Thursday, February 23, 2017

Tuesday, February 21, 2017

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


Saturday, February 18, 2017

*** 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

Friday, February 17, 2017

SimCenter talk


video recording

student signup sheet

acetaminophen
coin and dice for multinomial distribution demonstration.

45 minutes talk:
10
20 aging
10 controllability

Thursday, February 16, 2017

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.



Wednesday, February 15, 2017

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


Monday, February 13, 2017

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


Thursday, February 9, 2017

cpsc1100 ch2

Covered 1-4.
stopped at method. section 4.
Only 9 students are there. I went over exercises but most students are bored.

Going over book example are boring. I need to engage students in more hands-on exericises. 

Wednesday, February 8, 2017

BIOL3250 sex-linked inheritance


Respondus lockdown browser. Facial detection during exam.

Review meiosis vs mitosis


Monday, February 6, 2017

UTC SSB self service , undergraduate advising

Undergraduate advising

advising resources
http://www.utc.edu/college-engineering-computer-science/advising/advisingresources.php

student success collaborative

ssc.advisory.com/gsrc/students

catalogue.utc.edu

clear path for advising
http://www.utc.edu/advisement/advising-resources/clear-paths-for-advising/clear-paths-for-advising-2016-2017.php#engineering-and-computer-science

records office

pre-requisite and co-requisite (lab)

transfer equivalence charts (records office website,
https://www.utc.edu/records/transfer-information/transfer-equivalency-charts/

math placement char (search math placement at utc)
http://www.utc.edu/mathematics/students/placement.php

course overrides

change of major/minor/catalogue year (submitted online only by student)

myMocs degree

blank petition

Repeat policy for undergraduates: first 3 replaced, most recent one counted (not the highest)

Financial aids policy: (could change).

Center for student success (library)







Friday, February 3, 2017

host mac, virtual machine guest Ubuntu, share folders



See
https://youtu.be/TcrfrVNNGMU

After setting shared folder in VirtualBox,

in Virtual Ubuntu, $ sudo adduser hqin vboxsf



The restart virtual Ubuntu. Shared folder appear as added drives.


Wednesday, February 1, 2017

cpsc 1100 lab, nested loop, Youtube screencast


go over for loop print on windows

Use YouTube screencast for VisualLogic nested loop demo in class. The Youtube videos can then immediately be accessed by students. It worked well.



UTC CSE Mapping of Student Outcome to Competency for Cohort Courses



Mapping of Student Outcome to Competency for Cohort Courses
Course
Outcome
Competency
1100
A
  1. 1)  Demonstrate knowledge of and use program constructs: selection, switch, if/then, if/then/else, repetition, loops and do while
  2. 2)  Demonstrate knowledge of and use Object Oriented programming concepts, such as classes, to design programming solutions for problems
a) Students will be able to create their own classes and methods.
b) Students will be able to use the concepts of Object Oriented

Programming
1110
A
1) Demonstrate knowledge of and use basic data types
a) Students will be able to create, store, retrieve, and process data in an

array.
  1. 2)  Demonstrate knowledge of Object Oriented programming techniques, such
    as, encapsulation, polymorphism and inheritance.
  2. 3)  Demonstrate knowledge of and use recursion to develop programming
    solutions for problems
  3. 4)  Demonstrate knowledge of and use algorithms, such as those for sorting and
    searching, and analyze their performance and understand relationships and interpret materials
2100
B
1) Demonstrate knowledge and use of analysis techniques for software problems to identify and describe SDLC activities and phases.
  1. 2)  Ability to design an Object-Oriented solution to a software problem.
  2. 3)  Ability to produce specification documentation for a software product.
C
1) Demonstrate knowledge and design techniques to create different UML diagrams including class, object, use case, and state machines.
2) Ability to write a test harness for class implementations.
  1. 3)  Ability to design a solution to a software problem.
  2. 4)  Ability to create Graphical User Interface (GUI).
  3. 5)  Ability to create GUI Diagrams.
2800
E
1) Understand security issues in operating systems
I
1) Ability to work in a command-line Linux/UNIX environment
3200
B
  1. 1)  Understand and develop recursive algorithms.
  2. 2)  Understand and implement classical sorting and searching algorithms.
  3. 3)  Understand and implement classical data structures and associated
    algorithms (trees, heaps, linked lists, graphs).
  4. 4)  Understand and implement applications of classical data structures.
  5. 5)  Use the standard library and generic programming techniques appropriate for
    a modern programming language (such as the C++ STL).
J
  1. 1)  Demonstrate an understanding of "Big O" notation, and its mathematical definition.
  2. 2)  Determine the computational complexity of algorithms.
  3. 3)  Determine the memory storage requirements of data structures.
  4. 4)  Evaluate and compare options regarding algorithms, data structures and
    other aspects in the design, implementation and analysis of a software product.
3600
F
  1. 1)  Demonstrate ability to give an oral presentation, which is well organized, with a clear purpose.
  2. 2)  Demonstrate effective and professional delivery of an oral presentation.
  3. 3)  Demonstrate ability to write a paper, which is well organized, with a state
    purpose and clear organization of ideas.
  4. 4)  Demonstrate ability to write a paper whose content is detailed, accurate, and
    follows standard English usage.
  5. 5)  Demonstrate original thought.
  6. 6)  Demonstrate correct use of references, cited in a standard formatting style.
L
  1. 1)  Ability to know basic information security services
  2. 2)  Ability to know basic information security standards
  3. 3)  Ability to know sources of security threats
  4. 4)  Ability to know the frequent sources of system security problems
  5. 5)  Ability to assess system vulnerabilities
  6. 6)  Ability to understand the basics of cryptography
  7. 7)  Ability to know the basis of security laws
3610
E
  1. 1)  Differentiate between ethical theories
  2. 2)  Identify implicit assumptions and biases in arguments
3) Demonstrates an awareness and understanding of controversial issues relating to computing and society.
F
  1. 1)  Demonstrate ability to give an oral presentation, which is well organized, with a clear purpose.
  2. 2)  Demonstrate effective and professional delivery of an oral presentation.
  3. 3)  Demonstrate ability to write a paper, which is well organized, with a state
    purpose and clear organization of ideas.
  4. 4)  Demonstrate ability to write a paper whose content is detailed, accurate, and
    follows standard English usage.
  5. 5)  Demonstrate original thought.
  6. 6)  Demonstrate correct use of references, cited in a standard formatting style.
G
  1. 1)  Understand social issues of the Internet such as the Digital Divide and gender gap
  2. 2)  Understand issues surrounding intellectual property
  3. 3)  Become aware of and understand the ACM and IEEE codes of conduct
CE
  1. 1)  Students demonstrate a recognition of need to continue learning after graduation
  2. 2)  Students identify realistic strategies to continue learning after graduation
3700
J
3) Ability to design a combinational logic circuit to realize a specified function given constraints on gate type, fan-in, and/or delay, etc.
4) Ability to design a sequential logic circuit to realize a function given constraints on flip-flop type, etc.
CE
1) Students can design a physical lab experiment, including specifying equipment and detailing actions to be carried out.
4600
L
  1. 1)  Ability to know and be able to work with basic cryptography and biometrics a) Students will be able to understand various options of biometrics
    including fingerprint, face, voice, and DNA.
    b) Students will have the ability to implement an encryption algorithm

    such as AES, RSA
  2. 2)  Students will have the ability to analyze properties and vulnerability of
    certain ciphers such as error propagation of ASE or a short message attack to RSA.
4700
J
  1. 1)  Ability to evaluate CPU performance given clock frequency and a mix of several instruction types.
  2. 2)  Ability to evaluate pipeline throughput in machines with and without branch prediction
  3. 3)  Ability to determine key instruction set design parameters for a notional computer architecture
  4. 4)  Ability to evaluate various network topologies that may be used in parallel computer systems
4900
B
1) Ability to produce a requirements specification document for a complex software product
a) Students will be able to identify and describe the major activities that constitute requirements engineering.

b) Students will be able to describe and perform several different tasks related to requirements elicitation.
C
1) Ability to design a solution to a software problem.
2) Ability to create UML diagrams, including class, object, use case, interaction, and state machines.
3) Ability to identify various testing techniques and strategies and develop test cases for black box testing, white-box testing, and boundary testing.
K
  1. 1)  Demonstrate knowledge of the SDLC and associated activities
  2. 2)  Develop use case diagrams and scenarios that address a given software
    problem.
  3. 3)  Develop solutions to a software problem
  4. 4)  Demonstrate a knowledge of software development methodologies
4910
D
  1. 1)  Ability to work as a team to produce a software product
  2. 2)  Demonstrate an ability to produce a peer-rating report for each team
    member.
  3. 3)  Students will assume an assigned role in an SDLC team responsible for
    analyzing, designing, implementing, testing, and deploying a significant software product.
H
1) Uses new languages and technologies
I
  1. 2)  Demonstrate knowledge and use of various programming tools and skills like objects, classes, data types, iterations and program debugging and testing including use of SDE
  2. 3)  Demonstrate knowledge of and use of software project design skills like coding, documentation and related skills
    1. a)  Students will assume an assigned role in an SDLC team responsible for
      analyzing, designing, implementing, testing, and deploying a significant
      software product.
    2. b)  Students will work as a team to produce a project plan and System
      Requirements Specification (SRS)
    3. c)  Students will work as a team to produce a System Design Specification
      and source code
    4. d)  Student will work as a team to produce test plans and systems
      documentation
    5. e)  Students will work as a team to make a formal system demonstration
      and produce a peer-rating report for each member of their team
  3. 4)  Identify and describe the good and bad aspects of their experience

UTC, CPSC course assessment sheet




Computer and Engineering Course Assessment Sheet:
Course Number – Course Name

Outcome X: Definition of the Outcome:
Put definition of outcome here.  This should be the standard definition – no improvision
Course Number and Name of the Course: XXXXX
Catalog description of the course:

Catalog description goes here.  This should be taken from the most recent catalog

Competencies to measure Outcome X:

a)      You have been given a table of the outcomes and it should be exact here.

Target: Meets or exceed expectations is equal to or greater than 70% if 1000 or 2000 and 80% if 3000 or 4000.

Implementation Plan (timeline): semester and year
Key/Responsible Personnel: Your name

Competencies:

List the competency being assessed.  This should match one of the entries above.

Student Artifact Used: The exam or assignment used, the question number followed by the question written out.

Meets or Above Expectations: % (percentage for this question only)

Above Expectations:                           % (percentage for this question only)
            Meets Expectations:                            % (percentage for this question only)
Below Expectations:                            % (percentage for this question only)

Results: Target Achievement: Achieved or not achieved.
Recommendations: No recommendations are needed or specify recommendatiaon

A-1 Demonstrate knowledge of and use program constructs: selection, switch, if/then, if/then/else, repetition, loops and do while.

List the competency being assessed.  This should match one of the entries above.

Student Artifact Used: The exam or assignment used, the question number followed by the question written out.

Meets or Above Expectations: % (percentage for this question only)

Above Expectations:                           % (percentage for this question only)
            Meets Expectations:                            % (percentage for this question only)
Below Expectations:                            % (percentage for this question only)

Results: Target Achievement: Achieved or not achieved.
Recommendations: No recommendations are needed or specify recommendatiaon

A-1 Demonstrate knowledge of and use program constructs: selection, switch, if/then, if/then/else, repetition, loops and do while.

Summary of Findings for the outcome:

Meets or Exceeds Expectations:  86.6% (overall percentage)

Above Expectations:                 66.7% (overall percentage)
Meets Expectations:                  20.0% (overall percentage)
Below Expectations:                  13.3% (overall percentage)

Results: Target Achievement: Achieved

Recommendations: No action necessary.

Repeat as necessary.



Detailed Assessment of
Course Number and Name

Table 1 Course Assessment Plan

Student artifacts (assessment mechanism)
Target Student Outcomes/competencies
Exam name, Question Number
Outcome and competency such as A-1
Repeat as necessary
Repeat as necessary

Table 2 Spreadsheet for Student Performance on Student Artifacts

   Stud.  
         
Artifact
Student ID
Objective Competency
Exam or Assignment, question number
Need a new column for each
STU01


STU02


STU03


STU04


STU05


STU06


STU07


STU08


STU09


STU10


STU 11


STU12


STU13


STU14


STU15





Table 3 Summary of Findings
Objective Letter


     
Artifact
Rubric score
Objective and Number
Repeat for each above

Exam or Assignment, question number
Repeat for each above
Total Exceeds
Total number of students who exceed

Total Meets
  Total number of students who meet

Total Below
  Total number of students who are below
 
Total Students
Number of students

Exceeds %
# exceeds / total number of students

Meets %
# exceeds / total number of students

Below %
# exceeds / total number of students

Total % of Meets and Exceeds for the competency


Overall % of Meets and Exceeds for Outcome A