*** phylogenetic comparative method

Modern Phylogenetic Comparative Method

http://www.mpcm-evolution.org/

protein disorder, robustness

http://biorxiv.org/content/biorxiv/early/2015/11/25/032847.full.pdf

NIMBIoS undergraduate meeting 20151121

=> Mutation effect on cooperation. Two students from UNC Greensboro
 deterministic model, using Michanis-Menten style models.

=> invasive species and commodity flux
cargo shipping and invasive species
freight analysis framework FAF
http://ops.fhwa.dot.gov/FREIGHT/freight_analysis/faf/index.htm

S(t+1) = E * P g(St)
where g is the logistical growth, E: environmental matrix. P: transitional probability matrix.
Each state is a node.

"jump' from midwest to 'california'? through shipping, long-distrance dispersion.

=> Pakingson disease orthologs
human GWAS -> worm ortholog -> STRING -> pathway

=> Clinic gait analysis
quantify gait, using relfective markers. motion capture technique.
joint angle data, knee flexion/extension

Current analysis on adult males.
Modeling should be done before operational procedure.

Gage center for motion analysis.
Gillete Children's Healthcare.

software, SIM, openSIM
https://simtk.org/home/opensim_data

UTK Nimbios undergraduate research meeting, Nov 21-22, 2015

Nov 21-2, 2015
http://www.nimbios.org/education/undergrad_conf2015
http://www.nimbios.org/education/undergradconf

https://utconferences.outreach.utk.edu/ei/cm.esp?id=433&pageid=_30O0SBXXA

abstract submission before November 13
travel support before Sep 18

Confirmed students:
Christina Fennell, abstract received.  Maya L Bryant, abstrac received
Imani-Michelle White, abstract received, Bongeka Zuma, abstract received
Keyana Scott, Taylor William-Hamilton, abstract received.

data resources

Freight Analysis Framework
http://ops.fhwa.dot.gov/FREIGHT/freight_analysis/faf/index.htm#faf4

cargo shipping
http://arxiv.org/abs/1001.2172

G Graphics cookbook, website support

https://www.stat.auckland.ac.nz/~paul/RG2e/

KSU R Day

=> First talk
-> undergraduate minor in data analytics

->Analytics becomes the value driver:
raw data ^& report  = value
linking of multiple data source
predictive model, internal attrribute == trusted parter status
predictive attributes, insights == stickness and value

-> credit score modeling

-> insurance risk

-> insurance fraud detection, network based analysis, temporal information, identify potential ring leader.

-> vehicle risk, telematics
trip complexity: right-to-left ratio, local speeding, highway speeding, road feature, weather, hard breaking, night driving,

-> location risk in property insurance
weather-related peril, geo-spatial intelligence

-> life mortality modeling vs traditional accural model
factors: life style, MVRs, credit, prescription history, gender, age-buckets

-> Success in Data Analysis: understand what matters, details matter, understand connections, execution is key, learn the language.

-> drone technology may bring chagnes.

bio233 Thu 20151120 review

Go over exam 3 open book questions

Ch12, ch28 questions

Phylogeny, tree topology

Ortholog, paralogs

bio233, 20151117Tue

epidemiology, london cholera case

post-course survey

review

bio386, 20151117Tue

Bio386, computing survey

Computing project

Review student presentations.

bio233, lab, australian rabbit virus lab

Background of Austrilian rabbit virus

https://www.youtube.com/watch?v=Zl3bGWRrO1s

Lab report: Finish online exercises

Use past video link
https://www.youtube.com/watch?v=FqSDxGYu3K0&feature=youtu.be

references related to big data challenges

Berkeley Simons Institute for the theory of computing
https://simons.berkeley.edu/

bio233 20151109Mon lab, virus tradeoff paper, west-nile virus lab, streak plates.

=> virus tradeoff paper. (Students did not actually discuss the paper. They just went over the exercises).

=> west-nile virus lab,
Students worked on their own in groups.

=> streak plates. Most students work on their own.

*** bio386, Gordon exercise 20151105Thu

Gordon, file transfer

Procedure to transfer bio386.tar archives from QIN's directory to student directory: 

You can loginto Gordon using ssh or Putty directly

$ ssh username@gordon.sdsc.xsede.org

Then go to your file directory:  

$ cd /oasis/scratch/username/temp_project/

Then copy bio386.tar to your file directory

$  cp /oasis/scratch/hongqin/temp_project/bio386.tar . 

Then 

$ tar xvf bio386.tar 

Then

$ cd Slim-network-aging-bio386-fall-2015

Then 

$ nano -w  20151101-net-sim-ginppi.R

Inside of nano, you should change the username in the following line: 

mydir = '/oasis/scratch/username/temp_project/Slim-network-aging-bio386-fall-2015'

Then control-X save and exit nano

Now, we can need to change the working directory in PBS job script. 

$ nano -w netaging.pbs

Then change username in the following line

 cd /oasis/scratch/hongqin/temp_project/Slim-network-aging-bio386-fall-2015

Then exit and save. 

Then submit the job request

$ qsub netaging.pbs

If this runs, you are one of the first Spelman students to use a Federally funded super-computer. 

To check the status of your computing jobs

$ qstat -u username

bio386 20151105Thu

X student research project,

X data into R.

Gordon pbs job run.

Unix shell tutorial

http://www.tutorialspoint.com/unix/unix-loop-control.htm

made 2 liter YPD plates

8pm-10pm.

10g YE
20g Peptone
20g Dextrose
20g agar
add 1000 ml ddH2O
autoclave for 30 minutes (70 minutes)

30 minutues, weight ingredients, 1 hour autoclave, pour plates (about 30 minutes)

Poured about 5 sleeves of plates.

advising for spring 2016

For 42 students with course plans, I spent 8 hours, plus 4 hours in-person office hours.
Monday 4 hours
Tuesday 4 hours

For irregular students, changed majors, or seniors, it took much less time.

Wed 1-5pm, in-office advsing.

Spelman NSF day

* cost sharing is prohibited.

* NSF-wide and cross-cutting programs: HBCUs, RAPID/EAGER, ADVANCE, GRFP, MRI, RUI/ROA, REU/RET.

RAPID such as ebola virus in 2014, aspect of urgency.
https://www.nsf.gov/geo/plr/opp_advisory/briefings/may2010/gpg_rapid_eager.pdf
" PI(s) must contact the NSF program officer(s) whose expertise is most germane to the proposal topic before submitting a RAPID proposal. This will facilitate determining whether the proposed work is appropriate for RAPID funding."

EAGER, Early Concept Grants for Exploratory Research (EAGER), high risk and high reward. Internal review. 

ADVANCE: women in academics and science. 

MRI: an equipment to enhance "existing research" with more possibilities. 


For PUI: 
RUI: no more than 20 PhD degrees in 2 year period in all-NSF supported fields. 
ROA: research opportunity award, supplements to existing awards, such as support to visiting a large lab to learning new skills. 

RUI has better rate than regular proposals. 

bio125 todo list

=> ApE on Genbank file

=> Flow cytometer protocol, HU- cells in growth media

=> EdX and Couresra R-file