Posts on September 2011

A personal vision for the future of biology and medicine
Posted on Tue 20 Sep 2011 under Science

In the future, scientists will be able to simulate life in the computer using new theories on mechanisms of evolution coupled with advanced computer simulation technologies. No more real animal or cellular models. We will be able to investigate the causes of diseases by using virtual biological models of any organism to a resolution down to the molecular level. We can dissect the complete progression of any disease and be able to identify the macromolecular elements that are potentially involved.

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Snippet 3: A simple FASTA file parser in pure Python
Posted on Sat 17 Sep 2011 under Bioinformatics

I needed to have a simple FASTA file parser without using Biopython. There are just cases when you need to use some functions in Biopython but you can't install the whole package. In my case,  I wanted to handle and process sequences in FASTA format within a Google App Engine web app where it is not possible to install Python packages that have C extensions. Some of you may have other use cases, like when you want just the SeqIO.index() function to parse FASTA files. This is exactly what this short script tries to mimic. It has most of the methods and attributes of an indexed FASTA file using Bio.SeqIO in Biopython.

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