SysBio13 Asgn_14B_Class_18_Article_23_2013_10_24

Read Article 23  Hester, Brown, Husband, Iliescu, Pruett, Summers and Coleman, "HumMod: a modeling environment for the simulation of integrative human physiology,"  Frontiers in Physiology, 2(12): 1-12 (2011). Post a PCRC on the Blog

SysBio13 Asgn_14A_Class_18_Article_22_2013_10_24

Read Article 22  Hester, Iliescu, Summers and Coleman, "Systems biology and integrative physiological modelling," J Physiol 589.5 (2011) pp 1053–1060 1053. Post a PCRC on the Blog

SysBio13 Asgn_13_Class_17_Article_21_2013_10_22

Read Article 21  K. C. Chen, L. Calzone, A. Csikasz-Nagy, F. R. Cross, B. Novak, and J. J. Tyson. Integrative analysis of cell cycle control in budding yeast. Mol.Biol.Cell 15 (8):3841-3862, 2004. The objective is to appreciate the complexity of a detailed systems biology ODE model, not to be able to explain all the details. Post a PCRC on the Blog.

SysBio13 Asgn_12_Class_16_Article_20_2013_10_17

Read Article 20  J. J. Tyson, A. Csikasz-Nagy, and B. Novak. The dynamics of cell cycle regulation. BioEssays 24 (12):1095-1109, 2002.. Post a PCRC on the Blog

SysBio13 Asgn_11_Class_15_Article_19_2013_10_10

Read Article 19  B. Novak and J. J. Tyson. Design principles of biochemical oscillators. Nature Rev.Mol.Cell Biol. 9 (12):981-991, 2008. Answer the Pop Quiz before reading, and then read the article to obtain an overview of the concepts. We will drill down next class. Post a PCRC.

SysBio13 Pop Quiz - Why Oscillators?

Why do biological systems oscillate, i.e., What is the biological purpose of biological oscillators?
What features of biological oscillators would provide an evolutionary advantage?

SysBio13 Asgn_10_Class_11_Article_18_2013_09_26

Read Article 18  J. J. Tyson, K. C. Chen, and B. Novak. Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr.Opin.Cell Biol. 15 (2):221-231, 2003. Also read PPT-03 for for a compact summary.  We will discuss this article and the PPT in depth, which will take at least a full class. This should be a first reading to get an overview. Post a PCRC. We will have a second, more careful reading in a second class with a second PCRC.

SysBio13 Asgn_9D_Class_07_DTRA RFP__2013_09_17

Read DTRA RFP   X vivo Capability for Evaluation and Licensure (X.C.E.L.) Program DTRA BAA N66001-12-X-2002 Call Opportunity No. R001 . Post a PCRC on the Blog

SysBio13 Asgn_9C_Class_07_NIH RFP__2013_09_17

Read NIH RFP   Integrated Microphysiological Systems for Drug Efficacy and Toxicity Testing in Human Health and Disease (UH2/UH3) RFA-RM-11-022. Post a PCRC on the Blog

SysBio13 Asgn_9B_Class_07_DARPA RFP__2013_09_17

Read DARPA RFP   Microphysiological Systems DSO DARPA-BAA-11-73. Post a PCRC on the Blog

SysBio13 Asgn_9A_Class_06_Article_17_2013_09_17

Read Article 17  19368 Monya Baker. Tissue models: A living system on a chip. Nature 471 (7340):661-665, 2011. This is a news item, not a scientific paper, and gives a higher-level overview of the field than a detailed review. Post a PCRC on the Blog

SysBio13 Asgn_8B_Class_08_PPT_02_2013_09_14

Study PPT P02_SysBio_Is_Life_Control_2013_09_12_0639.pdf and decide what you need discussed in class. Post a PCRC on the Blog. Be sure to read and comment on the two papers on 7A and 7b.

SysBio13 Asgn_8A_Class_08_PPT_01_2013_09_14

Study PPT P1_SysBio_What_Is_Control_2013_09_12_1534.pdf and decide what you need discussed in class. Post a PCRC on the Blog. Be sure to read and comment on the two papers on 7A and 7b

SysBio13 Asgn_7B_Class_07_Article_16_2013_09_12

Article 16  T.G. Buchman, The Community of Selft, Nature, 420: 246-251, 2002 and study this in the context of what we have to do to maintain homeostasis in ATHENA.. Post a PCRC on the Blog

SysBio13 Asgn_7A_Class_07_Article_15_2013_09_12

Read Article 15  P. R. LeDuc, W. C. Messner, and J. P. Wikswo. How do control-based approaches enter into biology? Annu.Rev.Biomed.Engr. 13:369-396, 2011. This article addresses a problem central to much of existing biology, systems biology, and organs on a chip -- much of the work to date has been done in an open-loop manner, and hence does not adequately probe the system dynamics. Post a PCRC on the Blog.

SysBio13 Asgn_6F_Class_06_Article_14_2013_09_10

Read carefully Article 14  B. E. Clancy, W. M. Behnke-Parks, J. O. L. Andreasson, S. S. Rosenfeld, and S. M. Block. A universal pathway for kinesin stepping. Nat.Struct.Mol.Biol. 18 (9):1020-1028, 2011. This is the MAIN thrust of the class. It will be our canonical example of a molecular scale mathematical model. Imagine building a human at this detail. Don't get lost in the fine points - go for the big picture! Post a PCRC on the Blog.

SysBio13 Asgn_6E_Class_06_Article_13_2013_09_10

Scan Article 13  Neuman and Block, "Optical Trapping," RSI, 2004. to look at pictures and prose highlights of laser tweezers. Post a PCRC on the Blog.

SysBio13 Asgn_6D_Class_06_Article_12_2013_09_10

Scan Article 12  Visscher and Block, "Versatile optical traps with feedback control", MethsEnzymol, 1998. to look at pictures and prose highlights of laser tweezers. Post a PCRC on the Blog.

SysBio13 Asgn_6C_Class_06_Wikipedia_02_2013_09_10

Read Wikipedia  02: http://en.wikipedia.org/wiki/Optical_tweezers so that you can understand how optical tweezers work - they are a key tool in molecular motor biology. Post a PCRC on the Blog.

SysBio13 Asgn_6B_Class_06_YouTube_VideoV03_2013_09_10

Watch YouTube Video V03: http://www.youtube.com/watch?v=YAva4g3Pk6k. Post a PCRC on the Blog