INFO-I 400 INFO-H 400/ INFO-I 590

Systems Biology: A user’s guide

 

Instructor

 

Santiago Schnell

Office: Eigenmann Hall 906

Telephone: 821-856-1833

Email: schnell@indiana.edu

Website: www.informatics.indiana.edu/schnell

 

Classroom

 

Monday and Wednesday 9.00-10:00 am

Geology Building, Room 436

 

Course description

 

Systems Biology is in vogue – it is a catch-phrase in laboratories, grant applications and scientific journals.  So what exactly is systems biology?  What is the best plan for students interested in a career in systems biology?  In this seminar course, we will address these questions by introducing some of the major challenges in the discipline:  problems of computational, experimental and modelling natures will be addressed.  We will pay special attention to gene and protein networks, and cellular functions. Students will participate in the classes by presenting a seminar.  They are also expected to be active in class discussions.  Students will be asked to edit two articles from the online encyclopedia Wikipedia and then write their own article for the site.  Our aim is to improve the quality and balance of the systems biology articles on Wikipedia.

 

Course goals

 

Our goal is that each student will understand what systems biology is, the research problems and techniques in the field.  We encourage this by:

·        Fostering an understanding of the state of activity in the field by reading around specific topics each week, and teaching how to be the most effective consumer of systems biology research.

·        Giving the responsibility of writing balanced, good quality and academically rigorous articles, by making the work available to others and being subject to critical review.

·        Showing a deep appreciation of the diversity of the research traditions in systems biology.

·        Sharing experience of a systems biology practice that is both truly multidisciplinary and enthusiastic.

 

Specific abilities that each student should have upon completion of the course:

  1. To describe accurately the current state of knowledge in systems biology as a whole as well as in a wide selection of the diverse topics in the field.
  2. To evaluate information from disparate sources and bring it to bear on presenting a seminar to your peers and writing an article for the online encyclopedia.

 

 

Outline of topics and Schedule

 

Module 1: What is systems biology?   (1st - 2nd week)

 

Quick guide: Systems biology

Mitchell P. Levesque and Philip N. Benfey

Current Biology 14: R-179-R180.

http://dx.doi.org/10.1016/j.cub.2004.02.012

 

The evolution of molecular biology into systems biology

Hans V Wesherhoff and Bernhard O Palsson (2004)

Nature Biotechnology 22: 1249-1252.

http://dx.doi.org/10.1038/nbt1020

 

Computational systems biology

Hiroaki Kitano (2002)

Nature 420: 206-210.

http://dx.doi.org/10.1038/nature01254

 

Can a biologist fix a radio?

Yuri Lazebnik

Cancer Cell 2: 179-182

http://dx.doi.org/10.1016/S1535-6108(02)00133-2

 

Nature Podcast on Systems Biology

http://www.nature.com/focus/systemsbiologyuserguide/podcast/systems_biology_podcast.mp3

 

 

Module 2: Computational challenges  (3rd - 4th week)

 

Linking publication, gene and protein data

Paul Kersey and Rolf Apweiler (2006)

Nature Cell Biology 8: 1183-1189

http://dx.doi.org/10.1038/ncb1495

 

Modelling data across labs, genomes, space and time

Jason R. Swedlow, Suzanna E. Lewis and Ilya G. Goldberg (2006)

Nature Cell Biology 8: 1190-1194.

http://dx.doi.org/10.1038/ncb1496

 

 

Module 3: Data collection challenges (5th - 7th week)

 

Collecting and organizing systematic sets of protein data

John G. Albeck, Gavin MacBeath, Forest M. White, Peter K. Sorger, Douglas A. Lauffenburger and Suzanne Gaudet (2006)

Nature Reviews Molecular Cell Biology 7: 803-812.

http://dx.doi.org/10.1038/nrm2042

 

Imaging single molecules in living cells for systems biology

Yasushi Sako (2006)

Molecular Systems Biology 2: 1-6.

http://dx.doi.org/10.1038/msb4100100

 

Stochastic Gene Expression in a Single Cell

Michael B. Elowitz, Arnold J. Levine, Eric D. Siggia, Peter S. Swain (2002)

Science 297: 1183-1186

http://dx.doi.org/10.1126/science.1070919

 

Systems-level dissection of the cell-cycle oscillator: Bypassing positive feedback produces damped oscillations

Joseph R Pomerening, S. Y. Kim, James E. Ferrell (2005)

Cell 122: 565-578

http://dx.doi.org/10.1016/j.cell.2005.06.016

 

 

Module 4: Modelling strategies   (8th - 13th week)

 

What can systems biology do for you?

Jeffrey M. Perkel (2007)

The Scientist 21: 68-69

http://www.the-scientist.com/2007/3/1/68/1/

 

Modeling cellular machinery through biological network comparison

Roded Sharan and Trey Ideker (2006)

Nature Biotechnology 24: 427-433

http://dx.doi.org/10.1038/nbt1196

 

The topology of the regulatory interactions predicts the expression pattern of the segment polarity genes in Drosophila melanogaster

Reka Albert and Hans Othmer (2003)

Journal of Theoretical Biology 223: 1-18.

http://dx.doi.org/10.1016/S0022-5193(03)00035-3

 

Linking data to models: data regression

Khuloud Jaqaman and Gaudenz Danuser (2006)

Nature Reviews Molecular Cell Biology 7: 813-819

http://dx.doi.org/10.1038/nrm2030

 

Physicochemical modelling of cell signalling pathways

Bree B. Aldridge, John M. Burke, Douglas A. Lauffenburger and Peter K. Sorger (2006)

Nature Cell Biology 8: 1195-1203

http://dx.doi.org/10.1038/ncb1497

 

Cell-signalling dynamics in time and space

Boris N. Kholodenko (2006)

Nature Reviews Molecular Cell Biology 7: 165-176

http://dx.doi.org/10.1038/nrm1838

 

Multiscale modeling in biology

Santiago Schnell, Ramon Grima and Philip K. Maini (2007)

American Scientist 95: 134-142.

http://www.americanscientist.org/template/AssetDetail/assetid/54784

 

 

Course evaluation

 

  • Participation: 20%

Based upon attendance and class participation

  • Seminar and Discussion: 30%

Students will present an article (or articles) from one of the modules, and then lead the ensuing discussion

  • Articles and final paper: 50%

Students will edit two articles from the online encyclopedia Wikipedia and then write their own article on systems biology for the site.  Assessment will be on the ability to improve the quality and balance of the articles through additional reading.

 

 

Course Policies

 

Attendance:

We expect that students will approach the course as they should a professional job – attend every class. If you cannot attend class we would appreciate your notifying the instructor that you will not be present and why.  An email is sufficient.

 

Assignments:

Assignments will be turned in by the beginning of class on the date they are due.  Assignments which are late will not be graded unless you have requested an extension at least three days before the due date.  Each student may be granted only one extension. Not turning your assignment in the due date will mean that you will fail the assignment.  The final paper must be turned in on time.

 

Academic Integrity:

As with other aspects of professionalism in this course, you are expected to abide by the proper standards of professional ethics and personal conduct. This includes the usual standards on acknowledgment of joint work and other aspects of the Indiana University Code of Student Rights, Responsibilities, and Conduct (http://dsa.indiana.edu/Code/index.html). Cases of academic dishonesty will be reported to the Office of Student Ethics, a branch of the Office of the Dean of Students

 

Incomplete Grade:

An incomplete (‘I’) final grade will be given only by prior arrangement in exceptional circumstances conforming to university and departmental policy which requires, among other things, that the student must have completed the bulk of the work required for the course with a passing grade, and that the remaining work can be made up within 30 days after the end of the semester

 

Use of laptops in Class:

If the purpose of use is related to this class, students may use their laptops during class and discussion sections.  However, they should not be used if they distract your attention from what is going on in class, and use should be minimized, since it is distracting to other students. 

 

Accommodation:

We would like to hear from anyone who has a disability that may require some modifications of seating, or other class requirements so that appropriate arrangements can be made.  Please see the instructor after class or during office hours.

 

We would like to know early in the semester of any possible conflicts between course requirements/deadlines and religious holy days or holidays (http://www.indiana.edu/~deanfac/holidays.html), so that accommodations can be made. Please see the instructor after class or during office hours.

 

We welcome feedback on the class organization, material, lectures, assignments and exams. Please share your comments and suggestions so that we can improve the class.

 

Wikipedia guidelines

 

  • Keep it real. Please do not create nonsense pages or add junk to articles. You risk being blocked from editing Wikipedia for vandalism.  In egregious cases, this will result in your entire school being blocked.

 

  • Read The Fine Manual.  We encourage you to take a look at the pages linked from Wikipedia:Help — they should answer many immediate questions.

 

  • Testing and avoiding. It may be a good idea — though not necessarily easy — to run your own wiki and use it for experiments first.  If you are a wiki expert, please preview the material before you publish it in Wikipedia.  If you do not wish to submit material to Wikipedia, then you can turn in a paper instead.

 

  • Copyrights. Please do keep Wikipedia:Copyrights in mind. Not everything on the Web is free for the taking, and even that which is may not be compatible with Wikipedia licensing. This is true for both text and images.