Bio/CS 251

Introduction to Bioinformatics

Class Web Sitehttp://cs.gettysburg.edu/~leinbach/Bio_CS251/

• This site will contain all important documents related to the class.

Power points of all lectures

Labs

Exam Answer Keys (Posted after the exam)

Homework Assignments and Answer Keys

• Note the updated syllabus contained at this site. It super cedes the one distributed on paper. Difference: description of the final project. There are two options.

My Definition of BioinformaticsA study of the algorithms and programs that are used by Molecular Biologists and others in the Biological and Medical Sciences in their quest for understanding protein structure and function in living organisms.

This is just one of many definitions that may be found in text books, scientific papers, and on the web. The simplest definition is that it is an interdisciplinary subject drawing on material from Biology, Mathematics, and Computer Science. To me this is like saying that e = mc2 has something to do with relativity theory.

Some Implications of this Definition

• An individual studying Bioinformatics needs to have some understanding of the basic ideas of Molecular Biology research.

• They also need to have a familiarity with DNA sequences and how they contribute to 3D Protein Structure as well as gene identification and phylogenetics.

• They need to be familiar with the many “in silico” tools that are used and the parameters that control the output of the programs or algorithmically controlled devices.

• It is important for them to understand the objectives and limitations of both Computer Science and Molecular Biology.

• They need to have some experience with collecting biological data for analysis

Computational Biology

Micro Biology & Medical Science

Computational Biology

Computer Science Biology

Bioinformatics

Micro Biology & Medical Science

Computational Biology

(Note the two way arrow)

Some Timelines

Material taken from lecture given by

Lucy Skrabanek

Institute of Computational Biology at Weill Medical College of Cornell University

February 23, 2005

Early Pre History

Computer Science

Micro Biology

Bioinformatics

Late Pre History

Computer Science

Micro Biology

Bioinformatics

Recent History

Computer Science

Micro Biology

Bioinformatics

Two Scientists Who In ~900 Words Reshaped the Way In Which We View Life on Earth

With the power and storage capabilities of computers biological databases began to proliferate all around the world. By the mid 1980’s users were demanding access to the latest, up to date data.

In 1988, a network was established to link databases in European Molecular Biology and Bioinformatics Labs. It was called the European Molecular Biology network, or EMBnet. At the turn of the century it consisted of 34 national, specialist, and associate nodes.

In the United States the National for Biological Information of the National Laboratories of Medecine at the National Institutes of Health became the repository for sequence and protein information as well as a link to other databases around the world.

The World Wide Web (a sophisticated internet tool) has facilitated queries to these databases.

The Net (no pun intended) Result is an Asstounding Growth of Biological Information

Source: Scrabanek op. cit.

Protein Structure Data is Growing at a Slower Pace

As a result, DNA sequencing and Proteomics have had an increasing number of important applications in the life, medical and social sciences.

Pickup any scientific journal that deals with the life or medical sciences, any popular scientific magazine, or, for that matter, any daily newspaper and you will find an article where DNA or related issues play an important role

Why, it even makes the comic section: