While answering some reviewers comments, I pulled out this data about the instruments used to submit data to the SRA. Clearly the HiSeq and MiSeq are dominating the number of runs that people are submitting.
Monthly Archives: February 2017
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.
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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.
Globus Endpoint
We have a globus endpoint for large file transfers into and out of the lab. If you need to use it contact Rob for authorization. Here are some details about the endpoint.