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Searching Entrez using EUtils and Python

Tue, 2005-08-16 14:25 — Greg

I discovered a nice tutorial on searching Entrez using EUtils and Python. The tutorial is part of the larger Scripting Bioinformatics course, available from the University of Aarhus Department of Computer Science. What I liked about this tutorial was the inclusion of more advanced of python techniques such as generators and iterators.


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Wed, 2005-08-17 14:01 — Neil

wonders of the web

This is why I love the web - all this useful stuff, out there.

From the intro to the scripting course:

It's a sad fact of life that most scientific software packages are incompatible — if we wish to perform a number of calculations on a set of data, the output of one program never quite matches the input of the next, and although in many cases tools exist for translating one data format into another, often the translation looses information about the data. And although we often want to combine calculations in various tools, without manually inspecting the intermediate results, building a pipeline of calculations is often not immediately possible.
In this course we will see how we can use a "scripting language" such as Python, Perl, Ruby, etc., to translate data formats for use with different tools, how to wrap the tools so that they can be called and controlled from scripts for easy pipelining of calculations, and how we can use databases for keeping track of data.

That just about sums up bioinformatics in a nutshell for me. For all this talk of standardisation and data formats - it just ain't gonna happen! Which is why scripting skills will get you a long way.