Category Archives: Lab blog

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

How many bp of metagenomes are there in the SRA?

We were curious about how many bp of metagenomes in the SRA. This was partly inspired by our grant writing, and partly by this question on twitter from Tom Delmont:



This is how to answer the question!

Continue reading

CAMI challenge datasets

CAMI (Critical Assessment of Metagenome Interpretation) is a community-led initiative designed to help tackle the problems faced by metagenomics analyses, aiming for an independent, comprehensive and bias-free evaluation of these metagenomics pipelines [source]. As part of the challenge, several simulated datasets were generated in order to evaluate each of the assembly, profiling, and binning tools submitted for review. Three distinct datasets were generated simulating microbiomes of varying complexities: low, medium, and high complexity. A pre-print version of the CAMI manuscript can be found on bioRxiv here:
This blog post contains links to the binning and profiling results for those datasets. Continue reading

2017 Metagenomics Workshop

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.

Continue reading

iPython Notebook How-To: Gap-fill a model in PyFBA

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.

Continue reading