Computer Science 464/788: 

Introduction to Computational Biology
Lehman College, City University of New York
Fall 2003

Announcements:

• Some students cheated on the initial parts of the project.  As such, each project presentation is being double checked
  for plagiarism.  This is extremely time-consuming, and so, the grades for all presentations will not be ready until next week.  Sorry for the delay!  As each presentation is checked, it's grade will be posted.  So, some students already have their grades; others will be posted soon.
  
• The presentation schedule for the projects is now available, as the quizzes based on the projects and photos from the poster session.
  
• This course is being offered at the undergraduate level (CMP 464) and masters level (CMP 788).  The lectures for both courses will be the same.  Those taking the course for graduate credit will have extra reading and programming assignments (in addition to those for the undergraduates), will have quizzes that test the understanding of the material at a deeper level, and will give a presentation to the class.
  

Handouts:

• Syllabus
• Outline
• "Computers Are from Mars, Organisms are from Venus" by J. Kim, 2002.
• Handouts for lecture on Tuesday, 9 September:
  
  • "Introduction to DNA Structure" by Prof. Richard B. Hallick, U. Arizona.  
  • "Principle of Sequencing" by Dr. Andy Vierstraete, U. Ghent.
  • Pairwise Alignment: "Dynamic Programming Example" & "Advanced DP Example" by Dr. Eric C. Rouchka, Washington U.,  St. Louis.
    
• Quiz 1 (due 18 September)
• Handouts for lecture on Tuesday, 23 September:
  
  • Background on Dynamic Programming:
    
    • Definition from the National Institute of Standards and Technology (NIST
    • "Dynamic Programming: An Introduction"by David K. Smith and PASS Maths (Part of the Millennium Mathematics Project sponsored by the Univeristy of Cambridge).
    • Definition and Edit Distance example by Dr. Lloyd Allison, Monash U.
  • Scoring Matrices from Oxford University Bioinfomatics Centre.
    
• Quiz 2 (due 25 September)
• Handouts for lecture on Thursday, 2 October:
  
  • Chapter 3 & 4 Examples from Beginning Perl for Bioinformatics by James Tisdall
• Quiz 3 (due 2 October)
• Handouts for lecture on Thursday, 9 October:
  
  • Introduction to Phylogeny Lecture Notes 
  • Chapter 5 Examples (loop and decision statements) from Beginning Perl for Bioinformatics by James Tisdall
• Handouts for lecture on Tuesday, 14 October:
  
  • Project Information
    
  • Multiple Sequence Alignment:
    
    • Overview of Multiple Sequence Alignment by Dr. Guy Bottu for embnet.news.
      
    • Iterative Alignment Strategy  by Dr. Hannes Luz, German Cancer Research Center and the Max Planc Institute for Molecular Genetics.
  • Using software:
    
    • BLAST tutorial (pairwise sequence alignment)
      
    • Fasta overview and tutorial (pairwise sequence alignment)
      
    • Clustalw overview and tutorial (multiple sequence alignment)
      
  • Chapter 5 Examples (more on regular expressions and loops) from Beginning Perl for Bioinformatics by James Tisdall
• Handouts for lecture on Thursday, 16 October:
  
  • Phylogenetic Tree Notes (pdf version) from Prof. Daniel Huson, University of Tuebingen, Germany.
  • Chapter 5 Examples (subroutines) from Beginning Perl for Bioinformatics by James Tisdall
• Handouts for lecture on Tuesday, 21 October:
  
  • Phylogenetic Tree Notes (pdf version)and Phylogenetic Networks Notes (pdf version) from Prof. Daniel Huson, University of Tuebingen, Germany.
  • Chapter 6 Examples (command-line arguments & passing variables) from Beginning Perl for Bioinformatics by James Tisdall
• Quiz 4 (due 21 October)
• Handouts for lecture on Thursday, 23 October:
  
  • Phylogenetic Tree Notes (pdf version)and Phylogenetic Networks Notes (pdf version) from Prof. Daniel Huson, University of Tuebingen, Germany.
  • Lecture notes on consensus methods,
    
  • Chapter 7 Examples (subroutines & modules) from Beginning Perl for Bioinformatics by James Tisdall.
• Handouts for lecture on Tuesday, 28 October:
  
  • Phylogenetic Tree Notes (pdf version)and Phylogenetic Networks Notes (pdf version) from Prof. Daniel Huson, University of Tuebingen, Germany.
  • Lecture notes on networks and comparing trees,
    
  • "Case Study: Visualizing Sets of Evolutionary Trees" Amenta & Klingner, 2002,
    
  • TreeJuxtaposer. by Prof. Tamara Munzner, University of British Columbia, Canada
  • Chapter 7 Examples (random number generation) from Beginning Perl for Bioinformatics by James Tisdall.
• Programming Assignment 1 (target date of 28 October)
• Handouts for lecture on Thursday, 30 October:
  
  • Phylogenetic Tree Notes (pdf version)and Phylogenetic Networks Notes (pdf version) from Prof. Daniel Huson, University of Tuebingen, Germany.
  • Lecture notes on testing algorithm empirically.
  • Paper by Prof. Moret,   "Towards a discipline of experimental algorithmics,"   in Data Structures, Near Neighbor Searches, and Methodology:   Fifth and Sixth DIMACS Implementation Challenges, M.H. Goldwasser, D.S. Johnson, and C.C. McGeoch, eds, DIMACS Monographs 59 , 197-213,   American Mathematical Society, Providence, 2002. Available from http://www.cs.unm.edu/~moret/papers.html.
    
  • Chapter 7 Examples (random number generation) from Beginning Perl for Bioinformatics by James Tisdall.
• Quiz 5 (due 30 October)
• Handouts for lecture on Tuesday, 4 November:
  
  • Protein Secondary Structure  (pdf version) from Prof. Daniel Huson, University of Tuebingen, Germany.
  • Overview from Folding@Home (we'll discuss the overview plus background info (see sidebar) on amino acids, proteins, diseases, and molecular modeling)
    
  • Chapter 8 Examples (hashes) from Beginning Perl for Bioinformatics by James Tisdall.
• Handouts for lecture on Tuesday, 11 November:
  
  • Protein Tertiary Structure  (pdf version) from Prof. Daniel Huson, University of Tuebingen, Germany.
  • Chapter 8 Examples (more on hashes, genetic code, and FASTA format) from Beginning Perl for Bioinformatics by James Tisdall.
• Programming Assignment 2 (target date of 11 November)
• Handouts for lecture on Thursday, 13 November:
  
  • DNA Arrays  (pdf version) from Prof. Daniel Huson, University of Tuebingen, Germany.
  • microarray.com:  a source for information about microarray technology.
  • NCBI's primer on microarrays.
  • Chapter 10 Examples (Protein Data Bank) from Beginning Perl for Bioinformatics by James Tisdall.
• Quiz 6 (due 13 November)
• Handouts for lecture on Tuesday, 18 November:
  
  • DNA Arrays  (pdf version) from Prof. Daniel Huson, University of Tuebingen, Germany.
  • Yeast cell cycle analysis project via microarrays from Stanford University.
  • An Introduction to SNPs from the National Center for Biotechnology Information.
  • Haplotype Mapping Project Report from the National Human Genome Research Institute.
    
  • Chapter 12 Examples (BLAST) from Beginning Perl for Bioinformatics by James Tisdall.
• Handouts for lecture on Thursday, 20 November:
  
  • Genome Assembly  (pdf version) from Prof. Daniel Huson, University of Tuebingen, Germany.
  • An Introduction to Genome Mapping from the National Center for Biotechnology Information.
    
  • Chapter 9 Examples (restriction maps & regular expressions) from Beginning Perl for Bioinformatics by James Tisdall.
• Programming Assignment 3 (target date of 25 November)
  

Useful Links:

• Textbook: http://www.oreilly.com/catalog/bioskills/index.html
• Blackboard: http://blackboard.lehman.cuny.edu