Computational Biology Major

Tao Sheng

Computational Biology is a joint major offered by both the Department of Biological Sciences in the Dietrich School of Arts and Sciences and the School of Computing and Information. Students can declare this major after completing BIOSC 150 and 160; CHEM 110 and 120; and CS 0011 or an equivalent placement test with the Python language. Students may also declare the major and choose to be under the Dietrich or SCI. Note, there are substantial differences between the two which are outlined here.

Starting in 2018, the bioinformatics major was replaced by the new Computational Biology major. This new major offers more core computer science courses and decreases biology requirements. Many required courses are now aligned with most graduate health science schools (medical, dental, etc.) which allows more flexibility. In turn, it is now a popular track for students wishing to go into graduate research, industry, or aforementioned graduate health science schools. In addition, some courses are currently being streamlined and students will be the first to attend some of these “revamped” courses for the new major.

In general, this major is quite broad. Computational Biology has numerous sub categories ranging from evolutionary biology, systems biology, medicinal chemistry, and more. Consequently, this major isn’t the most specialized and students should expect a broad overview of methods in biology that computation is useful for rather than a specialization in a certain subfield.

Fun facts:

  • Completing CHEM 110, 120, 310, 320, and BIOSC 1000 is the same as the requirements for the chemistry minor. As always, contact the registrar or official advisor for confirmation to declare.
  • CS is increasingly becoming a valuable skill for healthcare workers and researchers.
  • Biomedical researchers with computer science knowledge are the most sought after in the field.
  • The core CS courses in the major overlap with all except CS 447 of the CS minor. Note: you may or may not be able to declare the minor with the computational biology major in DSAS because of the credits overlap rule. Ask your advisors for more up to date information on this.

Before Declaring:

  • CS 0011 or equivalent in Python: CS 0008 is a possible alternative (offered more often and more flexible timing). Contact your advisor to see if it’s suitable still. You can also contact the major advisors to ask for a placement test to skip this requirement.
  • BIOSC 150: This course covers biology topics such as cell structure, genetics, metabolism and photosynthesis, and foundational chemical concepts. This class is intended for natural science majors and is decently intensive. An honors course is available.
  • BIOSC 160: This course covers biology topics such as evolution, ecology, reproduction, and biotechnology. Similarly, this is somewhat intensive. An honors course is available.
  • CHEM 110: This covers the first half of chemistry topics from atomic theory to thermochemistry. An honors course is available. Note, a lab is included in the course. (4 hours once a week)
  • CHEM 120: This covers the second half of chemistry topics from acid base chemistry to thermochemistry, electrochemistry, and bonding theories. An honors course is available. Note, a lab is included in the course. (4 hours once a week).

Major Coursework

Co-requisites:

  • MATH 0220: Calculus 1
  • STAT 1000: Applied Statistics

Core CS:

  • CS 0011 or equivalent, CS 401, CS 441, CS 445, CS 1501. See the rest of the wiki for more information on these courses.
  • Note that CS 401, CS 445, and CS 1501 are currently offered only in java. It is recommended in the time between CS 0011 and CS 401 that you quickly learn java syntax and lower level computer science concepts.
  • CS 1656: Introduction to Data Science: Overview of data science technologies and techniques: data management, manipulation, analysis, and presentation. The course will cover SQL, XML, Xquery, RDF, SPARQL, Graph/Cypher along with topics such as information retrieval, data mining, and other topics. This course is taught in Python. 1501 is a prerequisite and statistics is highly recommended.

Core Science:

  • BIOSC 0350: Genetics

    • This is a somewhat advanced level genetics course that goes deeper into foundational concepts covered in BIOSC 150 and 160. Many students take this with organic chemistry 1. Jacobson is a popular professor choice.
  • BIOSC 1000: Biochemistry

    • This is the hardest science course of the major. I advise decreasing your credit load this semester to no more than 14-16.
    • It's extremely fast paced, combines advanced biology concepts mostly studied in BIOSC 150 with chemistry concepts from 110, 120, and organic concepts from 310 and 320. However, I would mention that it is much more focused on biology than chemistry. Also, this course is extremely important for studying physiology, systems biology, and metabolism. Erica Mcgreevy is the most popular professor.
  • CHEM 0310: Organic Chemistry 1

    • This is a notoriously difficult course which requires a deep understanding of chemistry fundamentals and the ability to visualize 3D structures of molecules in certain conditions, environments, and perspectives. It's recommended that the student takes a light schedule as well (13-16 credits) when taking this course. There will be a lot of studying required.
    • Topics covered: nomenclature, stereochemistry, radical chemistry, fundamental reaction mechanisms, alcohols, sulfur chemistry, alkenes and alkynes. It may optionally include lab spectroscopy techniques.
    • Most professors are fantastic choices: most notably: George Bandik, Paul Floreancig, Peng Liu, Tim Tseng, Scott Nelson, Lingfeng Liu, Seth Horne (Honors).

Core Bioinformatics

  • Computational Biology (BIOSC 1540) (fall only)

    • Very basic course intended to “give students a broad understanding of how computational approaches can be used to solve problems in biology. Both the biological and computational underpinnings of the methods will be addressed”
    • Will use R for projects
  • Computational Genomics (Spring in even catalog years) OR Simulation and Modeling (Spring in odd catalog years)

    • example: Spring 2019 was BIOSC 1542 (genomics). NOTE: in Spring 2020, Simulation and Modeling will NOT be offered because of an internal issue. Genomics will return in the following spring. Contact the major advisors for more information on substitute courses if needed.
    • Genomics: Computer-aided methods to generate and test biological hypotheses at whole-genome scales. Students will gain both a theoretical and practical understanding of working with genomic data typical of high-throughput sequencing technologies.
    • Simulation / Modeling: Computational structural biology, simulation and modeling, as seen through the lens of a rational, computer-aided drug discovery. Topics will include protein structure and modeling, cheminformatics, virtual small-molecule screening, molecular dynamics screenings, molecular visualization, and online resources for studying proteins and molecules. A class project will allow students to apply the relevant tools.
    • Both courses allow the student to choose which specialization interests them the most. Both courses are intensive given they are a high level course, but will be the most applicable of the core bioinformatics which should prove to be one of the most enjoyable ones.
    • Beacuse these courses are offered so rarely, cross registering with CMU can be an option to replace the requirement if you want to take a specific course. Additionally, taking a graduate level course is an option but the mathematics may be difficult. Always contact the major advisors to ask for explicit permission to take other courses to waive this requirement.
  • Capstone: BIOSC 1640 (spring only) or CS 1640 (both fall and spring)

    • Depends on if declared with DSAS or SCI; though if you feel strongly about a course over the other, it does not hurt to email around to ask for permission.
    • Courses are somewhat new and most students will be taking these as the courses’ first iterations. From first glance, it seems BIOSC 1640 may offer a research experience or opportunities to use real world research techniques on replicated projects. CS 1640 is the old version of BIOSC 1640 that was retired and seems more focused on software engineering.
  • Seminar Comp Bio BIOSC 1630 (fall only)

    • Writing requirement for the major. Not much information is available on this course, but it’s likely not intensive and can be thought of as the “CS1501 W-requirement” of the major.

Elective

  • These are too numerous to list here. Visit the program catalog for the comprehensive list here

Extra notes

General:

  • I would recommend using AP credit to skip any classes you can (especially calculus). Exceptions are for students applying to health graduate schools that would prefer to see college experience with a course over AP credit, but of course that varies on a case to case basis.
  • The major is quite broad and there are a lot of different biological topics covered but none of them in-depth. If you have room in your schedule, you could look into other departments that offer computational courses (ex: Linguistics, Chemistry, etc.) to get more specialized bioinformatics / computational biology knowledge.
  • This major is newly made as mentioned above. Contact the official comp bio advisors for the final say on any information.
  • Satisfactory/No Credit information: "One core course required for the major may be taken on an S/NC basis. Co-requisite courses may be taken on an S/NC basis subject to School limitations. Please check with your School for specific information on S/NC grades."

About UTAing for biology or chemistry courses:

  • UTA/UTUing varies with departments -- responsibilities, compensation (either by a letter grade, S/NC, or pay), and requirements differ depending on which course you wish to help teach. This is quite different from the CS department.
  • In some cases, professors will reach out to you if you achieved an A- / A grade in the course to ask if you would like to UTA. Othertimes it's easier to email the professor you wish to UTA for directly.
  • Check out the biology department's information on becoming a UTA [here] (https://www.biology.pitt.edu/undergraduate/uta)

    • Most introductory (BIOSC 150/160) UTAs should be receiving credit hours as S/NC. Different professors will have different responsibilities and these can range from handling recitations, creating worksheets/homework, proctoring exams, and holding reviews.
  • The chemistry department's contact for becoming a UTA is Dr. Tamika Madison (TAM7@pitt.edu) as of June 2020. Backup contact: Dr. George Bandik (bandik@pitt.edu). To UTA for organic chemistry, contacting individual professors is recommended.

    • Some introductory (CHEM 110/120) UTAs should be receiving full letter grades (affects GPA). Different professors will have different responsibilities and there are a few roles (active learning facilitator, recitation co-leader, laboratory co-teacher)
    • Active learning facilitators work with a lecturer to guide students through Process Oriented Guided Inquiry Learning (POGIL) activities with a 1-2 hour per week time commitment
    • Recitation co-leaders work with other UTUs to help small groups of students practice lecture concepts during recitation (my personal recommendation) with a 1+ hour per week time commitment.
    • Laboratory co-teachers work with a laboratory instructor to help students complete laboratory experiments with a 3 hour per week time commitment.
    • Organic chemistry (CHEM 310/320) UTAs should receive full letter grades (affects GPA). Responsibilities vary but on average your role will be very important beacuse of the nature of the course.
  • You can UTA for the separate biology labs and the compensation will be S/NC credit most likely and responsibilities will vary.

Electives, gen eds, and other courses are not explicitly listed here because it varies depending what else you choose to study (or if you're on a pre-professional track). Here is just my recommendations for the major courses.

Year 1 Fall

  • BIOSC 0150, CHEM 0110, CS 0011 or equivalent

Year 1 Spring

  • BIOSC 0160, CHEM 0120, CS 0401
  • Calculus 1

Year 2 Fall

  • CHEM 0310, CS 441,BIOSC 350, BIOSC 1540

Year 2 Spring:

  • CS 445, BIOSC 1542 / 1544 (depends on year)

Year 3:

  • Research / Software Design (depends on school)
  • STAT 1000
  • BIOSC 1000
  • BIOSC 1542 / 1544
  • CS 1501

Year 4:

  • Comp Bio Seminar
  • CS 1656
Last updated: Dec 30th 2020