F A M E  

Welcome to FAME, hosted on the SURF ResearchCloud

Welcome to FAME, the Flux Analysis and Modeling Environment!
FAME is your one stop shop for stoichiometric modeling and flux balance analysis. It features FBA model construction, model execution, results visualization, and friendly elephants.

If you are unsure what to do, have a look at the tutorial and/or manual, and you'll be on your way soon. If you can come up with questions or unexpected results that the manual didn't count on, please let me know by email: j.boele@vu.nl.
Warning sign FAME is under constant development. If you encounter any malfunctions, bugs, etc. in FAME, please be so kind as to inform me by email, so that I can fix the application if necessary. Please also send me an email (with a snippet of your model's SBML) if you cannot get your model to load properly.
© 2011-2014 Joost Boele / VU University Amsterdam     -     disclaimer, license, and info
Last update: July 27th, 2015

Data integration with Synechocystis

Proceed to the Synechocystis page and start modelling.
For more information the Synchocystis publication describing this model can be found here:
Maarleveld TR, Boele J, Bruggeman FJ, Teusink B (2014) A Data Integration And Visualization Resource for the Metabolic Network of Synechocystis sp. PCC 6803
Plant Phys 2014 pp.113.224394 (epub ahead of print)
If you use FAME in your research, please cite:
Boele J, Olivier BG, Teusink B (2012) FAME, the Flux Analysis and Modeling Environment. BMC Syst Biol 6:8.

Import an existing model

Back to top Import model to run
New: to save upload time, you can also upload zipped model files. Uploaded zip files must have a file name ending in .zip, may contain only one file, and that file must be a .xml file.
1. Select your file
    OR: enter file URL (include http://) (filename must end in .xml)
2. Set the default rate for new reactions (when unsure, just leave these values)
Max rate (normal reactions):
Max rate (boundaries):
3. Was this model generated or processed using FAME?

4. All set?
<-- or just click here to load a demo model!

Build new model

Back to top Build new model
1. Please select a species:
2. Please select any number of pathways to include in the model:
Pathway options will appear here when you select a species.
3. Choose a name for your model and default max rates for reactions.
You can change the rates for individual reactions later.
Model Name:
Max rate (normal reactions):
Max rate (boundaries):
4. Would you like some fixes?
  Include?MAX objective?
ATP + H2O -> ADP + Pi
DNA synthesis from dNTPs
RNA synthesis from NTPs
Malic enzyme w/ NADP+/NADPH
R00835 (fixes PPP)
FRUCTOSE (fixes PPP)  
PPi + H2O -> 2 Pi
Use FBC extension? (under development!)   

5. Ready to go?

Merge models

Back to top Merge models
Use this form to merge two models. Objectives from the slave model are ignored, constraints from the slave model are overwritten by those of the master model.
Note that if you have deleted reactions from either model, they may still exist in the other.
1. Select your model files
Master model:
Slave model:
2. Set the default rate for reactions (when unsure, just leave these values)
These will not affect reactions currently in the models.
Max rate (normal reactions):
Max rate (boundaries):
3. All set?


Lost your model?

If you have lost your model or would like to retrieve an old session, enter the model ID here to get the latest version of your model that was kept on our server.
Back to top Lost your model?
You can find your model ID in the XML in the following line:
<model id="MODEL-ID" name="MODEL-ID">
1. Enter your model ID:
2. All set?


Only visualize

To visualize data on KEGG-like maps, enter your data in the box below and select the appropriate KEGG maps. Make sure your data are of the form
and only enter one key-value pair per line.
Back to top Only visualize
1. Enter your data

2. Select pathways

3. All set?

© 2011-2015 Joost Boele / VU University Amsterdam. All rights reserved     -     disclaimer, license, and info
Last update: July 27th, 2015

FAME is almost ready for production again!

Welcome to FAME, now on the SURF ResearchCloud infrastructure! Status 07-01-2022 FAME is running but certain functionality is still being tested.
Thank you for your patience, Brett.