Difference between revisions of "BE 150/Bi 250b Winter 2012"

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| <center>'''WARNING: This page is for a previous year.'''<br> See [[BE 150/Bi 250b|current course homepage]] to find most recent page available.</center>
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* Michael Elowitz (Bi/BE/APh)
 
* Michael Elowitz (Bi/BE/APh)
 
* Richard Murray (CDS/BE)
 
* Richard Murray (CDS/BE)
* Lectures: MWF 10-11, 101 Kerckhoff
+
* Lectures: MW 10-11, 101 Kerckhoff
 
| width=50% |
 
| width=50% |
 
'''Teaching Assistants'''
 
'''Teaching Assistants'''
 
* Emzo de los Santos
 
* Emzo de los Santos
 
* Vanessa Jonsson
 
* Vanessa Jonsson
 +
* Recitation: F 10-11, 111 Keck (BE 150), 3 BBB (Bi 250)
 
|}
 
|}
 
=== Course Description ===
 
BE 150/Bi 250b is a jointly taught class that shares lectures but has different reading material and homework assignments.  Students in BE 150 are expected to have a more quantitative background and the course material includes a combination of analytical and conceptual tools.  Students in Bi 250b are expected to have more knowledge of basic biological processes and the course material focuses on the principles and tools for understanding biological processes and systems.
 
 
'''BE 150''': Quantitative studies of cellular and developmental systems in biology, including the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms.  Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness.  Organization of transcriptional and protein-protein interaction networks at the genomic scale.  Topics are approached from experimental, theoretical and computational perspectives.
 
 
'''Bi 250b''': The class will focus on quantitative studies of cellular and developmental systems in biology. It will examine the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. The course will approach most topics from both experimental and theoretical/computational perspectives. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. The course will also consider the organization of transcriptional and protein-protein interaction networks at the genomic scale.
 
 
===Announcements ===
 
* 0 Jan 2012: updated copy of BFS, Ch 2 has been posted
 
* 4 Jan 2012: course mailing list created; sign up at https://utils.its.caltech.edu/mailman/listinfo/be150-students
 
* 4 Jan 2012: course time and location have been updated
 
* 11 Dec 2011: updated syllabus (should be final now)
 
* 19 Nov 2011: added TAs; updated schedule
 
* 2 Oct 2011: web page creation
 
 
=== Textbook ===
 
 
The primary text for the BE 150 and Bi 250b is
 
{|
 
|- valign=top
 
| align=right | &nbsp;[Alon]&nbsp;
 
| U. Alon, ''An Introduction to Systems Biology: Design Principles of Biological Circuits'', CRC Press, 2006.
 
|}
 
Students in BE 150 should also obtain the following notes (freely downloadable from the web):
 
{|
 
|- valign=top
 
| align=right | &nbsp;[BFS]&nbsp;
 
| D. Del Vecchio and R. M. Murray, ''Biomolecular Feedback Systems''.  Available online at http://www.cds.caltech.edu/~murray/amwiki/BFS.
 
* Note: these notes are being written and will be updated during the course
 
* Class version (Caltech access only, 8 Jan 2012): {{be150 pdf|wi12|caltech/bfs-class-frontmatter_01Jan12.pdf|TOC}}, {{be150 pdf|wi12|caltech/bfs-class-intro_01Jan12.pdf|Ch 1}}, {{be150 pdf|wi12|caltech/bfs-class-coreproc_08Jan12.pdf|Ch 2}},  {{be250c pdf|wi12|caltech/bfs-class-dynamics_08Jan12.pdf|Ch 3}}, <!--{{be250c pdf|wi11|caltech/bfs-class-fbkexamps_25Jan11.pdf|Ch 5}}--> {{be150 pdf|wi12|caltech/bfs-class-backmatter_01Jan12.pdf|Refs}}
 
|}
 
 
The following additional texts and notes may be useful for some students:
 
{|
 
|- valign=top
 
| align=right | &nbsp;[FBS]&nbsp;
 
| K. J. Astrom and R. M. Murray, ''Feedback Systems''.  Available online at http://www.cds.caltech.edu/~murray/amwiki.
 
|- valign=top
 
| align=right | &nbsp;[Klipp]&nbsp;
 
| Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald, Hans Lehrach, Ralf Herwig, ''Systems biology: A textbook''.  Wiley, 2009.
 
|- valign=top
 
| align=right | &nbsp;[Strogatz]&nbsp;
 
| Steven Strogatz, ''Nonlinear Dynamics And Chaos: With Applications To Physics, Biology, Chemistry, And Engineering''.  Westview Press, 2001.
 
|}
 
 
=== Grading ===
 
The final grade will be based on biweekly homework sets.  The homework will be due in class one week after they are assigned. Late homework will not be accepted without prior permission from the instructor.  The lowest homework score you receive will be dropped in computing your homework average.
 
 
=== Collaboration Policy ===
 
Collaboration on homework assignments is encouraged. You may  consult outside reference materials, other students, the TA, or the instructor.  Use of solutions from previous years in the course is not allowed.  All solutions that are handed in should reflect your understanding of the subject matter at the time of writing.
 
  
 
=== Lecture Schedule ===
 
=== Lecture Schedule ===
Line 91: Line 46:
 
BE 150:
 
BE 150:
 
* {{be150 pdf|wi12|caltech/bfs-class-intro_01Jan12.pdf|BFS, Ch 1}}: Introductory Concepts
 
* {{be150 pdf|wi12|caltech/bfs-class-intro_01Jan12.pdf|BFS, Ch 1}}: Introductory Concepts
* {{be150 pdf|wi12|caltech/bfs-class-coreproc_08Jan12.pdf|BFS, Ch 2}}: Modeling of Core Processes
+
* {{be150 pdf|wi12|caltech/bfs-class-coreproc_18Jan12.pdf|BFS, Ch 2}}: Modeling of Core Processes
 
** Section 2.1: Modeling Techniques
 
** Section 2.1: Modeling Techniques
 
|  
 
|  
Line 108: Line 63:
  
 
BE 150:
 
BE 150:
* {{be150 pdf|wi12|caltech/bfs-class-coreproc_08Jan12.pdf|BFS, Ch 2}}: Modeling of Core Processes
+
* {{be150 pdf|wi12|caltech/bfs-class-coreproc_18Jan12.pdf|BFS, Ch 2}}: Modeling of Core Processes
 
** Sections 2.2-2.3: transcription and translation, transcriptional regulation
 
** Sections 2.2-2.3: transcription and translation, transcriptional regulation
  
Papers Discussed in Lecture:
+
Papers discussed in lecture:
 
* [http://www.nature.com/nature/journal/v403/n6767/abs/403339a0.html Construction of a genetic toggle switch in <i>Escherichia coli </i>], Gardner TS, Cantor CR, Collins JJ. ''Nature'', <b>403</b>:339-342, 2000.
 
* [http://www.nature.com/nature/journal/v403/n6767/abs/403339a0.html Construction of a genetic toggle switch in <i>Escherichia coli </i>], Gardner TS, Cantor CR, Collins JJ. ''Nature'', <b>403</b>:339-342, 2000.
* [http://www.nature.com/nature/journal/v426/n6965/abs/nature02089.html A positive-feedback-based bistable 'memory module' that governs a cell fate decision], Xiong and Ferrel. ''Nature'', <b>426</b>:460-465, 2003.
+
* [http://www.nature.com/nature/journal/v426/n6965/abs/nature02089.html A positive-feedback-based bistable 'memory module' that governs a cell fate decision], Xiong and Ferrell. ''Nature'', <b>426</b>:460-465, 2003.
 
|[https://www.cds.caltech.edu/~murray/wiki/images/c/c6/Hw1.pdf BEHW1] [https://www.cds.caltech.edu/~murray/wiki/images/e/e1/Hw1bio.pdf BIOHW1]
 
|[https://www.cds.caltech.edu/~murray/wiki/images/c/c6/Hw1.pdf BEHW1] [https://www.cds.caltech.edu/~murray/wiki/images/e/e1/Hw1bio.pdf BIOHW1]
 
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIOpenMain.m lacIOpenMain.m]
 
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/lacIOpenMain.m lacIOpenMain.m]
Line 135: Line 90:
 
|  
 
|  
 
Bi 250b:
 
Bi 250b:
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC349147/?tool=pmcentrez An amplified sensitivity arising from covalent modification in biological systems], Goldbeter A, Koshland DE.  ''Proc. Natl. Acad. Sci. U.S.A.'', 78 (11): 6840–4, 1981.
+
* Alon, Ch 4: The feed-forward loop network motif
<!-- * Alon, Ch 6: Network motifs in developmental, signal transduction, and neuronal networks -->
+
* Alon, Ch 6: Network motifs in developmental, signal transduction, and neuronal networks  
  
 
BE 150:
 
BE 150:
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC349147/?tool=pmcentrez An amplified sensitivity arising from covalent modification in biological systems], Goldbeter A, Koshland DE.  ''Proc. Natl. Acad. Sci. U.S.A.'', 78 (11): 6840–4, 1981.
+
* {{be250c pdf|wi12|caltech/bfs-class-coreproc_18Jan21.pdf|BFS, Ch 2}}: Modeling of Core Processes
* {{be250c pdf|wi12|caltech/bfs-class-coreproc_08Jan21.pdf|BFS, Ch 2}}: Modeling of Core Processes
+
 
** Section 2.4: post-transcriptoinal regulation
 
** Section 2.4: post-transcriptoinal regulation
 
** Section 2.5: cellular subsystems
 
** Section 2.5: cellular subsystems
| HW #2
+
 
 +
Papers discussed in lecture:
 +
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC349147/?tool=pmcentrez An amplified sensitivity arising from covalent modification in biological systems], Goldbeter A, Koshland DE.  ''Proc. Natl. Acad. Sci. U.S.A.'', 78 (11): 6840–4, 1981.
 +
* [http://www.nature.com/msb/journal/v5/n1/full/msb200930.html Protein sequestration generates a flexible ultrasensitive response in a genetic network], N. E. Buchler and F. R. Cross.  ''Molecular Systems Biology'', 5:272, 2009.
 +
| [https://www.cds.caltech.edu/~murray/wiki/images/7/74/Hw2.pdf BEHW2] [https://www.cds.caltech.edu/~murray/wiki/images/5/51/Hw2_bio.pdf BIOHW2]
 +
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/prob1.m prob1.m]
 +
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/plot1.m plot1.m]
 +
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/phosphoMainIO.m phosphoMainIO.m]
 
|- valign=top
 
|- valign=top
 
|
 
|
Line 150: Line 111:
 
| 23&nbsp;Jan <br> 25 Jan <br><br> MBE
 
| 23&nbsp;Jan <br> 25 Jan <br><br> MBE
 
| Biological clocks: how to produce oscillations in cells
 
| Biological clocks: how to produce oscillations in cells
 +
* Plant clocks/circadian rhythm
 
* Synthetic oscillators (repressilator, dual-feedback oscillator)
 
* Synthetic oscillators (repressilator, dual-feedback oscillator)
 
* Circadian clocks in cyanobacteria
 
* Circadian clocks in cyanobacteria
* Optional: plant clocks/circadian rhythm
 
Background slides on modeling and stability
 
* [http://www.cds.caltech.edu/~murray/books/AM08/pdf/bfs09-L1_modeling_26Aug09.pdf Modeling of core processes]
 
* [http://www.cds.caltech.edu/~murray/courses/cds101/fa08/pdf/L2-1_stability_h.pdf Dynamics and stability in ODEs]
 
 
|  
 
|  
 
* [http://www.nature.com/nature/journal/v403/n6767/full/403335a0.html A synthetic oscillatory network of transcriptional regulators], Elowitz and Leibler. ''Nature'', 403:335-338, 2000.
 
* [http://www.nature.com/nature/journal/v403/n6767/full/403335a0.html A synthetic oscillatory network of transcriptional regulators], Elowitz and Leibler. ''Nature'', 403:335-338, 2000.
 
* [http://www.nature.com/nature/journal/v456/n7221/full/nature07389.html A fast, robust and tunable synthetic gene oscillator], Stricker, ''et al.''.  ''Nature'',  456:516-519, 2008.
 
* [http://www.nature.com/nature/journal/v456/n7221/full/nature07389.html A fast, robust and tunable synthetic gene oscillator], Stricker, ''et al.''.  ''Nature'',  456:516-519, 2008.
 
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855407/ Cyanobacterial clock, a stable phase oscillator with negligible intercellular coupling], M. Amdaoud, M. Vallade, C. Weiss-Schaber, and I. Mihalcescu.  ''Proc Natl Acad Sci'', 104(17):7051–7056, 2007.
 
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855407/ Cyanobacterial clock, a stable phase oscillator with negligible intercellular coupling], M. Amdaoud, M. Vallade, C. Weiss-Schaber, and I. Mihalcescu.  ''Proc Natl Acad Sci'', 104(17):7051–7056, 2007.
| HW #3
+
BE 150:
 +
* {{be150 pdf|wi12|caltech/bfs-class-dynamics_18Jan12.pdf|BFS, Ch 3}}: Analysis of Dynamic Behavior
 +
** Sections 3.5: Oscillatory Behavior
 +
|[https://www.cds.caltech.edu/~murray/wiki/images/4/4b/Hw3.pdf BEHW3] [https://www.cds.caltech.edu/~murray/wiki/images/e/e1/Hw3bio.pdf BIOHW3]
 +
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/ddeoscillate.m  ddeoscillate.m]
 
|- valign=top
 
|- valign=top
|  
+
|
 +
 
 
===== 5 =====
 
===== 5 =====
 
| 30 Jan <br> 1 Feb <br><br> RMM
 
| 30 Jan <br> 1 Feb <br><br> RMM
Line 171: Line 134:
 
|
 
|
 
* Alon, Ch 7: Robustness of protein circuits : the example of bacterial chemotaxis
 
* Alon, Ch 7: Robustness of protein circuits : the example of bacterial chemotaxis
* BFS, Sec 5.4: Bacterial chemotaxis
+
* H. Kitano, [http://www.ncbi.nlm.nih.gov/pubmed/15520792 Biological robustness], Nat Rev Genet, vol. 5, no. 11, pp. 826–837, Nov. 2004.
* [http://www.pnas.org/content/97/9/4649.full Robust perfect adaptation in bacterial chemotaxis through integral feedback control], Tau-Mu Yi, Yun Huang, Melvin I. Simon and John Doyle. ''PNAS'', 97(9):4649-4653, 2000.
+
* N. Barkai and S. Leibler, [http://www.ncbi.nlm.nih.gov/pubmed/9202124 Robustness in simple biochemical networks], Nature, vol. 387, no. 6636, pp. 913–917, Jun. 1997.
| HW #4
+
* (optional) C. V. Rao, J. R. Kirby, and A. P. Arkin, [http://www.ncbi.nlm.nih.gov/pubmed/14966542 Design and diversity in bacterial chemotaxis: a comparative study in Escherichia coli and Bacillus subtilis], PLoS Biol, vol. 2, no. 2, p. E49, Feb. 2004.
 +
BE 150:
 +
* {{be150 pdf|wi12|caltech/bfs-class-dynamics_29Jan12.pdf|BFS, Ch 3}}: Sec 3.3 (Robustness) and Sec 3.6 (Bifurcations)
 +
* {{be150 pdf|wi12|caltech/bfs-class-chemotaxis_29Jan12.pdf|BFS, Sec 5.2}}: Bacterial chemotaxis
 +
* (optional) O. Shoval, L. Goentoro, Y. Hart, A. Mayo, E. Sontag, and U. Alon, [http://www.pnas.org/content/107/36/15995.long Fold-change detection and scalar symmetry of sensory input fields], Proceedings of the National Academy of Sciences, vol. 107, no. 36, pp. 15995–16000, Sep. 2010.
 +
| [https://www.cds.caltech.edu/~murray/wiki/images/d/d3/Be150hw4.pdf BE150 HW #4] [https://www.cds.caltech.edu/~murray/wiki/images/8/88/Bi250bHw4.pdf Bi250b HW#4]
 +
*[http://www.cds.caltech.edu/~murray/courses/be150/wi12/problem1.nb problem1.nb]
 +
*[http://www.cds.caltech.edu/~murray/courses/be150/wi12/chemotaxis.m chemotaxis.m]
 
|- valign=top
 
|- valign=top
|  
+
|
 +
 
 
===== 6 =====
 
===== 6 =====
 
| 6 Feb* <br> 8 Feb <br><br> RMM
 
| 6 Feb* <br> 8 Feb <br><br> RMM
Line 186: Line 157:
 
* [http://www.sciencemag.org/content/297/5584/1183 Stochastic Gene Expression in a Single Cell], Michael B. Elowitz, Arnold J. Levine, Eric D. Siggia and Peter S. Swain.  ''Science'', 297(5584):1183-1186, 2002.
 
* [http://www.sciencemag.org/content/297/5584/1183 Stochastic Gene Expression in a Single Cell], Michael B. Elowitz, Arnold J. Levine, Eric D. Siggia and Peter S. Swain.  ''Science'', 297(5584):1183-1186, 2002.
 
* [http://www.nature.com/nature/journal/v440/n7082/full/nature04599.html Stochastic protein expression in individual cells at the single molecule level], Long Cai, Nir Friedman and X. Sunney Xie.  ''Nature'', 440:358-362, 2006.
 
* [http://www.nature.com/nature/journal/v440/n7082/full/nature04599.html Stochastic protein expression in individual cells at the single molecule level], Long Cai, Nir Friedman and X. Sunney Xie.  ''Nature'', 440:358-362, 2006.
| HW #5
+
BE 150:
|- valign=top
+
* {{be150 pdf|wi12|caltech/bfs-class-stochastic_29Jan12.pdf|BFS, Ch 4}}: Stochastic behavior
 +
* {{be150 pdf|wi12|caltech/bfs-class-random_29Jan12.pdf|BFS, App C}}: Probability and random processes (optional)
 +
 
 
|  
 
|  
 +
[https://www.cds.caltech.edu/~murray/wiki/images/6/68/Hw5-be.pdf  BEHW5]  [https://www.cds.caltech.edu/~murray/wiki/images/a/a7/Hw5-bio.pdf BIOHW5]
 +
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/runner.m runner.m]
 +
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/hw5.sbproj hw5.sbproj]
 +
|- valign=top
 +
|
 +
 
===== 7 =====
 
===== 7 =====
 
| 13 Feb+ <br> 15 Feb <br><br> MBE
 
| 13 Feb+ <br> 15 Feb <br><br> MBE
Line 197: Line 176:
 
* [http://www.nature.com/nature/journal/v455/n7212/full/nature07292.html Frequency-modulated nuclear localization bursts coordinate gene regulation], Long Cai, Chiraj K. Dalal and Michael B. Elowitz.  Nature 455:485-490, 2008.
 
* [http://www.nature.com/nature/journal/v455/n7212/full/nature07292.html Frequency-modulated nuclear localization bursts coordinate gene regulation], Long Cai, Chiraj K. Dalal and Michael B. Elowitz.  Nature 455:485-490, 2008.
 
* [http://www.nature.com/nature/journal/v466/n7303/full/nature09145.html Single-cell NF-kB dynamics reveal digital activation and analogue information processing], S. Tay ''et al''.  ''Nature'', 466(7303):267-271, 2010
 
* [http://www.nature.com/nature/journal/v466/n7303/full/nature09145.html Single-cell NF-kB dynamics reveal digital activation and analogue information processing], S. Tay ''et al''.  ''Nature'', 466(7303):267-271, 2010
| HW #6
+
| [https://www.cds.caltech.edu/~murray/wiki/images/7/75/Hw6-be.pdf BEHW6] [https://www.cds.caltech.edu/~murray/wiki/images/f/fe/Hw6-bio.pdf BIOHW6]
 
|- valign=top
 
|- valign=top
 
|  
 
|  
 +
 
===== 8 =====
 
===== 8 =====
 
| <s>20 Feb</s> <br> 22&nbsp;Feb <br> 24&nbsp;Feb <br><br> RMM
 
| <s>20 Feb</s> <br> 22&nbsp;Feb <br> 24&nbsp;Feb <br><br> RMM
Line 210: Line 190:
 
* [http://linkinghub.elsevier.com/retrieve/pii/S0959437X04000887 Elucidating mechanisms underlying robustness of morphogen gradients], Avigdor Eldar, Ben-Zion Shilo and Naama Barkai. ''Curr Opin Genet Dev.'', 14(4):435-439, 2004.
 
* [http://linkinghub.elsevier.com/retrieve/pii/S0959437X04000887 Elucidating mechanisms underlying robustness of morphogen gradients], Avigdor Eldar, Ben-Zion Shilo and Naama Barkai. ''Curr Opin Genet Dev.'', 14(4):435-439, 2004.
 
* [http://www.pnas.org/content/107/15/6924.short Scaling of morphogen gradients by an expansion-repression integral feedback control], Danny Ben-Zvia and Naama Barkai.  ''PNAS'',  107(15):6924-6929, 2010.
 
* [http://www.pnas.org/content/107/15/6924.short Scaling of morphogen gradients by an expansion-repression integral feedback control], Danny Ben-Zvia and Naama Barkai.  ''PNAS'',  107(15):6924-6929, 2010.
| HW #7
+
| [https://www.cds.caltech.edu/~murray/wiki/images/d/df/Hw7-be.pdf BEHW7] [https://www.cds.caltech.edu/~murray/wiki/images/d/d5/Hw7-bio.pdf BioHW7]
 
|- valign=top
 
|- valign=top
|  
+
|
 +
 
 
===== 9 =====
 
===== 9 =====
 
| 27 Feb <br> 29 Feb*+ <br><br> MBK
 
| 27 Feb <br> 29 Feb*+ <br><br> MBK
Line 225: Line 206:
  
 
===== 10 =====
 
===== 10 =====
| 5  Mar <br> 7 Mar <br> MBE
+
| 5  Mar <br> 7 Mar+ <br> MBE
 
| Fine grain patterns
 
| Fine grain patterns
 
* Lateral inhibition
 
* Lateral inhibition
Line 232: Line 213:
 
* [http://www.ncbi.nlm.nih.gov/pubmed/9015458 Pattern formation by lateral inhibition with feedback: a mathematical model of delta-notch intercellular signalling], Collier et al. Journal of theoretical biology (1996) vol. 183 (4) pp. 429-46.
 
* [http://www.ncbi.nlm.nih.gov/pubmed/9015458 Pattern formation by lateral inhibition with feedback: a mathematical model of delta-notch intercellular signalling], Collier et al. Journal of theoretical biology (1996) vol. 183 (4) pp. 429-46.
 
* [http://www.ncbi.nlm.nih.gov/pubmed/20418862 Cis-interactions between Notch and Delta generate mutually exclusive signalling states], Sprinzak et al. Nature (2010) vol. 465 (7294) pp. 86-90
 
* [http://www.ncbi.nlm.nih.gov/pubmed/20418862 Cis-interactions between Notch and Delta generate mutually exclusive signalling states], Sprinzak et al. Nature (2010) vol. 465 (7294) pp. 86-90
| HW #8
+
| [https://www.cds.caltech.edu/~murray/wiki/images/d/d6/Hw8-be.pdf BEHW8] [https://www.cds.caltech.edu/~murray/wiki/images/e/ef/Hw8-bio.pdf BioHW8]
 +
* [http://www.cds.caltech.edu/~murray/courses/be150/wi12/NotchDeltaGui.m NotchDeltaGui.m]
 +
|}
 +
<br>
  
 +
=== Course Description ===
 +
BE 150/Bi 250b is a jointly taught class that shares lectures but has different reading material and homework assignments.  Students in BE 150 are expected to have a more quantitative background and the course material includes a combination of analytical and conceptual tools.  Students in Bi 250b are expected to have more knowledge of basic biological processes and the course material focuses on the principles and tools for understanding biological processes and systems.
 +
 +
'''BE 150''': Quantitative studies of cellular and developmental systems in biology, including the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms.  Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness.  Organization of transcriptional and protein-protein interaction networks at the genomic scale.  Topics are approached from experimental, theoretical and computational perspectives.
 +
 +
'''Bi 250b''': The class will focus on quantitative studies of cellular and developmental systems in biology. It will examine the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. The course will approach most topics from both experimental and theoretical/computational perspectives. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. The course will also consider the organization of transcriptional and protein-protein interaction networks at the genomic scale.
 +
 +
=== Textbook ===
 +
 +
The primary text for the BE 150 and Bi 250b is
 +
{|
 +
|- valign=top
 +
| align=right | &nbsp;[Alon]&nbsp;
 +
| U. Alon, ''An Introduction to Systems Biology: Design Principles of Biological Circuits'', CRC Press, 2006.
 
|}
 
|}
 +
Students in BE 150 should also obtain the following notes (freely downloadable from the web):
 +
{|
 +
|- valign=top
 +
| align=right | &nbsp;[BFS]&nbsp;
 +
| D. Del Vecchio and R. M. Murray, ''Biomolecular Feedback Systems''.  Available online at http://www.cds.caltech.edu/~murray/amwiki/BFS.
 +
* Note: these notes are being written and will be updated during the course
 +
* Class version (Caltech access only, 29 Jan 2012): {{be150 pdf|wi12|caltech/bfs-class-frontmatter_01Jan12.pdf|TOC}}, {{be150 pdf|wi12|caltech/bfs-class-intro_01Jan12.pdf|Ch 1}}, {{be150 pdf|wi12|caltech/bfs-class-coreproc_18Jan12.pdf|Ch 2}},  {{be150 pdf|wi12|caltech/bfs-class-dynamics_29Jan12.pdf|Ch 3}},  {{be150 pdf|wi12|caltech/bfs-class-stochastic_29Jan12.pdf|Ch 4}}, {{be150 pdf|wi12|caltech/bfs-class-chemotaxis_29Jan12.pdf|Sec 5.2}}, {{be150 pdf|wi12|caltech/bfs-class-random_29Jan12.pdf|App C}}, {{be150 pdf|wi12|caltech/bfs-class-backmatter_01Jan12.pdf|Refs}}
 +
|}
 +
 +
The following additional texts and notes may be useful for some students:
 +
{|
 +
|- valign=top
 +
| align=right | &nbsp;[FBS]&nbsp;
 +
| K. J. Astrom and R. M. Murray, ''Feedback Systems''.  Available online at http://www.cds.caltech.edu/~murray/amwiki.
 +
|- valign=top
 +
| align=right | &nbsp;[Klipp]&nbsp;
 +
| Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald, Hans Lehrach, Ralf Herwig, ''Systems biology: A textbook''.  Wiley, 2009.
 +
|- valign=top
 +
| align=right | &nbsp;[Strogatz]&nbsp;
 +
| Steven Strogatz, ''Nonlinear Dynamics And Chaos: With Applications To Physics, Biology, Chemistry, And Engineering''.  Westview Press, 2001.
 +
|}
 +
 +
=== Grading ===
 +
The final grade will be based on biweekly homework sets.  The homework will be due in class one week after they are assigned. Late homework will not be accepted without prior permission from the instructor.  The lowest homework score you receive will be dropped in computing your homework average.
 +
 +
=== Collaboration Policy ===
 +
Collaboration on homework assignments is encouraged. You may  consult outside reference materials, other students, the TA, or the instructor.  Use of solutions from previous years in the course is not allowed.  All solutions that are handed in should reflect your understanding of the subject matter at the time of writing.
 +
  
== Old Announcements ==
 
  
 
[[Category:Courses]]
 
[[Category:Courses]]

Latest revision as of 06:17, 31 January 2013

WARNING: This page is for a previous year.
See current course homepage to find most recent page available.

Systems Biology

Instructors

  • Michael Elowitz (Bi/BE/APh)
  • Richard Murray (CDS/BE)
  • Lectures: MW 10-11, 101 Kerckhoff

Teaching Assistants

  • Emzo de los Santos
  • Vanessa Jonsson
  • Recitation: F 10-11, 111 Keck (BE 150), 3 BBB (Bi 250)

Lecture Schedule

There will be two 1-hour lectures each week, as well as a 1-hour recitation section.

Week Date Topic Reading Homework
1
4 Jan
6 Jan+
MBE/RMM
Course overview
  • Principles in systems biology

Recitation section:

  • MATLAB tutorial (optional)

Matlab Tutorial

Bi 250b:

  • Alon, Ch 1: Introduction

BE 150:

  • BFS, Ch 1: Introductory Concepts
  • BFS, Ch 2: Modeling of Core Processes
    • Section 2.1: Modeling Techniques
2
9 Jan
11 Jan+

MBE
Gene circuit dynamics
  • Core processes in cells
  • Modeling transcription, translation and regulation using ODEs
  • Negative auto-regulation

Bi 250b:

  • Alon, Ch 2: Transcription networks : basic concepts
  • Alon, Ch 3: Autoregulation : a network motif

BE 150:

  • BFS, Ch 2: Modeling of Core Processes
    • Sections 2.2-2.3: transcription and translation, transcriptional regulation

Papers discussed in lecture:

BEHW1 BIOHW1
3
16 Jan
18 Jan*
20 Jan*

RMM
Circuit motifs
  • Feedforward loops (FFLs)
  • Phosphorylation cascades
  • Two-component signaling systems
  • Sequestration for ultrasensitivty

Bi 250b:

  • Alon, Ch 4: The feed-forward loop network motif
  • Alon, Ch 6: Network motifs in developmental, signal transduction, and neuronal networks

BE 150:

  • BFS, Ch 2: Modeling of Core Processes
    • Section 2.4: post-transcriptoinal regulation
    • Section 2.5: cellular subsystems

Papers discussed in lecture:

BEHW2 BIOHW2
4
23 Jan
25 Jan

MBE
Biological clocks: how to produce oscillations in cells
  • Plant clocks/circadian rhythm
  • Synthetic oscillators (repressilator, dual-feedback oscillator)
  • Circadian clocks in cyanobacteria

BE 150:

  • BFS, Ch 3: Analysis of Dynamic Behavior
    • Sections 3.5: Oscillatory Behavior
BEHW3 BIOHW3
5
30 Jan
1 Feb

RMM
Robustness
  • Chemotaxis and perfect adaptation
  • Fold change detection
  • Controls analysis of robustness

BE 150:

BE150 HW #4 Bi250b HW#4
6
6 Feb*
8 Feb

RMM
Noise
  • Random processes
  • Intrinsic and extrinsic noise
  • Stochastic modeling: master equation, SSA

BE 150:

BEHW5 BIOHW5

7
13 Feb+
15 Feb

MBE
Burstiness in gene expression and signalling
  • Birth-death processes
BEHW6 BIOHW6
8
20 Feb
22 Feb
24 Feb

RMM
Patterning
  • Morphogenesis
  • Robust morphagen gradient
  • Proportionality and scaling
BEHW7 BioHW7
9
27 Feb
29 Feb*+

MBK
Modeling of complex biological networks (Mary Kennedy)
10
5 Mar
7 Mar+
MBE
Fine grain patterns
  • Lateral inhibition
  • Notch-delta
BEHW8 BioHW8


Course Description

BE 150/Bi 250b is a jointly taught class that shares lectures but has different reading material and homework assignments. Students in BE 150 are expected to have a more quantitative background and the course material includes a combination of analytical and conceptual tools. Students in Bi 250b are expected to have more knowledge of basic biological processes and the course material focuses on the principles and tools for understanding biological processes and systems.

BE 150: Quantitative studies of cellular and developmental systems in biology, including the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. Organization of transcriptional and protein-protein interaction networks at the genomic scale. Topics are approached from experimental, theoretical and computational perspectives.

Bi 250b: The class will focus on quantitative studies of cellular and developmental systems in biology. It will examine the architecture of specific genetic circuits controlling microbial behaviors and multicellular development in model organisms. The course will approach most topics from both experimental and theoretical/computational perspectives. Specific topics include chemotaxis, multistability and differentiation, biological oscillations, stochastic effects in circuit operation, as well as higher-level circuit properties such as robustness. The course will also consider the organization of transcriptional and protein-protein interaction networks at the genomic scale.

Textbook

The primary text for the BE 150 and Bi 250b is

 [Alon]  U. Alon, An Introduction to Systems Biology: Design Principles of Biological Circuits, CRC Press, 2006.

Students in BE 150 should also obtain the following notes (freely downloadable from the web):

 [BFS]  D. Del Vecchio and R. M. Murray, Biomolecular Feedback Systems. Available online at http://www.cds.caltech.edu/~murray/amwiki/BFS.
  • Note: these notes are being written and will be updated during the course
  • Class version (Caltech access only, 29 Jan 2012): TOC, Ch 1, Ch 2, Ch 3, Ch 4, Sec 5.2, App C, Refs

The following additional texts and notes may be useful for some students:

 [FBS]  K. J. Astrom and R. M. Murray, Feedback Systems. Available online at http://www.cds.caltech.edu/~murray/amwiki.
 [Klipp]  Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald, Hans Lehrach, Ralf Herwig, Systems biology: A textbook. Wiley, 2009.
 [Strogatz]  Steven Strogatz, Nonlinear Dynamics And Chaos: With Applications To Physics, Biology, Chemistry, And Engineering. Westview Press, 2001.

Grading

The final grade will be based on biweekly homework sets. The homework will be due in class one week after they are assigned. Late homework will not be accepted without prior permission from the instructor. The lowest homework score you receive will be dropped in computing your homework average.

Collaboration Policy

Collaboration on homework assignments is encouraged. You may consult outside reference materials, other students, the TA, or the instructor. Use of solutions from previous years in the course is not allowed. All solutions that are handed in should reflect your understanding of the subject matter at the time of writing.