Course policies

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Dynamics of Biological Systems
Course Website
https://biol300.case.edu/
Instructors
Shared contact: biol300@case.edu
Dr. Hillel Chiel Jeffrey Gill Jon Sasse
DeGrace 304 DeGrace 310 --
hjc@case.edu jpg18@case.edu jps166@case.edu
216-368-3846 330-904-7963 --
Course Time and Location
Mon Tue Wed Thu Fri
-- 1:00 - 2:15 PM -- 1:00 - 2:15 PM --
Clapp 304 Clapp 304
Office Hours
Mon Tue Wed Thu Fri
3:30 - 4:30 PM 5:00 - 6:00 PM
Clapp 304 Clapp 405


Contacting the Instructors

biol300@case.edu

Unless you have reason to contact a specific instructor, please direct all your questions, comments, and concerns to the address above. Your correspondence to this address will be received by all instructors.

Textbook

  • Chapters from the textbook that Dr. Chiel has created for the course can be downloaded from the links on the syllabus.

Computers in Class

The course requires work on computer simulations, surveys and entries to the course wiki throughout the semester.

Please bring your laptop to class.

We will have a small number of laptops that we can lend to you if you need one.

Educational Goals

  • Learning the skills necessary to create models of the dynamical processes underlying biological systems.
  • Learning to analyze dynamical models both numerically and mathematically.
  • Learning to write about models clearly.

Structure of the Course

  • First half of the semester
    • Solving problems that teach you how to use Mathematica to create and analyze biological models
  • Second half of the semester
    • Reconstructing, analyzing and writing about a model of a biological system that you have chosen, which was previously published in the technical literature, using Mathematica

Student Guide to the Course

  • To master Mathematica and modeling, you need to practice regularly, develop a "feel" for both the modeling language and the models, and thus make the transition from novice to expert in the course of a single semester.
  • Accomplishing these goals requires steady application throughout the semester.
  • We have done our best to break down the process of learning to build models into small, manageable pieces
  • We also are available to answer your questions, provide you with useful hints, and the book itself provides you working code that you can use for your own models.
  • Each part of the course builds on the next. If you master one part, you will find it much easier to master the next part; by the end of the semester, you will find that tasks you thought you couldn't possibly do are now relatively easy.


  • In the first half of the semester:
    • Read the chapter section before class.
    • Be an active reader; try to understand the ideas presented in the chapter; take the code that's in the chapter, paste it into a new notebook, and activate it. Look at the code and see if you can understand how it works.
    • Look at the problems and think about them before class.
    • Once you are in class, spend your time focused on the problems.
    • Solving a problem requires formulating a plan, trying different approaches, and not giving up too quickly.
    • If you start to feel frustrated, talk about the problem with your teammate, with the other members of the class at your table, and with your instructors.
    • Don't give up; all these problems can be solved. For many of the problems, there is more than one right answer.
    • Never be afraid to ask questions.
    • Instructors will give you hints and suggestions; these will help you learn to solve problems yourself.
    • During conceptual check offs, make sure to ask questions about aspects of the results, or material in the chapter, that weren't clear to you.
    • Take advantage of office hours.
    • Budget time every week to do the reading before class, and to work on problems that you didn't finish in class so you are ready for the lightning and conceptual checkoffs at the beginning of the next class.
    • Come to class; skipping class will ensure that you fall further and further behind.
    • Regularly check how you are doing. We give points after every class, so you can always check your progress, class by class.
    • If you feel you need additional points, do the extra credit work.
    • Well before Spring break, start looking at potential papers for your term paper model.
    • Choose a topic that really interests you; we will help you determine if it is feasible to reproduce the model.


  • In the second half of the semester:
    • Formulate a plan and a timetable for model reconstruction, and keep track of how you are doing.
    • Make sure to submit the term paper benchmarks on time; they will increase the chances that you submit an excellent term paper.
    • If you are stuck on a problem, work with your teammate to solve it, and talk to the instructors so that you can get unstuck and make progress.


Stay caught up with the course through the semester!


A Quick Guide for Failing the Course

  • Ignore the rules, rubrics and deadlines
  • Skip class
  • Don't read the book chapters
  • Never prepare for class
  • Use class time to work on other things or for leisure time activities
  • Don't master key concepts
  • Ignore your partner
  • Ignore suggestions and advice from the instructors
  • Never go to office hours especially if you don't understand material or are having trouble reconstructing your model
  • Don't read the paper whose model you are reconstructing carefully or at all
  • Don't hand in benchmarks for the term paper
  • Don't do an extension for the term paper
  • Plagiarize text or code for the term paper
  • Don't submit most or all of the final term paper
  • Wait to submit your final term paper until 5 minutes before the final deadline and encounter a technical error

Assessment

  • You may earn up to 50 points for class participation.
  • You may earn up to 50 points for the term paper.
  • You may also earn extra credit points.

Class Participation

Class participation can be earned for

Term Paper

Term paper points can be earned for doing each of the following by the appropriate deadline:

Extra Credit Points

Extra credit points can be earned by

  • Providing helpful suggestions to improve the course book or the course wiki (up to 5 points); make sure you are looking at the most recent versions of the book chapters and the wiki, as corrections are added throughout the semester!
  • Filling out the course evaluation form at the end of the semester, and certifying that you have done so (1 point);
  • Identifying plagiarism on the wiki (1 point for each instance identified);
  • Commenting on another student's Discussion benchmark by the deadline to do so (up to 1/2 point);
  • Comment on another student's final Term paper by the deadline to do so (up to 2 points);
  • Presenting your term project to the class (up to 3 points).

Editing the class wiki

  • To obtain credit for the term paper components, and to provide comments on other students' writing, you will need to edit the course wiki.
  • All term paper components must be submitted using the links that you created at the time that you created the Term paper proposal.
  • Because you must sign in with your CWRU ID to edit, no edits will be anonymous.
  • Each edit will be recorded, so that we can keep track of and evaluate what you've done (as can other students).
  • When you provide comments on other students' term paper proposals, benchmarks, or final term papers, please do not edit their text directly. Instead, select the Discussion tab on the appropriate page, and enter your comments and suggestions there.
  • Visit Editing help for help with writing on the wiki.


Notice the tabs at the top of each page. Here are brief descriptions of the tabs that you will use:

  • Page and Read display the fully formatted page.
  • Discussion allows you to discuss material on a page without altering the page itself.
  • Edit allows you to edit the text that appears on the page.
    • In edit mode, a set of small icons appears above the box into which you can enter or change text.
    • These icons allow you to change the font face (e.g., bold, italic) to add links within the BIOL 300 wiki or to external pages, change headings, insert horizontal lines, or embed files.
    • View Editing help for explanations of each icon.
  • View history provides a full history of the edits to that page, including the author of the edits and the time the edit was done.

At the bottom of the page, there are three very useful buttons that appear in edit mode:

  • Save page saves all of your edits
  • Show preview allows you to view the page before saving your changes; you should use this frequently, especially at the beginning
  • Show changes shows the changes since the last edit
  • Cancel will remove your changes
  • Editing help provides useful tips on editing

Team Assignment

  • During the semester, you will work in teams of two.
  • Although some students prefer to work alone, we have found that teamwork has great benefits:
    • Explaining a problem to someone else, discussing results and their meaning, and helping another person understand a key concept reinforces knowledge.
    • Students often have different learning styles, and can learn a great deal from paying attention to how someone else learns and understands material.
    • Being able to work with others is a skill that can be invaluable for the future.
  • Students will be assigned to teams randomly:
    • We found that students felt left out if others could choose friends as teammates.
    • Students' own choices were rarely better than random assignments.
    • If students add or drop the course, we will adjust the teams.
  • On rare occasions, we may consider allowing two students to select one another as teammates. To do this,
    • The prospective teammates must have complementary skills (e.g., one is a biologist, the other is an engineer);
    • The prospective teammates must have a specific project that they have agreed to work on together;
    • The prospective teammates must certify to the instructors that they are willing to do a more complex and elaborate model extension for their term project;
    • The prospective teammates must receive approval from the instructors for their specific project before the end of the Add/Drop period in the first two weeks of the semester.

Course Topics

  • Rationale for modeling and modeling tools;
  • Introduction to biological models and to the modeling process;
  • Introduction to Mathematica for modeling;
  • A case study in descriptive model development: Bacterial growth;
  • Introduction to one-dimensional nonlinear dynamical systems theory;
  • A mechanistic model of cell replication: Chemical kinetics and metabolic pathways;
  • Introduction to two-dimensional nonlinear dynamical systems theory;
  • An introduction to the dynamical theory of oscillatory phenomena;
  • A case study in agent-based model reconstruction: Flocking behavior.

Modeling Sites

Academic Integrity

Code that you create for problem benchmarks must be your own; if someone else asks you to share code, offer to look at what they have written and to help them, but do not give them your code.

If they persist, please speak to one of the instructors.

It is a violation of the academic integrity rules to use text or figures from a previously published paper or from the Internet in a term paper or on the course wiki unless you

  • provide appropriate citations in both text and bibliography, and
  • place the text from the other sources within quotation marks.

You may not obtain the program files for a model that you have proposed to reconstruct from another source (e.g., from the author of the published paper), run them with parameter changes, and hand in the results as your own work. The point of the project during the second half of the semester is for you to build the model yourself. It is fine to obtain model files to compare them to your own model, of course; you should report these comparisons as part of your term paper if you do this.

The work you present for the term paper proposal, benchmarks, and the final term paper must be your own. Handing in a paper that was done for another class (even if it is your own work), reproducing text and/or equations from a web site or a paper without proper attribution (plagiarism), or presenting work that was done by another (e.g., friend, roommate, faculty member, or other member of the class) as your own is a violation of academic integrity.

It is important to understand that taking other people's ideas and/or words without proper attribution is a form of stealing, and is unacceptable.

Here is a detailed description, with examples, of Plagiarism.

See the CWRU Academic Integrity Board Website for details of the official Case policy on Academic Integrity.

Please realize that ignorance of the law is no excuse.

If we discover a violation of the integrity policies, we will be required to give a zero on the assignment, and to report the students who were involved in the integrity violation to the appropriate Dean (either Undergraduate or Graduate).

For instances of plagiarism between students,

  • If the source can be clearly identified, whether by the self-incrimination from the plagiarizer or by dates or other means, then the culprit alone receives a 0 and is reported to the academic integrity board.
  • If it is unclear who committed the plagiarism, the situation is reported to the academic integrity board and both parties receive a 0 unless advised otherwise by the board.

Reporting of an integrity violation will require that a special form be filled out, and will become part of the student's permanent record.

This is especially important for this course, as there is no final exam.

Remember these two principles:

Don't Cheat.

The rules apply to everyone, including you.

Letters of Recommendation

Dr. Chiel receives many requests for letters of recommendation.

He does not wish to write letters that will not help a student.

Thus, he will not write a letter unless he knows the student well (i.e., he has had the student for at least two different classes, or the student has worked in his lab) and he can write a strongly positive letter on their behalf.

You may also find it useful to look at this essay to determine how not to behave if you hope to ask him for a letter of recommendation some time in the future: How Not to Get a Letter of Recommendation. This essay is contained in "Great Letters of Recommendation" by Dan Osborne and Lilly Chow.

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