BING 6004 – Principles of Computational BioEngineering (Spring 2016)

This course introduces the basic computational issues and methods employed in molecular biology.  Biological data sources available on the Internet will be utilized and analyzed.

General Information

  • Course Information Sheet A.K.A. Prontuario (PDF)

Lecture Tu & Th (6:30 – 7:45) @ Stefani 207

  • Lecture 0 – Course Introduction and Administrivia
  • Lecture 1 – Python Programming Basics: Expressions and Variables (Slides PPT)
  • Lecture 2 – Controlling the Flow of your Program (Slides PPT)
  • Lecture 3 – Container Objects (Slides PPT)
  • Lecture 4 – Manipulating Files (Slides PPT)
  • Lecture 5 – Sequence Alignment and Sequence Database Seaching (Slide PPT)
  • Lecture 6 – Introduction to Next Generation Sequencing NGS by Dr. Ricardo González  (Slides PART1, PART2)
  • Lecture 7 – NGS Algorithms and Tools by Dr. Ricardo González (Slides PART1, PART2)
  • Lecture 8 - Using Relational Databases To Analyze Bioinformatics Data (Slides PDF blast2TSV.py, P00624.fasta, P0064.tsv, SQLModuleSampleDB, trinotate.db)

Exams

  • Partial Exam : To be announced (TBA). During lab session.
  • Final Exam: TBA

Programming Assignments

  • Programming Assignment 1.  (PDF, SourceCode)
  • Programming Assignment 2.  (PDF, SourceCode)
  • Programming Assignment 3.  (PDF, SourceCode)

Software Development Tools

  • PyCharm IDE