Overview of the Workflows
The following workflows are currently available:
More information about these differnt types of workflows can be found below.
Hint
Which type of workflow to use is heavily dependent on your organism, available information for your organism and the data you wish to use as input.
CarveMe + ModelPolisher based (CMPB) workflow
The CMPB workflow is based on generating a draft model using CarveMe and subsequently extending and polishing
the model using various tools.
This workflow can be run on an annotated genome or an already generated CarveMe model and requires very little additional information to be run on its base settings. However, additional information can be added from e.g. KEGG or BioCyc to perform an automated gap filling using refineGEMs [1].
Note
Currently, the ModelPolisher connection is still under construction, but the workflow can already be run.
High-quality template based (HQTB) workflow
Warning
Due to chances in refineGEMs, this workflow is under heavy
developement and may not work as expected.
The HQTB workflow curates a new model from an annotated genome based on a high-quality template model
(plus corresponding annotated genome) and additional database information.
This workflow aims to profit from already performed (manual) curation of an already existing model, to carry this knowledge into the new model. The closer the template is to the original, the more knowledge can potentially be carried over. Therefore, this workflow is more useful, if the user already has a model of a similar organism compared to the one for which the new model should be curated for.
More ideas for workflows
Below are some ideas for workflows, to be implemented in future update(s):