Last modified: 06 September 2014
MetNetMaker is the only free software designed solely to create metabolic networks based on the KEGG LIGAND database ready for Flux-Balance Analysis in the COBRA toolbox.
If you use the software in published work please cite the following
paper in Bioinformatics,
If we want to understand metabolism we need to understand not just the reactions in it but also the interactions between those reactions. Flux-balance analysis (FBA) is one way, although there are plenty of others, to look at these interactions. The drawback of FBA is that it requires a metabolic network to be created for the organism studied that contains no holes in the path connecting nutrients and growth.
MetNetMaker helps with creating a Metabolic Network by keeping track of the details, like naming conventions, cellular compartments and network subdivisions so that FBA-ready networks in SBML format can be created by anyone familiar basic concepts of metabolism.
All versions of MetNetMaker are backwards compatible with previous versions. If you require a previous version for any reason please email me.
Make sure you have Microsoft Access or Access Runtime installed first.
(The Access Runtime (Install_AccessRuntime.exe) is included if you don't have it.)
Unzip and double-click MetNetMakerv1.6.2.accdr to run MetNetMaker.
New versions of cytoscape may not work with the visualisation tools. Use v2.8.3 for best results.
The newest version of MetNetMaker integrates with Cytoscape to allow metabolic network to be visualised during creation. Cytoscape can be downloaded from www.cytoscape.org for free and is required to use the visualisation features.
The installer includes some example files and a brief tutorial that should help a new user get used to how MetNetMaker works and produce their first SBML models.
If you try using MetNetMaker and come across any problems please don't hesitate to email me. Up to date contact information is kept on my personal page.
Note: The installation process has changed. KEGG LIGAND no longer needs downloading and the software ships in the state shown at the end of the first video.
The videos below show the installation process, how to create your first model and how to perform FBA on your models, including simulating gene deletions. All the files created in this videos are included with the software.
The installer version is recommended as it has been more thoroughly tested.
Both versions of MetNetMaker are the same but the method of installation differs. If you have admin rights on your computer and you don't have Microsoft Access or Microsoft Access Runtime installed then use the Installer. If you already have Microsoft Access or the Microsoft Access Runtime installed then just download the standalone, unzip it and double click on the MetNetMaker.accdb icon to start. With both methods of installation the MetNetMaker.accdb (or MetNetMaker.accdr, the two are interchangeable) is fully portable and can be run on any computer with Microsoft Access or Microsoft Access Runtime installed.
I know there are problems with requiring Windows to run the software but in my experience it is the least bad of all the options. MAC OS X is only legally installable on Apple hardware making it prohibitively expensive to those with existing non-Apple hardware. Linux is freely available and installable anywhere but in my experience it is not a stable platform to rapidly develop rich applications on (page upon page of unfriendly linux forums describing conflicts between hardware, distribution and software combinations have taught me this). Windows is stable, efficient, reasonably priced and able to run on almost all existing hardware, that's why I use it. With virtualisation software like Parallels, and Sun's free VirtualBox it is easy to install Windows anywhere. Most Universities have site licenses and individual copies of Windows 7 are not very expensive.
In writing MetNetMaker I have learnt that MS Access is a long way from being the perfect database and that VBA is a long way from being a perfect development language. Nevertheless, I have not come across any better way of writing an application so closely tied to a database. Cross platform development in languages like Java are aimed at people with a lot of programming experience and I passionately believe that programming needs to be more integrated into the way Biologists work if we're going to make real progress across disciplines. When I started my PhD, I had not written an application or used anything more than a very simple database before. Access provides a well-supported and well-documented graphical introduction to SQL and theories in relational databases and provides a way to build GUI applications on top of those databases. Perhaps most importantly it runs in the MS Access 2007 or 2010 runtime providing a stable and well-supported base for the software to run on.
Yes MetNetMaker is free but it does require some non-free software to run. It can only run on Windows (XP SP2 or better) so you'll need a computer with that on. To use the software you only need the free Microsoft Office Access 2007 Runtime which is included with the installer but if you want to view and/or edit the source code you'll need the full version of Microsoft Access 2007 or 2010. The full version of Access is available for a free 60-day trial so you can try before you buy.
It does. I fixed this in version 1.5.2. MetNetMaker now ships with the last free version of the LIGAND ontology.
I found the KEGG LIGAND system easier to parse and I found the naming convention easier to understand. There is no reason why BioCyc could not be used if it were correctly parsed and imported into the database but rewriting MetNetMaker to support this would not be a trivial task.
SBML is a language for describing models in terms of compounds and reactions (and more) but it doesn't say how the compounds and reactions themselves should be defined. Importing a model defined in terms of BioCyc reactions and compounds (for example) and then adding KEGG defined reactions would make a very confusing model and so I don't think it's the worth the considerable effort required to support it. MetNetMaker can load, edit and combine networks that were created with it from the *.xls format files used internally for saving.
If you want to write SBML then libSBML is the best way to do it, so why doesn't MetNetMaker use libSBML? There are a few reasons. The first is related to me not being a computer scientist. I wanted to learn how XML worked and specifically how SBML worked so I wrote the SBML export layer myself. I think it works well. The second reason is that my choice of MS Access and VBA would make using libSBML difficult and require some calls to the Windows API, increasing the complexity and reducing the stability of the software.
Prior to version 1, MetNetMaker was licensed under the Creative Commons GPL.
MetNetMaker versions 1.0, 1.5 and later are licensed under a Creative Commons license that allows free non-commercial use on condition of attribution and release of derivative works under a similar license.
If for any reason you would prefer to use the software under a different license please contact me and I will be happy to sort something out. I am also happy to discussing adding features where requested.