Asgn_24B_Class_33_Article_21_2012_04_04

Read Article  21: Meindert Danhof, Joost de Jongh, Elizabeth C. M. De Lange, Oscar Della Pasqua, Bart A. Ploeger, and Rob A. Voskuyl. Mechanism-Based Pharmacokinetic-Pharmacodynamic Modeling: Biophase Distribution, Receptor Theory, and Dynamical Systems Analysis. Annu.Rev.Pharmacol.Toxicol. 47 (1):357-400, 2007. (RefID_20183). Get an overview of the content and be prepared to discuss each figure in detail. Post a PCRC.

Asgn_24A_Class_33_Article_20_2012_04_04

Read Article  20: Nicolas Bertrand and Jean Christophe Leroux. The journey of a drug-carrier in the body: An anatomo-physiological perspective. Journal of Controlled Release In press.  DOI: 10.1016/j.jconrel.2011.09.098, 2012. (RefID20179). Get an overview of the content and be prepared to discuss each figure in detail. Post a PCRC.

Asgn_23_Class_28_Article_18_2012_03_23

Article  18: Dynamical Systems Approach to Endothelial Heterogeneity by Erzsébet Ravasz Regan, PhD, and William C. Aird, MD, Preprint. Post a PCRC.

Asgn_22_Class_27_2012_03_21

Class will be a review of revised presentations and one-page reports. Post a PCRC on Monday's discussions - standard questions.

Asgn_19_Class_24_Article_17_2012_03_14

Read Article  17: Lahav,G, Rosenfeld,N, Sigal,A, Geva-Zatorsky,N, Levine,AJ, Elowitz,MB, Alon,U. Dynamics of the P53-Mdm2 Feedback Loop in Individual Cells, Nat.Genet., 36, 147-150, 2004. This is the first paper in the series. Try to figure out what was learned between 2004 and 2010. Post a PCRC.

Asgn_18_Class_24_Article_16_2012_03_14

Read Article  16: Loewer,A, Batchelor,E, Gaglia,G, Lahav,G. Basal Dynamics of P53 Reveal Transcriptionally Attenuated Pulses in Cycling Cells, Cell, 142, 89-100, 2010. This is the most recent paper in a long series. Read it to get an overview. Post a PCRC.

Asgn_17_Class_23_Article_15_2012_03_12

Read Article  15: S. Huang. The molecular and mathematical basis of Waddington's epigenetic landscape: A framework for post-Darwinian biology? BioEssays 34 (2):149-157, 2012.
Read the article and the supplementary material. Post a PCRC.

Asgn_16_Class_21_Article_14_2012_02_29

Read Article 14: S. Huang, G. Eichler, Y. Bar-Yam, and D. E. Ingber. Cell fates as high-dimensional attractor states of a complex gene regulatory network. Phys.Rev.Lett. 94 (12):128701, 2005. Check out the supplementary material in DropBox. Post a PCRC.

Asgn_15_Class_20_Article_13_2012_02_27

Read Article  10: S. Huang. Appendix A Primer for Biologists on:  Nonlinear dynamics, multistability and noise. 2007.. Post a PCRC.

Asgn_14_Class_19_Kaneko_Ch3_2012_02_24

Read Kaneko Chapter 3: Basic Concepts in Dynamical Systems and Statistical Physics for Biological System. Pages 47-79. Post a PCRC.

Asgn_13_Class_18_Kaneko_Ch2_2012_02_22

Read Kaneko Chapter 2: Constructive Biology. Pages 37-46. Post a PCRC.

Asgn_12_Class_17_Kaneko_Ch1_2012_02_20

Read Kaneko Chapter 1: How Should Living Systems Be Studied?. Pages 1-16., Post a PCRC.

Asgn_11_Class_17_Kaneko_Preface_2012_02_20

Read Kaneko Preface  Life: An Introduction to Complex Systems Biology  K. Kaneko.. Pages i-vii. Post a PCRC.

Asgn_10B_Class_16_Organ-on-a-Chip_2012_02_17

Update Organ-on-a-Chip   Present your progress on your organ-on-a-chip proposal, with references.. Post  on blog:  Input, Output, Feedback/Control, Your Plan. Email PPT and drop into your student folder.

Asgn_10A_Class_16_Article_12_2012_02_17

Article  12: Chen KC, Calzone L, Csikasz-Nagy A, et al.,Integrative analysis of cell cycle control in budding yeast, MOLECULAR BIOLOGY OF THE CELL, 15(8) 3841-3862 (2004). Review this to get a general idea of the complexity of the model that Tyson has assembled to explain the cell cycle. Do not attempt to master the details. Post a PCRC.

Asgn_9_Class_14_Article_11_2012_02_13

Article  11: Béla Novák and John J. Tyson, Design principles of biochemical oscillators, Nat Rev Mol Cell Bio, 9: 981-991 (2008).

Asgn_8_Class_11_Article_10_2012_02_06

Article  10: 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.. We will discuss this article 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.

Asgn_7_Class_10_Organ-on-a-Chip_Intro1_2012_02_03

Present Organ-on-a-Chip Intro 1: your choice for an organ-on-a-chip proposal, with references.. Post  on blog:  Input, Output, Feedback/Control, Your Plan. Email PPT and drop into your student folder.

Asgn_6_Class_6_Article_9_2012_01_23

Read Article  9: 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. Post a PCRC on the Blog.

Asgn_5_Class_5_Article_8_2012_01_20

Read Article  8: J. P. Wikswo, A. Prokop, F. Baudenbacher, D. Cliffel, B. Csukas, and Momchil. Velkovsky. Engineering challenges of BioNEMS: the integration of microfluidics, and micro- and nanodevices, models, and external control for systems biology. IEE Proc.-Nanobiotechnol. 153 (4):81-101, 2006. Post a PCRC on the Blog.

Asgn_4D_Class_4_Article_7_2012_01_18

"Scan Article 7: Vance A. Tucker. The energetic cost of moving about.  Sci.Am. 63:413-420, 1975. Be sure to understand Figs. 1-3 and 5, and the concept that energy has to be expended to stretch active muscle."

Asgn_4C_Class_4_Article_6_2012_01_18

Read Article  6: Knut. Schmidt-Nielsen. Organ size and tissue metabolism. In: Scaling:  Why is animal size so important?,Anonymous  New York:Cambridge University Press, 1984, p. 90-98.. The primary goal is for you to be able to explain the challenges in building multiple, compatible organs on a chip.

Asgn_4B_Class_4_Article_5_2012_01_18

Scan Article  5: Knut Schmidt-Nieldon, Scaling in Biology: The Consequences of Size, J. Expt. Zoology, pp 287-307 (1975). Don't sweat the small details - focus on how scaling works.

Asgn_4A_Class_4_Article_4_2012_01_18

Read Article  4: Wikipedia article on Allometry. Try to gain an understanding of the concept of scaling laws.

Asgn_3E_Class_3_Organ Selection_2012_01_13

Which organs you are interested in studying in greater depth, and why? Enter your choice in the Blog

Asgn_3D_Class_3_DTRA RFP_2012_01_13

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

Asgn_3D_Class_3_DTRA RFP_2012_01_13

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

Asgn_3C_Class_3_NIH RFP__2012_01_13

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.

Asgn_3B_Class_3_DARPA RFP__2012_01_13

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

Asgn_3A_Class_3_Article_Baker 2011_2012_01_13

Read 19368 Monya Baker. Tissue models: A living system on a chip. Nature 471 (7340):661-665, 2011. Post a PCRC on the Blog

Whole Pancreatic Beta

http://www.youtube.com/watch?v=-OI6QILPDlo

Put up by Brad Noske.

Gives a better idea of the relative sizes of the objects as compared with the cell.

Asgn_2B_Class_2_Article_Kitano-2002:_2012_01_11

Read Article Kitano-2002:  Hiroaki Kitano. Computational systems biology. Nature 420 (6912):206-210, 2002.. Post a PCRC on the Blog

Asgn_2A_Class_2_Article_Five Dimensions:_2012_01_11

"Read Article Five Dimensions:  S. Huang and J. Wikswo. Dimensions of systems biology. In: Reviews of Physiology, Biochemistry and Pharmacology, edited by S. G. Amara, E. Bamberg, T. Gudermann, S. C. Hebert, R. Jahn, W. J. Lederer, R. Lill, A. Miyajima, and S. Offermanns, 2006, p. 81-104. Post a PCRC on the Blog"

Survey

Name: Shane Weller Emmons

Preferred firstname: Weller

Year: Senior

School (A&S / Engineering / Medicine):

Engineering

Degree Program/Major(s): Biomedical Engineering

Minor(s): Engineering Management

Hometown:

Hattiesburg, MS

Campus Address:

Off campus

Campus Phone: _

601-408-5083

E-Mail Address(s):

weller.emmons@gmail.com

Career Plans(if known):

Healthcare Industry

Physics, Mathematics, and Biolog Background(Course names or description, please):

Phys 116a/b, Bio 110a/b, Math 175, Math 198, Systems Physiology, Physiological Transport Phenomena

What do you already know about biophysics, bioengineering, or biology?

Alot?

What is your experience in computer programming or mathematical modeling?

Designed an isoelectric point calculator for peptide identification in tandem MS/MS (C++)

Currently research protein protein signaling networks of invadapodia.

Why are you taking this class? What do you hope to get out of it?

BME elective required. I hope to understand one of the developing technologies that is redefining biology.

What is your teaching experience?

None

Questionnaire

Name: Ayeeshik Kole

Preferred firstname: Ayeeshik

Year: Senior

School (A&S / Engineering / Medicine): Engineering

Degree Program/Major(s): Biomedical Engineering, Communication of Science and Technology

Minor(s): N/A

Hometown: Columbia, MD

Campus Address: 2301 Vanderbilt Pl PMB 354431

Campus Phone: N/A

E-Mail Address(s): ayeeshik.kole@vanderbilt.edu

Career Plans(if known): Medical Scientist

Physics, Mathematics, and Biology Background(Course names or description, please): PHYS 116 A/B (General Physics), MATH 175 (Multivariable Calculus), MATH 196 (DiffEq and Linear Algebra), BSCI 110 A/B (Biological Sciences), BME 251/2 (Systems Physiology), BME-210 (Biotransport), BME-280 (Tissue Engineering)

What do you already know about biophysics, bioengineering, or biology?
I am familiar with microfluidics and microtechnology research, the field of tissue engineering, and basic cell receptor biology. I am also familiar with the concept of automated systems biology and attended computational biology conferences.

What is your experience in computer programming or mathematical modeling?
MATLAB

Why are you taking this class? What do you hope to get out of it?
BME Elective and Honors fulfillment. I hope to learn more about systems biology. My research project in SyBBURE has dealt with building a means to experimentally develop better system models, but I don't have a thorough understanding of the depths of systems biology research.

What is your teaching experience?
I have done equipment training for SyBBURE on microscopes, mass spec software, 3-D printing, photolith/microfab. I have also tutored for many introductory engineering classes.

CLASS BACKGROUND

Name: Kris T. Hardy

Preferred firstname: Tom

Year: Senior

School (A&S / Engineering / Medicine): Engineering

Degree Program/Major(s): Biomedical Engineering

Minor(s): N/A

Hometown: Augusta, GA

Campus Address: 2301 Vanderbilt Pl PMB 353697

Campus Phone: n/a

E-Mail Address(s): tmhardy309@gmail.com

Career Plans(if known): Physician

Physics, Mathematics, and Biolog Background(Course names or description, please): PHYS 116 A and B: MATH 155B, 175, 196, and 234; BSCI 110 A and B, BME 251 and 252 (systems physio)

What do you already know about biophysics, bioengineering, or biology?

Not familiar with biophysics; As a BME undergrad I have some experience in bioengineering including working in a lab in the BME department; my experience in biology is limited to the classes that I have taken

What is your experience in computer programming or mathematical modeling?

I took CS 103 (matlab) and I did some computer programming in the lab I worked in (C/C++)

Why are you taking this class? What do you hope to get out of it?

This class fulfills my BME elective requirement and I hope to learn more about the subject

What is your teaching experience?

I have no extensive teaching experience. I have done some tutoring

Class Background

Please provide the following information by copying this list to your response and filling in the blanks:

CLASS BACKGROUND

Name:

Preferred firstname:

Year:

School (A&S / Engineering / Medicine):

Degree Program/Major(s):

Minor(s):

Hometown:

Campus Address:

Campus Phone: _

E-Mail Address(s):

Career Plans(if known):

Physics, Mathematics, and Biolog Background(Course names or description, please):

What do you already know about biophysics, bioengineering, or biology?

What is your experience in computer programming or mathematical modeling?

Why are you taking this class? What do you hope to get out of it?

What is your teaching experience?