Tag Archives: metabolic models

Installing PyFBA (and necessary modules) without admin permissions

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

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.

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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.
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