http://wiki.genedrift.org/ 2012-05-19T09:07:53-04:00 http://wiki.genedrift.org/ http://wiki.genedrift.org/lib/images/favicon.ico text/html 2010-08-18T09:26:44-04:00 Paulo Nuin http://wiki.genedrift.org/doku.php?id=bioinformatics_workshop_2010_-_department_of_pathology_and_molecular_medicine&rev=1282138004&do=diff Thursday August 5th Topics covered: Basic Linux/Unix commands: cd - ls - mkdir - wc - grep Introduction to the BASH shell - online book Simple for loops in BASH Simple FASTA file manipulation in BASH BioMart - Martview Blast+ - Blast book, based on the legacy version but still relevant text/html 2010-08-05T19:39:54-04:00 Paulo Nuin http://wiki.genedrift.org/doku.php?id=gd_wiki&rev=1281051594&do=diff This wiki will contain entries from Beginning Python for Bioinformatics and some information about software projects. Beginning Python for Bioinformatics Software Bioinformatics Workshop 2010 - Department of Pathology and Molecular Medicine text/html 2010-01-24T13:51:27-04:00 Julia Williams http://wiki.genedrift.org/doku.php?id=part1&rev=1264359087&do=diff Part 1 Hands on code: Sequences and strings 1 As pointed in Beginning Perl for Bioinformatics, a large percentage of bioinformatics procedures deals with strings, especially DNA and amino acids sequence data. As is largely known DNA is composed of four different nucleotides: A, C, T and G and proteins can contain up to 20 amino acids. Each one of these elements have one letter of the alphabet assigned to them. In the DNA case some letters represent one or more nucleotides that can be present a… text/html 2009-05-22T11:36:18-04:00 Paulo Nuin http://wiki.genedrift.org/doku.php?id=part16&rev=1243006578&do=diff 1 Let's check some database topics in Python. I was asked to create a simple database to organize wet-lab stuff. No relationships needs, no relational tables required. Just a simple table with determined columns, and a nice GUI to go with it so people can edit, search and use. text/html 2009-05-22T11:29:23-04:00 Paulo Nuin http://wiki.genedrift.org/doku.php?id=beginning_python_for_bioinformatics&rev=1243006163&do=diff The posts from Beginning Python for Bioinformatics are and will be included here, allowing for a better experience when reading the entries. Beginning the begin This website uses as a premise the book: Beginning Perl for Bioinformatics by James Tisdal text/html 2009-05-22T11:28:24-04:00 Paulo Nuin http://wiki.genedrift.org/doku.php?id=part15&rev=1243006104&do=diff 1 We created a very elegant script in Python that efficiently counts words in FASTA sequences and then using a basic statistical method, calculates the significance of each word and output the overrepresented ones. Our script used a little bit less than 50 lines, and if you include the imported fasta module, it won't top 100. But the number of lines is not important. The efficiency, clarity and speed are key here. At the same time, running a script from the command line is not something every…