Once again we are offering a one week workshop on metagenomics data analysis at San Diego State University from June 26th to June 30th. The course will have a focus on random metagenomics sequencing and data analysis (not 16S sequencing). The course will cover sequencing technologies and sequencing approaches, data analysis using the linux command line, paired end sequencing, sequence assembly, mapping reads and visualization, population genomics, and extracting data from the sequence read archive. If you are interested, click the read more.
The metadata in the SRA is not all the data you can get about a run. Here is how to get more data about a run from the SRA without going to the SRA website.
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.
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.
Gap-fill a model in PyFBA
by Daniel Cuevas
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.
Generating, saving, loading models in PyFBA
by Daniel Cuevas
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.
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.
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.