Friday, August 31, 2018

Whole Blood Gene Expression Associated With Clinical Biological Age

Simcenter conference room monitor
Remote control: Input -> pick laptop for VGA.

Thursday, August 30, 2018

Wednesday, August 29, 2018

cpsc2100 20180830Thu

OpenTron github example.

Exericse 4, 6, 7, string

https://courses.edx.org/courses/course-v1:MITx+6.00.1x+2T2017_2/courseware/fc8f42302c644118adfcfa720f9f403e/35f82f6c3ecb4e9e913dc279a9b73a9f/?child=last

https://medium.com/cyberdoggo/mit-6-00-1x-problem-set-1-c5ba79ae2aad

Tuesday, August 28, 2018

全自动微生物生长曲线分析仪

differential privacy

http://www.win-vector.com/blog/2015/11/our-differential-privacy-mini-series/

nested models

Cite Ziheng Yang's codeML, nested model test approaches

https://stats.stackexchange.com/questions/4717/what-is-the-difference-between-a-nested-and-a-non-nested-model

Thursday, August 23, 2018

Genomelink Hackathon 2.0:

genomelink API and hackthons

https://www.awakens.co/

Genomelink Hackathon 2.0: Build hyper-personalized consumer applications using insights from DNA data with Genomelink API

Genomelink Hackathon 2.0 follows the successful launch of the first edition of our online hackathon, also hosted on Devpost. If you are in the San Francisco Bay Area, consider joining our in-person hackathons. Sign up for our mailing list to stay tuned for future online & offline events.

The Genomelink Hackathon, hosted by venture-backed genomic startup, AWAKENS, is a developer competition leveraging Genomelink API, to seek out novel use cases for how insights from genomic data can be applied -- to provide actionable insights and access to hyper-personalized services, and education on genomics.

The number of consumers who had their DNA analyzed more than doubled in 2017, with more than 1 in 25 US adults now with their genetic data on hand. The information in our genomic data has the potential to inform on our nutrition, fitness, personality, cognition, and more. Yet, the insights available from genomic data are not yet made relevant or useful to people’s lives. How can we use this data effectively?

Genomelink API enables any developer/company to create apps or services that are hyper-personalized, based on their users’ DNA data. Here’s how: Genomelink API provides insights on genetic traits of interest with just a few lines of code -- without advanced requirements like genomics expertise or how to securely handle raw DNA data. This means that you’ll be able rapidly integrate DNA-personalization into your new or existing app. With APIs like Genomelink API, the opportunity for developers to contribute to the exciting new field of personal genomics has become wide open!

What kind of personalized app will you create, to enhance people’s lives through improving our health, wellness, lifestyle, and learning experience?

Get started now by creating your free Genomelink developer account, learning how to use Genomelink API(review the list of genetic traits available here), and reading about apps developed in previous Genomelink hackathons.

About AWAKENS:
AWAKENS has built Genomelink, a Stripe-type API solution that enables any developers / companies to build hyper-personalized apps based on the consumer’s DNA data. Supported by Illumina Accelerator, Berkeley SkyDeck, key Berkeley and Stanford faculties in nutrition and genomics, AWAKENS is building an infrastructure that will fuel the creation of diversified value-producing use cases of personal genomics. Read about the team here.

View full rules

ELIGIBILITY

The Hackathon IS open to:

Individuals who are at least 18 years of age as of the time of entry ("Eligible Individuals")
Teams of Eligible Individuals ("Teams")
Teams of Eligible Individuals entering on behalf of Organizations (including corporations, not-for-profit corporations and other nonprofit organizations, limited liability companies, partnerships, and other legal entities) that exist and have been organized or incorporated at the time of entry ("Organizations")

REQUIREMENTS

Main Requirement: Create or update a functioning software application that integrates Genomelink API. Your application may not use genetic insights to discriminate or otherwise harm users.

Your app should help DNA data holders make DNA relevant to their life. This could include helping them learn about themselves, intepret their data better, or access more personalized services.

To get started, check out Submissions from our previous Genomelink Hackathon. We especially like novel solutions & use cases, or original twists to existing solutions. We also encourage the use of other apis in conjuction with Genomelink api. We encourage past participants of Genomelink Hackathon (previously named GENOME LINK Challenge) to submit updates to their existing Genomelink applications or create an entirely new solution. Entrants will be required to explain updates made if submitting an existing Application.

What to include in your submission:

Include a video demo (max 5 min) + screenshots of your app demonstrating how it works.
Written description of your solution: Complete and enter all of the required fields on the “Enter a Submission” page.
Link to availability: including login credentials to private website or access to private repositories if applicable.
Entrant's (including each team member's) full name and email address

HOW TO ENTER

Register for the hackathon on Devpost.
Create your free Genomelink Developer accountResources can be found in the developer dashboard
Find a teammate (optional) by reaching out to other developers on the Participants tab.
Create or update an awesome DNA-personalized app!
Shoot your demo video and take screenshots of your functioning app.
Provide a way to access your project for judging and testing (The Github code repository may be public or private. If the repository is private, share access with @knmkr).
Submit your application on genomelink2.devpost.com before August 28, 2018 @ 5:00PM PT for consideration in the hackathon!

JUDGES

Austin Noronha
Vice President, Sony Innovation Fund

Kensuke Numakura
CTO, Awakens

Yuta Matsuda
COO & Product Manager, Awakens

JUDGING CRITERIA

Quality of idea
Includes the creativity and originality of the idea.
Implementation
Includes how well the developer leveraged the Genomelink API.
Feasibility & Viability in market
Can this idea be implemented in the real world? How will users interact with and gain information from the application? Judges will evaluate both the practicality of the solution and how significant an impact it will have.

Sunday, August 19, 2018

UTC data science BS and MS

https://www.utc.edu/college-engineering-computer-science/programs/computer-science-engineering/masters-ds.php

ABET computing programs

http://www.abet.org/

http://www.abet.org/accreditation/accreditation-criteria/criteria-for-accrediting-computing-programs-2016-2017/

Applied and Natural Science Accreditation Commission (ANSAC); Computing Accreditation Commission (CAC); Engineering Accreditation Commission (EAC)

Friday, August 17, 2018

UTC honor code,

incident report form
https://cm.maxient.com/reportingform.php?UTChattanooga

Wednesday, August 15, 2018

CECS new faculty and staff

New Faculty

· Dr. Hamdy Ibrahim – Mechanical Engineering

· Dr. Seong Dae Kim – Engineering Management and Technology

· Dr. Mohamad Mahtabi – Mechanical Engineering

· Dr. Mengjun Xie – Computer Science and Engineering

· Dr. Deborah Mudali – Computer Science and Engineering, Visiting Professor

New Staff

· Mr. Philip Bonfiglio - Development

· Ms. Amber Burdsall – Dean’s Office

· Ms. Alanna Hunnicutt – Student Success Center

· Ms. Sara Jackson – Student Success Center

· Ms. Ghorashi Maryam – Dean’s Office

· Mr. Jason McDowell - IT and Laboratories

Monday, August 13, 2018

computational R21 examples

REPORT search %R21% in "project number"

https://projectreporter.nih.gov/project_info_description.cfm?aid=9600834&icde=40721728&ddparam=&ddvalue=&ddsub=&cr=31&csb=default&cs=ASC&pball=

Project Number:	1R21LM012759-01A1	Contact PI / Project Leader:	OTU, HASAN
Title:	IDENTIFICATION AND CHARACTERIZATION OF INTERACTION ATLASES IN HUMAN	Awardee Organization:	UNIVERSITY OF NEBRASKA LINCOLN

https://projectreporter.nih.gov/project_info_description.cfm?aid=9146395&icde=40721728&ddparam=&ddvalue=&ddsub=&cr=29&csb=default&cs=ASC&pball=

Project Number:	5R21LM012271-02	Contact PI / Project Leader:	MYNENI, SAHITI
Title:	CONTENT-BASED SOCIAL NETWORK ANALYSIS METHODS FOR DATA-DRIVEN HEALTH PROMOTION	Awardee Organization:	UNIVERSITY OF TEXAS HLTH SCI CTR HOUSTON

https://projectreporter.nih.gov/project_info_description.cfm?aid=9351565&icde=40721728&ddparam=&ddvalue=&ddsub=&cr=26&csb=default&cs=ASC&pball=

Project Number:	5R21LM012448-02	Contact PI / Project Leader:	MCCOY, ALLISON B
Title:	ELECTRONIC HEALTH RECORD SAFETY: DEVELOPING FRAMEWORK-BASED MEASURES AND IDENTIFYING BEST PRACTICES	Awardee Organization:	TULANE UNIVERSITY OF LOUISIANA

https://projectreporter.nih.gov/project_info_description.cfm?aid=9302040&icde=40721728&ddparam=&ddvalue=&ddsub=&cr=22&csb=default&cs=ASC&pball=

Project Number:	6R21LM011664-03	Contact PI / Project Leader:	LASKO, THOMAS
Title:	SCALABLE BIOMEDICAL PATTERN RECOGNITION VIA DEEP LEARNING	Awardee Organization:	VANDERBILT UNIVERSITY MEDICAL CENTER

https://projectreporter.nih.gov/project_info_description.cfm?aid=8925916&icde=40721728&ddparam=&ddvalue=&ddsub=&cr=15&csb=default&cs=ASC&pball=

Project Number:	5R21LM012060-02	Contact PI / Project Leader:	JIANG, XIAOQIAN
Title:	PROTECT PRIVACY OF HEALTHCARE DATA IN THE CLOUD	Awardee Organization:	UNIVERSITY OF CALIFORNIA, SAN DIEGO

https://projectreporter.nih.gov/project_info_description.cfm?aid=8926467&icde=40721728&ddparam=&ddvalue=&ddsub=&cr=11&csb=default&cs=ASC&pball=

Project Number:	5R21LM011667-02	Contact PI / Project Leader:	GRANDO, MARIA ADELA
Title:	PATIENT-CENTERED DECISION SUPPORT BASED ON DEVICE EVIDENCE (I DECIDE)	Awardee Organization:	ARIZONA STATE UNIVERSITY-TEMPE CAMPUS

https://projectreporter.nih.gov/project_info_description.cfm?aid=8899626&icde=40721728&ddparam=&ddvalue=&ddsub=&cr=9&csb=default&cs=ASC&pball=

Project Number:	5R21LM011941-02	Contact PI / Project Leader:	GEREK INCE, ZEYNEP NEVIN
Title:	COMPUTATIONAL DIAGNOSIS OF NON-SYNONYMOUS VARIATIONS USING STRUCTURAL DYNAMICS	Awardee Organization:	TEMPLE UNIV OF THE COMMONWEALTH

https://projectreporter.nih.gov/project_info_description.cfm?aid=8952547&icde=40721728&ddparam=&ddvalue=&ddsub=&cr=7&csb=default&cs=ASC&pball=

Project Number:	1R21LM012219-01 Former Number: 1R21GM116019-01	Contact PI / Project Leader:	DIXON, BRIAN E.
Title:	ADVANCING METHODS TO MEASURE AND IMPROVE THE QUALITY OF LARGE SCALE HEALTH DATA	Awardee Organization:	INDIANA UNIV-PURDUE UNIV AT INDIANAPOLIS

https://projectreporter.nih.gov/project_info_description.cfm?aid=9108437&icde=40721728&ddparam=&ddvalue=&ddsub=&cr=3&csb=default&cs=ASC&pball=

Project Number:	5R21LM012197-02	Contact PI / Project Leader:	CHU, HAITAO
Title:	STATISTICAL METHODS AND SOFTWARE FOR MULTIVARIATE META-ANALYSIS	Awardee Organization:	UNIVERSITY OF MINNESOTA

https://projectreporter.nih.gov/project_info_description.cfm?aid=8919947&icde=40721728&ddparam=&ddvalue=&ddsub=&cr=1&csb=default&cs=ASC&pball=

Project Number:	5R21LM011937-02	Contact PI / Project Leader:	ARNOLD, COREY WELLS
Title:	A TOPIC MODEL AND VISUALIZATION FOR AUTOMATIC SUMMARIZATION OF PATIENT RECORDS	Awardee Organization:	UNIVERSITY OF CALIFORNIA LOS ANGELES

https://projectreporter.nih.gov/project_info_description.cfm?aid=9528022&icde=40721418&ddparam=&ddvalue=&ddsub=&cr=39&csb=default&cs=ASC&pball=

Project Number:	1R21LM012615-01A1	Contact PI / Project Leader:	TYLER, ANNA L.
Title:	INFERRING MOLECULAR MECHANISMS OF COMPLEX DISEASE BY INTEGRATING PATTERNS OF EPISTASIS WITH FUNCTIONAL GENOMIC NETWORKS	Awardee Organization:	JACKSON LABORATORY

https://projectreporter.nih.gov/project_info_description.cfm?aid=8929294&icde=40721418&ddparam=&ddvalue=&ddsub=&cr=42&csb=default&cs=ASC&pball=

Project Number:	5R21LM011919-02	Contact PI / Project Leader:	WONG, CAROLYN
Title:	VISUALIZING HIGHWAY POLLUTION: A STUDY OF INTER-GENERATIONAL HEALTH COMMUNICATION	Awardee Organization:	UNIVERSITY OF MASSACHUSETTS BOSTON

https://projectreporter.nih.gov/project_info_description.cfm?aid=9509775&icde=40721418&ddparam=&ddvalue=&ddsub=&cr=46&csb=default&cs=ASC&pball=

Project Number:	1R21GM127915-01	Contact PI / Project Leader:	ZHANG, YU
Title:	NEW IDEAS FOR GWAS LOCI: PREDICT FUNCTIONAL MUTATIONS, TARGET GENES AND TISSUES DRIVING DISEASE ASSOCIATION	Awardee Organization:	PENNSYLVANIA STATE UNIVERSITY-UNIV PARK

https://projectreporter.nih.gov/project_info_description.cfm?aid=9431714&icde=40721418&ddparam=&ddvalue=&ddsub=&cr=4&csb=default&cs=ASC&pball=

Project Number:	1R21LM012744-01	Contact PI / Project Leader:	CHU, HAITAO
Title:	JOINT META-REGRESSION METHODS ACCOUNTING FOR POSTRANDOMIZATION VARIABLES	Awardee Organization:	UNIVERSITY OF MINNESOTA

https://projectreporter.nih.gov/project_info_description.cfm?aid=9600808&icde=40721418&ddparam=&ddvalue=&ddsub=&cr=11&csb=default&cs=ASC&pball=

Project Number:	1R21LM012763-01A1	Contact PI / Project Leader:	GRANT, GREGORY R
Title:	THE NEXT GENERATION OF RNA-SEQ SIMULATORS FOR BENCHMARKING ANALYSES	Awardee Organization:	UNIVERSITY OF PENNSYLVANIA

https://projectreporter.nih.gov/project_info_description.cfm?aid=9348928&icde=40721418&ddparam=&ddvalue=&ddsub=&cr=13&csb=default&cs=ASC&pball=

Project Number:	1R21LM012578-01	Contact PI / Project Leader:	JANULIS, PATRICK FRANCIS
Title:	IMPLEMENTING AND EVALUATING A MACHINE LEARNING TOOL FOR ENTITY RESOLUTION IN DRUG USE AND SEXUAL CONTACT NETWORKS OF YMSM	Awardee Organization:	NORTHWESTERN UNIVERSITY AT CHICAGO

https://projectreporter.nih.gov/project_info_description.cfm?aid=9601437&icde=40721418&ddparam=&ddvalue=&ddsub=&cr=16&csb=default&cs=ASC&pball=

Project Number:	1R21LM012772-01A1	Contact PI / Project Leader:	KORKIN, DMITRY
Title:	FUNCTIONAL CHARACTERIZATION OF GENETIC AND POST-TRANSCRIPTIONAL VARIATION USING MACHINE LEARNING METHODS	Awardee Organization:	WORCESTER POLYTECHNIC INSTITUTE

Scientific name: Saccharomyces cerevisiae: culture from type material of Saccharomyces cerevisiae: ATCC 18824
culture from type material of Saccharomyces cerevisiae: CBS 1171
culture from type material of Saccharomyces cerevisiae: NRRL Y-12632

Genbank common name: baker's yeast
Inherited blast name: ascomycetes
Rank: species
Genetic code: Translation table 1 (Standard)
Mitochondrial genetic code: Translation table 3 (Yeast Mitochondrial)
Other names:

synonym:	Saccharomyces oviformis
synonym:	Saccharomyces italicus
synonym:	Saccharomyces capensis
synonym:	Saccharomyces uvarum var. melibiosus
common name:	brewer's yeast
common name:	S. cerevisiae
anamorph:	Candida robusta

biomodeling center, University of Washington

whole cell modeling
http://reproduciblebiomodels.org/

Wednesday, August 8, 2018

UTC guest parking

$3 per day per guest

Tuesday, August 7, 2018

privacy tutorial

http://cseweb.ucsd.edu/~kamalika/pubs/WIFStutorial.pdf

http://www.cis.upenn.edu/~aaroth/courses/privacyF11.html

Campus cyber infrastructure CC*

Campus Cyberinfrastructure (CC*), this is one of four areas:

Data Driven Networking Infrastructure for the Campus and Researcher awards will be supported at up to $500,000 total for up to 2 years;

Monday, August 6, 2018

measurable words for learning outcomes

Good:
explain, define, describe

Bad:
learn, understand,

Saturday, August 4, 2018

web crawler

wget

https://github.com/QinLab/Rcrawler