BIO3250 Ch5, chisquare independent test,

Explain homework settings

Socrative

YouTube recording

QubeHub Rstudio demo

BIOL3250 review of exam 1, continued, bonus points, ch5 started.

review learning pyramid,
active learning
prepare exams

review of exam 1.

talk bonus point explanation
learning R bonus points

ch5, linkage and recombination

*** network controllability researchers

Albert-László Barabási 

Yang-yu Liu

Ying-Cheng Lai
http://chaos1.la.asu.edu/~yclai/pub.html#sect7

Wen-Xu Wang

Zuno albert

Japan NIG


Atsushi Mochizuki

SimCenter talk

video recording

student signup sheet

acetaminophen
coin and dice for multinomial distribution demonstration.

45 minutes talk:
10
20 aging
10 controllability

cpsc1100 Ch2, 2.8, 2.9

2.8 Object references

2.9 Draw two-shapes.

Go over homework and lab.

Skip ch2.10.

controversies on driver node identificaiton

In a PONE paper on driver node in cancer networks, a reader commented on different ways to identify driver nodes.

http://journals.plos.org/plosone/article/comment?id=10.1371/annotation/fa7b59e2-c5b0-4e34-b2bc-da5d4eef0ee5


Nacher J, Akutsu T (2012) Dominating scale-free networks with variable scaling exponent: heterogeneous networks are not difficult to control - Abstract - New Journal of Physics - IOPscience. New Journal of Physics 14.

There more recent papers on controllability outside of Liu and Barabasi group. 

bio3250, 20170216 Thu

Consent form for survey.

Review exam 1, average 65. Highest 88.

Retake for makeup points.

directed yeast/human nework

directed yeast network
https://www.ncbi.nlm.nih.gov/pubmed/21900206

directed TF and their target networks
http://europepmc.org/abstract/MED/16762362
(network are provided in suppmentary information).

Controllability analysis, yeast PPI

Liu11 code input format

TextWrangler replace ',' in pairs.csv to white space, save as 'pair.txt'.

applejack:run.ppi hqin$ Parse pairs.txt 

pairs.txt

# N= 4478, E= 13667

In total it takes 0.20 s

applejack:run.ppi hqin$ head pairs.txt.nodemap 

0 YMR047C

1 YGR218W

2 YOR128C

3 YCR067C

4 YLL028W

5 YHR188C

6 YMR292W

7 YDR414C

8 YNL078W

9 YHR187W

applejack:run.ppi hqin$ ControllabilityAnalysis pairs.txt > _typscript.txt 

_typescript.txt

Read Standard Elist:

N= 4478

E= 13667

<k> = 6.10406

Number of driver nodes: Nd= 2295

Control profile (Ns, Ne, Ni)=(1321,0,974)

Nd= 2295

Type-I node classification: (Ncn, Nrn, Non)=(460,1961,2057)

Type-II node classification: (Ncn, Nrn, Non)=(1321,1526,1631)

Link classification: (Ncl, Nrl, Nol)=(796,6079,6792)

Clustering Coefficient: <LCC>= 0.0806148; GCC=0.0604306; <LCC>_d=0.0403074; GCC_d=0.0302153

0 72348.1

1 53025.5

2 5971.48

3 10

4 3242.97

5 705.874

6 0

7 7391.21

8 2264.2

... ... 

... ... 

<Betweeness Centrality> = 1085.74<Closeness Centrality> = 1085.74

<Hub Centrality> = 0.00255414

<Authority Centrality> = 0.00232173

In total it takes 4.87 s.

applejack:run.ppi hqin$ ll

total 1328

-rw-r--r--  1 hqin  staff    42K Feb 15 06:51 _typscript.txt

lrwxr-xr-x  1 hqin  staff    17B Feb 15 06:48 pairs.txt -> ../data/pairs.txt

-rw-r--r--  1 hqin  staff   107K Feb 15 06:49 pairs.txt.elist.b

-rw-r--r--  1 hqin  staff   117K Feb 15 06:49 pairs.txt.elist.t

-rw-r--r--  1 hqin  staff   240K Feb 15 06:51 pairs.txt.linktype

-rw-r--r--  1 hqin  staff    56K Feb 15 06:49 pairs.txt.nodemap

-rw-r--r--  1 hqin  staff    80K Feb 15 06:51 pairs.txt.nodetype

-rw-r--r--  1 hqin  staff   213B Feb 15 06:51 pairs.txt.output

applejack:run.ppi hqin$ wc -l pairs.txt.linktype 

   13668 pairs.txt.linktype

applejack:run.ppi hqin$ head pairs.txt.linktype 

#source  target  LinkType 

YMR047C YGR218W 1

YOR128C YCR067C 2

YLL028W YHR188C 1

Q: Liu11 treat PPI as directed graph. How did PNAS16 paper deal with this problem? 

Reference
Liu 2011 Nature.

human chimera, interesting topics for lectures

http://www.medicaldaily.com/human-chimera-paternity-test-reveals-child-fathered-long-lost-vanished-twin-absorbed-359050

bio3250 review for exam 1

Learning outcomes in exam 1

Exam 1 policy.

Respondus lockdown browser usage

cpsc1100 java, ch2.4, 2.5 using objects. part2

using variables
Java Tutor visualize
http://www.pythontutor.com/java.html#mode=display

Java API
https://docs.oracle.com/javase/8/docs/api/


Accessor and mutator methods.

UTC announcement email-lists

To send an email to all faculty and staff, email utcinfo@raven.utc.edu.

To send an email to all students, email scrappy@raven.utc.edu.

Write the email exactly as you want it to appear to the recipient. Please don't attach files or insert images, though you can copy and paste the text into the body of the email. 

Your message dated Mon, 13 Feb 2017 18:16:17 +0000 with subject "Toward a

new kind of medicine: Biology +  Computer Science + Engineering" has been

successfully distributed to the SCRAPPY list (16093 recipients).

genetics, exam 1, concepts and skills

common model organisms

mitosis, cell cycle
meiosis, chromosomal change during meiosis

alleles, genotype, phenotype

homologous chromosome, crossing over

principle of segregation, principle of independent assortment
monohybrid cross
dihybrid cross
Punnett square
chi-sqaure, p-value

pedigree, probability

Barr body
ABO
SRY

recessiveness, dominance, codominance, sex-linked inheritance

UTC email mobile setting

username: first-last@utc.edu
password: (from iam.utc.edu)
server: outlook.office365.com