Difference between revisions of "Bi/BE 250c Winter 2011"
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'''Instructors'''  '''Instructors'''  
−  * Michael Elowitz (Bi/  +  * Michael Elowitz (Bi/APh) 
* Richard Murray (CDS/BE)  * Richard Murray (CDS/BE)  
* Lectures: Tu/Th, 12:30 pm, 151 Braun  * Lectures: Tu/Th, 12:30 pm, 151 Braun  
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'''Teaching Assistants'''  '''Teaching Assistants'''  
−  * Vanessa Jonsson  +  * Vanessa Jonsson (OH: M 3:304:30, Steele 3) 
−  * Fiona Chandra  +  * Fiona Chandra (OH: W 4:305:30, Steele 3) 
}  }  
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===Announcements ===  ===Announcements ===  
+  * 20 Jan 2011: HW #3 is now posted  
+  * ODE and MATLAB Tutorial will be held Friday, Jan 7 at 1 pm in Steele 214  
* 24 Oct 2010: web page creation  * 24 Oct 2010: web page creation  
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The following additional texts and notes may be useful for some students:  The following additional texts and notes may be useful for some students:  
{  {  
+   valign=top  
+   align=right  [FBS]  
+   K. J. Astrom and R. M. Murray, ''Feedback Systems''. Available online at http://www.cds.caltech.edu/~murray/amwiki.  
 valign=top   valign=top  
 align=right  [BFS]   align=right  [BFS]  
 D. Del Vecchio and R. M. Murray, ''Biomolecular Feedback Systems''. Available online at http://www.cds.caltech.edu/~murray/amwiki/BFS.   D. Del Vecchio and R. M. Murray, ''Biomolecular Feedback Systems''. Available online at http://www.cds.caltech.edu/~murray/amwiki/BFS.  
+  * Class version (Caltech access only): {{be250c pdfwi11caltech/bfsclassfrontmatter_23Jan11.pdfTOC}}, {{be250c pdfwi11caltech/bfsclassintro_01Jan11.pdfCh 1}}, {{be250c pdfwi11caltech/bfsclasscoreproc_01Jan11.pdfCh 2}}, {{be250c pdfwi11caltech/bfsclassdynamics_25Jan11.pdfCh 3}}, {{be250c pdfwi11caltech/bfsclassfbkexamps_25Jan11.pdfCh 5}}, {{be250c pdfwi11caltech/bfsbackmatter_23Jan11.pdfRefs}}  
 valign=top   valign=top  
 align=right  [Klipp]   align=right  [Klipp]  
−   Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald, Hans Lehrach, Ralf Herwig, ''Systems biology:  +   Edda Klipp, Wolfram Liebermeister, Christoph Wierling, Axel Kowald, Hans Lehrach, Ralf Herwig, ''Systems biology: A textbook''. Wiley, 2009. 
+   valign=top  
+   align=right  [Strogatz]  
+   Steven Strogatz, ''Nonlinear Dynamics And Chaos: With Applications To Physics, Biology, Chemistry, And Engineering''. Westview Press, 2001.  
}  }  
+  
+  SAMPLE MATLAB ODE FILES:  
+  [http://www.its.caltech.edu/~fiona/be250c_TA/runfun.m runfun.m]  
+  [http://www.its.caltech.edu/~fiona/be250c_TA/fun.m fun.m]  
+  
+  === 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. In addition, if your score on the ﬁnal is higher than the weighted average of your homework and ﬁnal, your ﬁnal will be used to determine your course grade.  
+  
+  === 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 ===  
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Recitation sections (TAs):  Recitation sections (TAs):  
* Ordinary differential equations  * Ordinary differential equations  
−  * MATLAB tutorial  +  * [http://www.cds.caltech.edu/~vjonsson/bi250c2011/lectures/MATLABTutorial.pdf MATLAB tutorial ] 
    
* Alon, Ch 2: Transcription networks : basic concepts  * Alon, Ch 2: Transcription networks : basic concepts  
−  * BFS, Ch 2: Modeling of Core Processes  +  * {{be250c pdfwi11caltech/bfsclasscoreproc_01Jan11.pdfBFS, Ch 2}}: Modeling of Core Processes 
* Alon, Ch 3: Autoregulation : a network motif  * Alon, Ch 3: Autoregulation : a network motif  
 <! Homework >   <! Homework >  
+  [http://www.cds.caltech.edu/~vjonsson/bi250c2011/hw/hw1.pdf hw1]  
+  [http://www.cds.caltech.edu/~murray/courses/bibe250c/wi11/caltech/Hw1Sol.pdf Solutions]  
 valign=top   valign=top  
 2   2  
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* Alon, Ch 6: Network motifs in developmental, signal transduction, and neuronal networks  * Alon, Ch 6: Network motifs in developmental, signal transduction, and neuronal networks  
 <! Homework >   <! Homework >  
+  [http://www.cds.caltech.edu/~murray/wiki/images/5/5f/Hw2.pdf HW2]  
 valign=top   valign=top  
 3   3  
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* Circadian clocks in cyanobacteria  * Circadian clocks in cyanobacteria  
* Optional: plant clocks/circadian rhythm  * Optional: plant clocks/circadian rhythm  
+  Background slides on modeling and stability  
+  * [http://www.cds.caltech.edu/~murray/books/AM08/pdf/bfs09L1_modeling_26Aug09.pdf Modeling of core processes]  
+  * [http://www.cds.caltech.edu/~murray/courses/cds101/fa08/pdf/L21_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'', 403:335338, 2000.  * [http://www.nature.com/nature/journal/v403/n6767/full/403335a0.html A synthetic oscillatory network of transcriptional regulators], Elowitz and Leibler. ''Nature'', 403:335338, 2000.  
* [http://www.nature.com/nature/journal/v456/n7221/full/nature07389.html A fast, robust and tunable synthetic gene oscillator], Stricker, ''et al.''. ''Nature'', 456:516519, 2008.  * [http://www.nature.com/nature/journal/v456/n7221/full/nature07389.html A fast, robust and tunable synthetic gene oscillator], Stricker, ''et al.''. ''Nature'', 456:516519, 2008.  
−  * [http://www.  +  * [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1855407/ Cyanobacterial clock, a stable phase oscillator with negligible intercellular coupling], M. Amdaoud, M. Vallade, C. WeissSchaber, and I. Mihalcescu. ''Proc Natl Acad Sci'', 104(17):7051–7056, 2007. 
 <! Homework >   <! Homework >  
+  [http://www.cds.caltech.edu/~murray/wiki/images/4/41/HW3_final.pdf HW3]  
+  [http://www.cds.caltech.edu/~murray/courses/bibe250c/wi11/caltech/hw3Sol.pdf Solutions]  
 valign=top   valign=top  
 4   4  
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* [http://www.pnas.org/content/97/9/4649.full Robust perfect adaptation in bacterial chemotaxis through integral feedback control], TauMu Yi, Yun Huang, Melvin I. Simon and John Doyle. ''PNAS'', 97(9):46494653, 2000.  * [http://www.pnas.org/content/97/9/4649.full Robust perfect adaptation in bacterial chemotaxis through integral feedback control], TauMu Yi, Yun Huang, Melvin I. Simon and John Doyle. ''PNAS'', 97(9):46494653, 2000.  
 <! Homework >   <! Homework >  
+  [http://www.cds.caltech.edu/~murray/wiki/images/d/d4/Hw4.pdf HW4]  
+  [http://www.cds.caltech.edu/~murray/courses/bibe250c/wi11/caltech/hw4Sol.pdf Solutions]  
 valign=top   valign=top  
 5   5  
Line 112:  Line 144:  
* [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'', 440:358362, 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'', 440:358362, 2006.  
 <! Homework >   <! Homework >  
+  [http://www.cds.caltech.edu/~murray/wiki/images/8/8e/Hw5.pdf HW5]  
+  [http://www.cds.caltech.edu/~murray/courses/bibe250c/wi11/caltech/hw5Sol.pdf Solutions]  
 valign=top   valign=top  
 6   6  
Line 118:  Line 152:  
    
* [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2920833/ Computational Models of HIV1 Resistance to Gene Therapy Elucidate Therapy Design Principles], Sharon Aviran, Priya S. Shah, David V. Schaffer, Adam P. Arkin. ''PLoS Comput Biol.", 2010.  * [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2920833/ Computational Models of HIV1 Resistance to Gene Therapy Elucidate Therapy Design Principles], Sharon Aviran, Priya S. Shah, David V. Schaffer, Adam P. Arkin. ''PLoS Comput Biol.", 2010.  
−  +   <! Homework >  
−  +  [http://www.cds.caltech.edu/~murray/wiki/images/3/32/Hw6.pdf HW6]  
 valign=top   valign=top  
 7   7  
−   15 Feb <br> 17 Feb <br><br> MBE  +   <s>15 Feb</s> <br> 17 Feb <br><br> MBE 
 Dynamic signal coding   Dynamic signal coding  
* PWM  * PWM  
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* [http://www.pnas.org/content/107/15/6924.short Scaling of morphogen gradients by an expansionrepression integral feedback control], Danny BenZvia and Naama Barkai. ''PNAS'', 107(15):69246929, 2010.  * [http://www.pnas.org/content/107/15/6924.short Scaling of morphogen gradients by an expansionrepression integral feedback control], Danny BenZvia and Naama Barkai. ''PNAS'', 107(15):69246929, 2010.  
 <! Homework >   <! Homework >  
+  [http://www.cds.caltech.edu/~murray/wiki/images/b/b1/Hw7.pdf HW7]  
+  [http://www.cds.caltech.edu/~murray/courses/bibe250c/wi11/caltech/hw7Sol.pdf Solutions]  
 valign=top   valign=top  
 9   9  
−   1 Mar <br> 3 Mar <br><br>  +   1 Mar <br> 3 Mar <br><br> RMM 
 Fine grain patterns   Fine grain patterns  
* Lateral inhibition  * Lateral inhibition  
* Notchdelta  * Notchdelta  
−    +   
+  * [http://www.ncbi.nlm.nih.gov/pubmed/9015458 Pattern formation by lateral inhibition with feedback: a mathematical model of deltanotch intercellular signalling], Collier et al. Journal of theoretical biology (1996) vol. 183 (4) pp. 42946.  
+  * [http://www.ncbi.nlm.nih.gov/pubmed/20418862 Cisinteractions between Notch and Delta generate mutually exclusive signalling states], Sprinzak et al. Nature (2010) vol. 465 (7294) pp. 8690  
 <! Homework >   <! Homework >  
+  [https://www.cds.caltech.edu/~murray/wiki/images/a/a1/Hw8.pdf HW8 ]  
 valign=top   valign=top  
 10   10  
−   8 Mar <br> <br>  +   8 Mar <br> <br> MBE 
 Epistasis and modularity   Epistasis and modularity  
* Flux balance analysis and yeast metabolism  * Flux balance analysis and yeast metabolism  
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}  }  
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== Old Announcements ==  == Old Announcements ==  
[[Category:Courses]]  [[Category:Courses]] 
Latest revision as of 04:54, 27 June 2021
Systems Biology  
Instructors

Teaching Assistants

Course Description
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 higherlevel circuit properties such as robustness. The course will also consider the organization of transcriptional and proteinprotein interaction networks at the genomic scale.
Announcements
 20 Jan 2011: HW #3 is now posted
 ODE and MATLAB Tutorial will be held Friday, Jan 7 at 1 pm in Steele 214
 24 Oct 2010: web page creation
Textbook
The primary text for the course (available via the online bookstore) is
[Alon]  U. Alon, An Introduction to Systems Biology: Design Principles of Biological Circuits, CRC Press, 2006. 
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. 
[BFS]  D. Del Vecchio and R. M. Murray, Biomolecular Feedback Systems. Available online at http://www.cds.caltech.edu/~murray/amwiki/BFS. 
[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. 
SAMPLE MATLAB ODE FILES: runfun.m fun.m
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. In addition, if your score on the ﬁnal is higher than the weighted average of your homework and ﬁnal, your ﬁnal will be used to determine your course grade.
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
Week  Date  Topic  Reading  Homework 
1  4 Jan 6 Jan MBE 
Course overview; gene circuit dynamics
Recitation sections (TAs):



2  11 Jan 13 Jan MBE 
Circuit motifs



3  18 Jan 20 Jan RMM 
Biological clocks: how to produce oscillations in cells
Background slides on modeling and stability 


4  25 Jan 27 Jan RMM 
Robustness



5  1 Feb 3 Feb MBE 
Noise
Probabilistic differentiation (?) 


6  8 Feb 10 Feb TAs 
Population dynamics and Evolution 


7  17 Feb MBE 
Dynamic signal coding



8  22 Feb 24 Feb RMM 
Patterning



9  1 Mar 3 Mar RMM 
Fine grain patterns



10  8 Mar MBE 
Epistasis and modularity

