As easy as it is to install PyFBA using the pip
command, it can be quite cumbersome to do so when you are working on a system without granted administrative or sudo
permissions. Here is a quick guide that has worked for me when installing PyFBA on a CentOS 6.3 system running a SunGrid Engine cluster system. If you are working on a Linux system and you do have admin and sudo
permissions, please follow the install guide here. Continue reading
Tag Archives: metabolic models
PyFBA 1.2 release
Our genome-scale metabolic model software, PyFBA, has been upgraded to version 1.2 recently. With new features ranging from a new Model class to Python 3 support, this release expands the usefulness of PyFBA. Version 1.2 has been updated on our GitHub master branch and PyPI. Read further to see more details.
iPython Notebook How-To: Gap-fill a model in PyFBA
Gap-fill a model in PyFBA
by Daniel Cuevas
Introduction
In this notebook, we will present the steps to generate a genome-scale metabolic model from RAST annotations, gap-fill the model on rich LB type media, and save the model to hard disk.
iPython Notebook How-To: Generating, saving, and loading models in PyFBA
Generating, saving, loading models in PyFBA
by Daniel Cuevas
Introduction
In this notebook, we will present the steps to generate a genome-scale metabolic model from RAST annotations, save the model on your computer, and load the model from your computer.
Continue reading