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 one of the most sought after
  • 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.

Declaration Requirements:

  • CS 0011 or equivalent in Python: CS 0008 may be 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: Foundations of Biology 1: 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: Foundations of Biology 2: This course covers biology topics such as evolution, ecology, reproduction, and biotechnology. Similarly, this is somewhat intensive. An honors course is available.
  • CHEM 110: General Chemistry 1: This covers the first half of chemistry topics from atomic theory to thermochemistry. An honors course is available. A lab is included in the course (4 hours once a week) unless it's a retake.
  • CHEM 120: General Chemistry 2: This covers the second half of chemistry topics from acid base chemistry to thermochemistry, electrochemistry, and bonding theories. An honors course is available. A lab is included in the course (4 hours once a week) unless it's a retake.

Major Coursework - excluding declaration requirements

Co-requisites:
  • MATH 0220: Calculus 1
  • STAT 1000: Applied Statistics
  • CHEM 110 & 120 (required for declaration too), 310 (organic 1)

    • CHEM 0310: Organic Chemistry 1 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 if no prior organic experience or not confident in general chemistry yet. Topics covered: nomenclature, stereochemistry, radical chemistry, fundamental reaction mechanisms, alcohols, sulfur chemistry, alkenes and alkynes. It may optionally include lab spectroscopy techniques.
Core CS:
  • CS 0011 or equivalent or placement test, 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, so a transition to java may require extra learning to catch up.
  • 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 Biological Sciences:
  • 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 since it is fundamental for higher level biology.
  • BIOSC 1000: Biochemistry

    • This is the hardest science course of the major. Word on the street is that this is the "biology" equivalent of 1501, and that 1501 is the "CS" equivalent of biochemistry. I advise decreasing your credit load this semester to no more than 14-15.
    • 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.

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”
    • Currently uses 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 extenuating circumstances. 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.
    • Because 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)

    • DSAS = BIOSC 1640, SCI = CS 1640; though if you feel strongly about a course over the other, one can get permission to take another school's capstone requirement to fulfill their own requirement.
    • Courses are somewhat new and most students graduating in 2022 will be taking these as the courses’ first iterations. The following information must be taken with a grain of salt. Although this likely varies, BIOSC 1640 may offer real research experience on real projects or "curated" projects for the course. Contacting the professor teaching it next term to get more details is always recommended. CS 1640 seems to be a combined section with CS 1980 and there should be available real world projects (either in software engineering or bioinformatics). As of 2021, this website hosts information on the SCI comp. bio. capstone here
  • Comp Bio Seminar BIOSC 1630 (fall only)

    • Includes (W) writing requirement for the major. This course focuses on reading and analyzing primary research literature in the field of computational biology, with an emphasis on effective techniques for communicating about the associated science both verbally but also in writing. Many articles are to be read and critiqued and discussed.

Electives

  • These are too numerous to list here. Visit the program catalog for the comprehensive list here. Lots of overlap with pre-professional course requirements.

Extra notes

  • 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, Neuroscience 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. Other times 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 should be findable on their website. 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. Always consult with an advisor or re-evaluate if you feel a different path is better for your personalized plan.

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 Fall and Spring:

  • BIOSC / CS 1640 - Research / Software Design (depends on school)
  • STAT 1000
  • BIOSC 1000
  • BIOSC 1542 / 1544
  • CS 1501

Year 4 Fall and Spring:

  • Comp Bio Seminar
  • CS 1656
Last updated: Sep 13th 2021