Category Archives: Lab blog

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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Software Engineering

So you have written some software and want to release it to the world! Congratulations!

You’re not done yet. Now you need to document your software and make a release so that everyone knows how to use it. Here are the minimal set of files that you should include and a discussion about each.

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Describing metagenomes in the SRA

I love standards; there are always so many to choose from. The sequence read archive strives hard to capture appropriate information about the sequences that people deposit, but in the end scientists are people too, and they are never uniform and standard. This means there are a lot of ways to describe metagenomes. To get your data used by other people (and cite your papers), make sure you tag it so we can find it!

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