Guide Computational Methods for Bioinformatics. Python 3.4

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What is "Bioinformatics"? Description of Course Contents The lecture portion of the course serves two purposes and click here for Projects and Presentations : 1 to introduce you to the basic, core concepts of Bioinformatics , which underlie the many, many applications used by computational biologists to extract knowledge and understanding from myriads of databases.

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How is sequence information collected, stored and organized, managed and distributed? Which bioinformatic methods best reveal and conceptualize the raw information provided by genomics and proteomics research?

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See Course Outline in FlowChart format. T ogether we will try to get at least a glimpse of the subtle variations in relatively simple biological structures, and how these variations combine in numerous ways to contribute to a wonderful and exciting biological complexity and hence diversity.

As always with all my courses , the pedagogy rests on two main themes: 1 Knowing, understanding, and analyzing major concepts , and how these concepts relate to each other, to the major concepts of all biology, and to disciplines and ideas outside the normal realm of biological science; 2 Understanding the theory and practice of the scientific method , and then how it transforms questions, observations, problems, etc.

Every attempt will be made to integrate major concepts to show the unity of the various sub-disciplines comprising molecular biology by applying the knowledge and techniques of genomics and bioinformatics. Every attempt will be made to collect a seemingly overwhelming amount of details into regular, concept-based patterns forming the over-arching themes and principles of modern biology.

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Yes, these patterns and themes exist! Reductionism will lead to Holism, especially by way of Bioinformatics, and to an increased awareness of how sets of regularly repeating themes and patterns, first observed in macromolecular sequences, combine in myriad ways to generate the wonderful, rich diversity of living organisms. Then you will embark on a new and exciting adventure into Systems Biology A note about your texts for this course: a constant, repeating theme throughout the texts, in each chapter, almost like a fractal image , and this site too, and this one is the fundamental relationship of structural genomics to functional genomics to comparative genomics, which is interlaced always with computational analyses.

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Please Note: each of the following sections is divided into Reading Assignments and Web-links; the reading assignments can be found by clicking the listed links, while the Web-links and other useful information are located on the Resources for BIO page. Pairwise Sequence Comparisons.


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Protein Sequence and Structure Analyses. This textbook is designed for students that have some background in biological sciences but very little in computer programming.

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Python scripting, however, is definitely a pre-requisite. This book considers three main tools by which computations and data analysis of biological data may be performed. These core competencies are the use of a spreadsheet, the use of a computer language, and the use of a database engine.


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  • This text assumes that the reader has very little experience in using a spreadsheet and no experience in the programming language or the use of a database engine. Advanced readers might find this text a bit frustrating as many of the examples do not use the most efficient coding possible.

    pierreducalvet.ca/206491.php The purpose of this text is to relay an understanding of how algorithms work and how they can be employed.