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Problem sets and lecture materials from Spring 2015 iteration of MCB 135: Introductory Systems Biology
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README.md
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README.md

Course materials from Harvard's MCB 135: Introductory Systems Biology

Spring 2015

Instructor: Mary Wahl

These course materials were developed for the first (spring 2015) offering of MCB 135: Introductory Systems Biology. They are shared under the MIT license as described in the file LICENSE.md in this repository. The syllabus for the course is included below.

Suggested prior coursework

An introductory college-level biology course such as LS 1a, LPS A, or AP Biology will be helpful. MCB 135 will use methods commonly taught in introductory linear algebra and differential equations courses: students concurrently enrolled in Ma 19a (Modeling and Differential Equations for the Life Sciences) will encounter the necessary techniques before they appear in MCB 135.

Readings

We strongly recommend that you obtain a copy of the following textbooks, from which a majority of suggested readings will be drawn:

  • Ingalls, Brian. Mathematical Modeling in Systems Biology. MIT Press, 2013.
  • Alon, Uri. An Introduction to Systems Biology: Design principles of biological circuits. Chapman & Hall/CRC, 2007.

Suggested readings from other sources will be posted in PDF format on the course website. Steven Strogatz's Non-linear Dynamics and Chaos (2014) is an excellent resource for those less familiar with linear algebra, differential equations, and stability analysis.

Lecture

Location: Biolabs (16 Divinity Ave. in Cambridge), Room 1075 (Note location change, effective 2/18/15) Meeting Time: MWF 2:30 - 3:30 PM

Discussion section

Sections will meet once per week to discuss a primary literature article relevant to recent lecture topics. Each student will lead discussion of one paper (chosen through sign-ups) and participate actively during other weeks. Preferences for section meeting times will be collected by survey through the course website during the first week using this confidential Doodle poll (Links to an external site.).

Location and meeting time: Fridays from 11 AM - noon in Biolabs 1075

Problem sets

In the wild, scientists address open questions with ample time and resources, including textbooks, notes, peers, experts, and computers. It is our conviction that learning and assessment should occur under similar circumstances. MCB 135 has no timed, closed-book, or explicitly cumulative assessments such as midterm or final exams, favoring instead a larger than typical number of problem sets.

Problem sets are assigned weekly and due at the start of class on the specified date. Collaboration is encouraged provided that each student's submission is written up independently and lists all collaborators/outside sources. Students should not submit jointly-obtained responses that they do not understand sufficiently well to explain or re-derive on their own if asked. Please seek clarification immediately if you find this policy unclear.

Final project

The final project, due during finals period (exam group 18), will be an original research proposal similar in structure to the NSF Graduate Research Fellowship application. Guidance will be provided on topic selection, format, and revisions. Producing a polished proposal typically requires multiple rounds of content editing: you are highly encouraged to seek advice from the course staff as well as researchers in related disciplines. As with problem sets, all sources should be adequately cited and the final submission should reflect the student's own work. A more detailed description of the research proposal assignment is available on the course website.

Grading policy

The grade breakdown is as follows:

  • 60% Problem sets, with the lowest problem set grade dropped
  • 20% Discussion section participation, with the lowest participation score dropped
  • 20% Final project

Extensions or alternative arrangements may be granted by the course head under exceptional circumstances. Once the answer key has been posted, late problem sets cannot be accepted for credit.

Accommodations for students with disabilities

Students needing academic adjustments or accommodations because of a documented disability must present their Faculty Letter from the Accessible Education Office (AEO) and speak with the course head by the end of the second week of the term, February 6. Failure to do so may result in an inability to respond in a timely manner. All discussions will remain confidential, although faculty may contact the AEO to discuss appropriate implementation.

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