SysBio19 Asgn_9_Due_5:00PM Monday Nov 11: Gates article in Boolean_Read folder_2019_11_12 Lead: Kyle

Structural and Dynamic Network Control: Read carefully Gates article in Boolean_Read folder  Gates and Rocha, SciRpts (2016) "Control of complex networks requires both structure and dynamics.". Answer the questions: 1) What did you already know? 2) What did you learn? 3) What is your most pressing question that you would like Kyle to explain in class? 4) How does this relate to your project?

Class GRN Interest Poll

List the regulatory/differentiation networks that are of greatest interest to you and most closely related to your overall educational goals: Please respond before class tomorrow (Tuesday, October 29).

SysBio19 Asgn_8_Due_Tuesday_43767__Liu_article_in_Control_Folder_2019_10_29 Lead: Javier

Network Observability: Read carefully Liu article_in_Control_Folder  Liu, Y. Y., et al. (2013). "Observability of complex systems." PNAS 110(7): 2460-2465.. Answer the questions: 1) What did you already know? 2) What did you learn? 3) What is your most pressing question that you would like Jaview to explain in class? 4) How does this relate to your project?

SysBio19 Asgn_7_Due_Tuesday_43767__Liu_article_in_Control_Folder_2019_10_29 Lead: Aiden&Nilai

Network Controllability: Read carefully Liu article_in_Control_Folder  Liu, Y. Y., et al. (2011). "Controllability of complex networks." Nature 473(7346): 167-173.. Answer the questions: 1) What did you already know? 2) What did you learn? 3) What is your most pressing question that you would like Aiden and Nilai to explain in class? 4) How does this relate to your project?

SysBio19 Asgn_6_Due_Sunday_20-0ct-2019__LeDuc_article_in_Control_Folder_2019_10_22

Read carefully LeDuc article_in_Control_Folder  Control of biology. Answer the questions: 1) What did you already know? 2) What did you learn? 3) What is your most pressing question that you would like Nicole to explain in class? 4) How does this relate to your project?

SysBio19 Asgn_5_Class__Woo_article in Networks Folder_2019_10_17 - Due, Tuesday, Oct 15!

Read carefully Woo article in Networks Folder:  Elucidating Compound Mechanism of Action byNetwork Perturbation Analysis. Answer the questions: 1) What did you already know? 2) What did you learn? 3) What is your most pressing question that you would like Blake, Cody, and Tejas to explain in class? 4) How does this relate to your project?

SysBio19 Asgn_4_Class__Yachie-Kinoshita_article

Browse Yachie-Kinoshita article  Modeling signaling-dependent pluripotency with Boolean logic to predict cell fate transitions. Scan this article to familiarize yourself with the contents. Answer the questions: 1) What did you already know? 2) What did you learn? 3) What is your most pressing question that you would like Kyle to explain in class? 4) How does this relate to your project?

SysBio19 Asgn_3_Class__Tyson_article

Browse Tyson article  Modeling the dynamic behavior of biochemical regulatory networks. Scan this article to familiarize yourself with the contents. Answer the questions: 1) What did you already know? 2) What did you learn? 3) What is your most pressing question that you would like Kyle to explain in class? 4) How does this relate to your project?

SysBio19 Asgn_2_Class__Bornholdt_article

Browse Bornholdt article  Ensembles, dynamics, and cell types: Revisiting the statistical mechanics perspective on cellular regulation. Scan this article to familiarize yourself with the contents. Answer the questions: 1) What did you already know? 2) What did you learn? 3) What is your most pressing question that you would like Kyle to explain in class? 4) How does this relate to your project?

SysBio19 Asgn_1_Class__Joo_article_2019_10_10

Read carefully Joo article  Probabilitic Boolean Networks. Answer the questions: 1) What did you already know? 2) What did you learn? 3) What is your most pressing question that you would like Kyle to explain in class? 4) How does this relate to your project?

Greetings to SysBio19

Folks -
This is the forum that we will use to exchange observations about the reading.
Please confirm by commenting on this post.
John

SysBio18 Asgn_9C_Class_25_List_01_2018_11_27 Control In/Of GLBA

Build a class list of examples of control IN the GLBA, and what are examples OF external control of the GLBA. Read the comments by your classmates and post a PCRC on the Blog that lists additional 1) Examples of control IN the GLBA. 2) Examples of how one might control the GLBA.

SysBio18 Asgn_9B_Class_25_PPT_03_2018_11_27 Examples of Control

Study PPT 03  PPT03_SysBio_Examples_of_Control_2018_11_15_0601. Review the PPT, which includes general responses from prior classes. Be sure to study slides 36-42. Post a PCRC on the Blog.

SysBio18 Asgn_9A_Class_25_Article_08_2018_11_27 Control Overview

Read Article 08  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.

SysBio18 Asgn_8_Class_18_Article_07_2018_10_25_Vernetti_Coupled_MPS

Coupled Organ Chips: Read Article 07  Vernetti, L, et al. Functional Coupling of Human Microphysiology Systems: Intestine, Liver, Kidney Proximal Tubule, Blood-Brain Barrier and Skeletal Muscle. Sci. Rep. 7: 42296. 2017. PMCID: PMC5235976. 

Think about how this approach could be used to study the Gut-Liver-Brain axis! 

Look at the Del Rio, et al., Nutrients, 2017 to get some idea of how much work was required to confirm the prediction regarding CSF TMAO.

Post a PCRC on the Blog. 

SysBio18 Asgn_7B_Class_17_Article_06_2018_10_23: Gut-Brain Review-2

Gut-Brain Review: Read Article 05  E.E. Mayer, "Gut feelings: the emerging biology of gut-brain communication," NatRevNeuro, 12: 453-466 (2011) . Post a PCRC on the Blog. We need a volunteer to moderate the blog and guide the discussion of the blog postings!

SysBio18 Asgn_7A_Class_17_Article_05_2018_10_23: Gut-Brain Review-1

Gut-Brain Review: Read Article 05  E.E. Mayer, "Gut feelings: the emerging biology of gut-brain communication," NatRevNeuro, 12: 453-466 (2011) . Post a PCRC on the Blog. We need a volunteer to moderate the blog and guide the discussion of the blog postings!

SysBio18 Asgn_6B_Class_15_Wikipedia_Enteric nervous system, etc._2018_10_11

Enteric nervous system: Read Wikipedia Enteric nervous system, etc.  https://en.wikipedia.org/wiki/Enteric_nervous_system https://en.wikipedia.org/wiki/Basal_electrical_rhythm  https://en.wikipedia.org/wiki/Neurogastroenterology. 
Post a PCRC on the Blog.

SysBio18 Asgn_6_Class__Blog Papers_Gut-Brain Papers_2018_10_11

Gut-Brain Axis overview papers: Read one or more papers that one of your classmates found interesting! Blog Papers Gut-Brain Papers  Report on your reading:1)  Paper title, first author, journal name, year. 2) Sentence or two on the relevance of the paper to our class. 3)  Recommendation for future action.

SysBio18 Asgn_5_Class__Wikipedia_Autonomic_2018_10_09

Autonomic nervous system: Read Wikipedia Autonomic  Autonomic nervous system https://en.wikipedia.org/wiki/Autonomic_nervous_system. Post a PCRC on the Blog.