• About Us
    • Leadership
    • What is Computational Biology?
    • What is Automated Science?
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    • Ph.D. in Computational Biology
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    • Undergraduate Program in Computational Biology
      • Why Major in Computational Biology?
      • Degree Requirements
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    • Minor in Computational Biology
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    • Courses Offered
      • Undergraduate Courses Offered
      • Graduate Courses Offered
      • Course Profiles
        • 02-201/601 Programming for Scientists
        • 02-250 Introduction to Computational Biology
        • 02-261 Quantitative Cell and Molecular Biology Laboratory
        • 02-402/702 Computational Biology Seminar
        • 02-425/725 Computational Methods for Proteogenomics and Metabolomics
        • 02-450/750 Automation of Biological Research: Robotics and Machine Learning
        • 02-500 Undergraduate Research in Computational Biology
        • 02-510/710 Computational Genomics
        • 02-602 Professional Issues in Computational Biology
        • 02-604 Fundamentals of Bioinformatics
        • 02-613 Algorithms and Advanced Data Structures
        • 02-700 M.S. Research
        • 02-701 CPCB Course / Current Topics in Computational Biology
        • 02-715 Advanced Topics in Computational Genomics
        • 02-760 Laboratory Methods for Computational Biologists
        • 02-801 Computational Biology Internship
        • 02-900 Ph.D. Thesis Research
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Find us
help@cbd.cmu.edu
Computational Biology Department Computational Biology Department
  • About Us
    • Leadership
    • What is Computational Biology?
    • What is Automated Science?
    • Computational Biology Careers Website
    • List of Educational Programs in Computational Biology
    • The Hillman Center
    • History
    • CBD at a Glance
    • News and Events
      • News
      • Calendar
      • Departmental Seminars
      • Meetings
    • Department Resources
  • Education
    • Ph.D. in Computational Biology
    • M.S. in Automated Science
    • M.S. in Computational Biology
    • Undergraduate Program in Computational Biology
      • Why Major in Computational Biology?
      • Degree Requirements
      • Sample Course Sequence for Computational Biology Majors
      • Guidelines for Transfer to Major in Computational Biology
      • Additional Major in Computational Biology
      • Visit Us
    • Minor in Computational Biology
    • Pre-College Program in Computational Biology
    • Courses Offered
      • Undergraduate Courses Offered
      • Graduate Courses Offered
      • Course Profiles
        • 02-201/601 Programming for Scientists
        • 02-250 Introduction to Computational Biology
        • 02-261 Quantitative Cell and Molecular Biology Laboratory
        • 02-402/702 Computational Biology Seminar
        • 02-425/725 Computational Methods for Proteogenomics and Metabolomics
        • 02-450/750 Automation of Biological Research: Robotics and Machine Learning
        • 02-500 Undergraduate Research in Computational Biology
        • 02-510/710 Computational Genomics
        • 02-602 Professional Issues in Computational Biology
        • 02-604 Fundamentals of Bioinformatics
        • 02-613 Algorithms and Advanced Data Structures
        • 02-700 M.S. Research
        • 02-701 CPCB Course / Current Topics in Computational Biology
        • 02-715 Advanced Topics in Computational Genomics
        • 02-760 Laboratory Methods for Computational Biologists
        • 02-801 Computational Biology Internship
        • 02-900 Ph.D. Thesis Research
  • Research
    • Software
    • Faculty Research Pages
    • Computational Biology Technical Reports
    • White Papers
  • People
    • Faculty
      • Voting Faculty
      • Affiliated Faculty
      • Visiting Faculty
      • Adjunct Faculty
    • Staff
      • Department Staff
      • Research Staff
    • Fellows and Special Faculty
      • The Lane Fellows Program
      • Current Lane Fellows
      • Past Lane Fellows
      • Postdoctoral Fellows
      • Past Postdoctoral Fellows
      • Special Faculty
    • Alumni
      • Ph.D. Graduates
      • Alumni Profiles
  • Join Us!
    • Life in Pittsburgh
      • Neighborhoods Near Carnegie Mellon University
      • Things to Do in Pittsburgh
    • Positions Available
    • Apply to Ph.D. Program
    • Apply to MSAS
    • Apply to MSCB
    • Apply to Undergraduate Program
    • Apply to be a Lane Fellow

02-250 / 03-250 Introduction to Computational Biology

02-250 COURSE PROFILE

Return to Courses Offered

Course Level Undergraduate
Units 12
Special Permission Required? (If yes, see “Notes:) No
Frequency Offered Spring
Course Relevance (who should take this course?)
  • Computational biology Majors
    • 02-250 is a required course
  • Biological Sciences Majors
    • 03-250 is a required course that is recommended to be taken in the spring of the second year (after taking 02-201, 15-110 or 15-112).
  • Computational Biology Minors
    • 02-250 OR 02-251 is required for the minor and should be taken early enough to be able to take the advanced elective course.
Key Topics
  • DNA and RNA sequence analysis
  • Sequence databases
  • Gene expression analysis
  • Genome assembly
  • Binding site prediction
  • Phylogenetics and human genetic variation
  • Difference and differential equation-based biological models
  • Biochemical, neuronal, cell cycle models
  • Compartmental models and pharmacodynamics
  • Biological image analysis
Background Knowledge
  • Basic familiarity with cell and molecular biology (e.g., 03-121 Modern Biology or Biology Advanced Placement), including the central dogma, Mendelian genetics, cell structure, biochemical reactions, and the cell cycle
  • Familiarity with concepts of imperative (procedural) programming (prerequisite: 02-201, 15-110, or 15-112), including flow control, loops, function and arguments, data types, program structure and modularity
  • Ability to write short programs in a procedural language, preferably Python, and familiarity with basic Unix commands (cd, ls, cp, mv)
Assessment Structure
  • Grades are determined 50% by homeworks, 10% by participation in recitations, 15% by a midterm exam, and 25% by a final exam.
  • Homework is assigned in class each Friday and is due by 10:30 am on the due date (usually the following Thursday). All assignments are submitted electronically through Canvas. 3 late days total can be used without penalty during the semester, but only 1 late day can be used per assignment. There are no partial late days. Late homeworks will not otherwise be accepted unless you have made prior arrangements for an extension.  Please note that extensions will only be granted under exceptional circumstances.
Most Recent Syllabus  Course Schedule (from Spring 2017 – dates to be updated)
Course Goals/Objectives
  1. Learn major biological data types, the methods by which they are produced, and their uses.
  2. Learn to critically assess the reliability of biological data sources.
  3. Learn essential concepts of statistics and algorithms needed to productively use database search and inference tools and interpret their results.
  4. Learn to synthesize results from different data sources and select sources appropriate to a given problem.
  5. Learn about of the major repositories of biological data and the tools to access them.
  6. Learn to independently research a biological question using online resources.
  7. Learn how to pose biological questions through mathematical models and reason about the assumptions and limitations of those models.
  8. Learn to simulate the behavior of simple biological models.
  9. Learn basic image processing methods and concepts of biological image analysis.
  10. Learn concepts behind supervised and unsupervised machine learning as applied to biological problems.
Course Website  http://www.cbd.cmu.edu/education/undergraduate-courses/introduction-to-computational-biology/
Learning Resources

PiazzaAutolab

Instructors and TA office hours

Prof. Pfenning Tuesdays 10AM-11AM GHC 7711                        Prof. Murphy Mondays 3:30-5:00 GHC 7723
Easwaran Ramamurthy  Wednesdays 5:00-7:00                      NSH 1505
Allyson Lawler  Tuesdays Tuesdays 3:00-5:00
MI 290

Pre-reqs, Cross List, Related Pre-requisite: 02-201, 15-110, or 15-112
Suggested co-requisite: 03-12102-250 is intended primarily for computational biology, computer science, statistics or engineering majors at the undergraduate or graduate level who have had prior experience with computer science or programming. 03-250 is intended primarily for biological sciences or biomedical engineering majors who have had limited prior experience with computer science or programming. Students may not take both 02-250 and 03-250 for credit.  The lectures are the same for both but recitations are separate.Cross-listed with 03-250 (see Notes)
Notes

The course is taught under two different numbers.  The lectures are the same for both but recitations and examinations are separate.

02-250 is intended primarily for computational biology, computer science, statistics or engineering majors at the undergraduate or graduate level who have had prior experience with computer science or programming.

03-250 is intended primarily for biological sciences or biomedical engineering majors who have had limited prior experience with computer science or programming.

Students may not take both 02-250 and 03-250 for credit. Prerequisite: (02-201 or 15-110 or 15-112), or permission of the instructors.

Department Website https://cbd.cmu.edu
College Website https://cs.cmu.edu
Updated January 2018

 

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  • This is the January cover of PLoS Computational Biology. It illustrates the significant pairwise relationships in influenza virus infected cells that were learned following the research of Dr. Bob Murphy, Xiongtao Ruan, and Dr. Seema Lakdawala from the University of Pittsburgh School of Medicine.

Read more on our website:
http://www.cbd.cmu.edu/paper-on-influenza-virion-assembly-grabs-cover-of-plos-computational-biology/
  • Happy Holidays from the Computational Biology Department! Here are some shots from our holiday party on Wednesday:
  • Reminder: The early application deadline for the MSAS (Masters of Science in Automated Science) is this Friday, November 30th at NOON EST!
  • It's #givingCMUday! Please visit the web site https://t.co/6nySgIlcez and consider making a donation to the CMU Computational Biology Department!
  • Getting into the holiday spirit! Thanks to all of our students for coming to our annual MSCB Thanksgiving event!
  • #BSCB at Fright Night 💀👻🎃
  • Two #BSCB accolades to announce in one day - hilighting Winston Grenier for making Dean’s List last spring. Here he is celebrating at the SCS Dean’s List Party this evening. Way to go Winston! 👏👏👏 #cmusocial
  • Congrats to BSCB senior Wendy Yang on her election to Phi Beta Kappa honor society! 🎉🏆 read more on our website - link in bio
  • First day of student orientation week 🍂📚✏️ Welcome to the largest ever incoming class of @CMUPittCompBio students! #backtoschool #cmusocial

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