Lecture 1: Overview and organization

  1. Discuss course goals and syllabus
  2. Some biology and motivation

What is bioinformatics?

The use of computer science, mathematics, and information theory to model and analyze biological systems, especially systems involving genetic material. ---The Free Dictionary

An interdisciplinary field that develops and improves on methods for storing, retrieving, organizing and analyzing biological data. A major activity in bioinformatics is to develop software tools to generate useful biological knowledge. --- Wikipedia

Why is data central? Data is fundamentally changing the way research is being done:

Example: In his thoughtful and provocative 2012 TedMed talk (14:08 min) Atul Butte, Chief of Systems Medicine at Stanford University, discusses the field of translational bioinformatics and introduces the idea that big data is fundamentally changing the way science is being done. A more in depth NIH lecture: Translational Bioinformatics: Transforming 300 Billion Points of Data (1:07:02) is also available on YouTube.
Data Mining to Recruit Sick People
Companies Use Information From Data Brokers, Pharmacies, Social Networks
Joseph Walker, Dec. 17, 2013, Wall Street Journal 

Some basic biology:
 Term What is it CS analog
 Nucleotides A, T, C, G - basic subunits of encoding instructions of lifeReserved words in a programming language
 DNAMolecule that encodes genetic instructions - usually double stranded -- has nucleotides and other structureA program consisting of many functions
 Chromosome Organized structure of DNA found in cellsLibrary of programs
 GeneRegion DNA that corresponds to a unit of inheritance and which produces a proteinFunction in a program (code that does something)
 RNA(Ribonucleic acid) Molecule that performs functions such as coding of proteinsFunction code (after compilation)
 ProteinMacromolecule that performs must functions within an organismExecuting function (after compilation and linking)
 Central dogma"DNA makes RNA (transcription) makes protein (translation)"Process of compiling and linking code to make an executable program and then running it

Rethinking the genome and genetics as a space opera:

Space opera I: The great machine
Transcription - Central Dogma Part 1: http://www.youtube.com/watch?v=DA2t5N72mgw
Translation - Central Dogma Part 2 (2:28 min): http://www.youtube.com/watch?v=WkI_Vbwn14g
Molecular Visualizations of DNA (7:47 min): http://www.youtube.com/watch?v=4PKjF7OumYo

Electron micrograph of decondensed chromatin from chicken erythrocytes. 
Beads on a string

Where is the chromosome in the nucleus?