Go to EC2 management console, Security groups and add a Custom TCP inbound rule with port 8000. Select “Anywhere” from the list.
Update and upgrade packages:
Go to EC2 management console
R, especially with lots of Bioconductor packages, provides nice tools to load, manage and analyze microarray data. If you are trying to load NCBI GEO data into R, use GEOquery package. Here, I’ll describe how to start with it and probably in my future posts I’ll mention more.
Use following code to get the path to or directory of current (running) script in R:
Mezzanine is a CMS application built on Django web framework. The installation steps are easy but your environment may not just suitable enough for it work without a problem. So, here I’m going to describe complete installation from scratch on a virtual environment.
Let’s say you created a Django app and ran
python manage.py syncdb and created its table. Everytime you make a change in the table, you’ll need to drop that table and run
python manage.py syncdb again to update. And how you drop a table of a Django app:
We’re almost done with the analyses and we’re making the final visualization of the network. As I previously posted, the network was clustered and visualized by time points. After that, we have done several more analyses and here I report how we visualized them. I’m going to post more about how we did the analyses separately.
Assume you have a large network and you want to find k-cores of each node and also you want to compute clustering coefficient for each one. Python package NetworkX comes with very nice methods for you to easily do these.
In my previous post, I mentioned how I clustered the network we obtained at the end. For functional annotation gene ontology (GO) enrichment has been done on these clusters.