Computing for Life Sciences
Feel free to contact and ask me questions: dkihara at purdue.edu
Mon/Wed/Fri 11:30am-12:20pm, LWSN 1106
This is a core course in the CLS Program.
Purpose of the course
to expose students to computational concepts, algorithms, basic programming, and tools used in computational life sciences.
Students will learn bioinformatics research topics, basic programming, and how computational methods are applied to address the research questions.
These techniques are applied for answering questions including the followings:
- unix system, programming in Python
- basic background about proteins, DNA, and RNA
- biological databases
- algorithms for biological sequence (DNA, protein) sequence alignment & database search
- algorithms for sequence motif search
- protein tertiary (3D) structure comparison
- protein 3D strucure prediction from amino acid sequence
- protein-protein interaction
- biological network analysis
- systems biology
- drug protein interaction
These topics will be introduced through recent research papers and through mini projects.
- How function of genes can be predicted once a genome sequence of an organism (e.g. human) is determined?
- How function of a protein can be predicted when its 3D structure is known?
- How can we predict 3D structure of proteins? How well can we predict it?
- How can we investigate evolution of proteins using sequence and structure information?
- How protein structures are described and compared?
- How different is human genome from Chimpanzee genome?
- How did organisms (genomes) evolve?
- how does a protein move to carry out its biological function?
- What is the principle for computational drug design?
30% homeworks +
30% projects +
40% midterm & final exam
We don't use a specific textbook. Lecture notes will suffice.
Good Books to refer to
- "Learning Python", 2nd edition, Mark Lutz, David Ascher, O'Reilly, ISBN: 0-596-00281-5.
- "Biological Sequence Analysis", Durbin, Eddy, Krogh, Mitchison, ISBN 0-521-62971-3
- "Protein Bioinformatics", Eidhammer, Jonassen, Taylor, ISBN 0-470-84839-1
- "Algorithms on Strings, Trees, and Sequences" Gusfied, ISBN 0-521-58519-8
Last Modified: August/09/2011