellNetAnalyzer [146] | MATLAB | Script/GUI | Closed source | AllM |
| FBA-SimVis [147] | MATLAB/Java | GUI | Closed source | Windows |
| OptFlux [148] | Java | Script | Open source | All |
| Sybil [149] | R | Script | Open source | All |
| CBMPy [150] | Python | Script | Open source | All |
| SurreyFBA [151] | C++ | Script/GUI | Open source | All |
| FASIMU [152] | C | Script | Open source | Linux |
| FAME [153] | Web-based | GUI | Open source | All |
| PathwayTools [154] | Web-based | GUI/script | Closed source | All |
| Kbase [155] | Web-based | Script | Open source | All |
| AutoKEEGRec [156] | MATLAB | Script | Open source | AllM |
| AuReMe [157] | Python | GUI | Open source | All |
| CarveMe [158] | Python | Script | ||
| MetaDraft [159] | Python | Script | Open source | All |
| ModelSEED [160] | Web-based | GUI | Open source | All |
| PathwayTools [161] | Common Lisp | GUI (API) | Open source | All |
| Merlin [162] | Java | GUI | Open source | All |
| CoReCO [163] | Python | Script | Open source | All |
| MEMOSys [164] | Java | GUI | Proprietary source | All |
| GEMSiRV [165] | Java | GUI | Open source | All |
| MetExplore [166] | Web-based | GUI | Open source | All |
| RbioNet [167] | Part of the COBRA ToolBox | Script | Open source | All |
| MetaFlux [168] | Web-based | GUI | Open source (distributed as part of Pathways tools) | All |
Abbreviations: (AllM) all operative systems in which it can run MATLAB, (API) Application Programming Interface, (GUI) Graphic User Interface, (OS) operative system.