Friday, August 31, 2018

Tuesday, August 28, 2018

Chinese bio equipment site



http://www.bio-equip.com/show1equip.asp?equipid=424615

微生物生长曲线测定仪
微生物生长曲线测定仪
英文名称:Microbial growth curve test equipment总访问:6462
国产/进口:进口半年访问:88
产地/品牌:英国DWS产品类别:微生物仪器
型       号:Rabit最后更新:2018-8-29
货       号:
参考报价:询价



全自动微生物生长曲线分析仪


opentrons, robot


http://opentrons.com/

github API

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.

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

  1. Register for the hackathon on Devpost.
  2. Create your free Genomelink Developer accountResources can be found in the developer dashboard
  3. Find a teammate (optional) by reaching out to other developers on the Participants tab.
  4. Create or update an awesome DNA-personalized app!
  5. Shoot your demo video and take screenshots of your functioning app.
  6. 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).
  7. Submit your application on genomelink2.devpost.com before August 28, 2018 @ 5:00PM PT for consideration in the hackathon!

JUDGES

Austin Noronha
Austin Noronha
Vice President, Sony Innovation Fund
Kensuke Numakura
Kensuke Numakura
CTO, Awakens
Yuta Matsuda
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.

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:1R21LM012759-01A1Contact PI / Project Leader:OTU, HASAN
Title:IDENTIFICATION AND CHARACTERIZATION OF INTERACTION ATLASES IN HUMANAwardee 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:5R21LM012271-02Contact PI / Project Leader:MYNENI, SAHITI
Title:CONTENT-BASED SOCIAL NETWORK ANALYSIS METHODS FOR DATA-DRIVEN HEALTH PROMOTIONAwardee 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:5R21LM012448-02Contact PI / Project Leader:MCCOY, ALLISON B
Title:ELECTRONIC HEALTH RECORD SAFETY: DEVELOPING FRAMEWORK-BASED MEASURES AND IDENTIFYING BEST PRACTICESAwardee 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:6R21LM011664-03Contact PI / Project Leader:LASKO, THOMAS
Title:SCALABLE BIOMEDICAL PATTERN RECOGNITION VIA DEEP LEARNINGAwardee 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:5R21LM012060-02Contact PI / Project Leader:JIANG, XIAOQIAN
Title:PROTECT PRIVACY OF HEALTHCARE DATA IN THE CLOUDAwardee 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:5R21LM011667-02Contact 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:5R21LM011941-02Contact PI / Project Leader:GEREK INCE, ZEYNEP NEVIN
Title:COMPUTATIONAL DIAGNOSIS OF NON-SYNONYMOUS VARIATIONS USING STRUCTURAL DYNAMICSAwardee 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: 1R21GM116019-01Contact PI / Project Leader:DIXON, BRIAN E.
Title:ADVANCING METHODS TO MEASURE AND IMPROVE THE QUALITY OF LARGE SCALE HEALTH DATAAwardee 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:5R21LM012197-02Contact PI / Project Leader:CHU, HAITAO
Title:STATISTICAL METHODS AND SOFTWARE FOR MULTIVARIATE META-ANALYSISAwardee 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:5R21LM011937-02Contact PI / Project Leader:ARNOLD, COREY WELLS
Title:A TOPIC MODEL AND VISUALIZATION FOR AUTOMATIC SUMMARIZATION OF PATIENT RECORDSAwardee 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:1R21LM012615-01A1Contact PI / Project Leader:TYLER, ANNA L.
Title:INFERRING MOLECULAR MECHANISMS OF COMPLEX DISEASE BY INTEGRATING PATTERNS OF EPISTASIS WITH FUNCTIONAL GENOMIC NETWORKSAwardee 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:5R21LM011919-02Contact PI / Project Leader:WONG, CAROLYN
Title:VISUALIZING HIGHWAY POLLUTION: A STUDY OF INTER-GENERATIONAL HEALTH COMMUNICATIONAwardee 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:1R21GM127915-01Contact PI / Project Leader:ZHANG, YU
Title:NEW IDEAS FOR GWAS LOCI: PREDICT FUNCTIONAL MUTATIONS, TARGET GENES AND TISSUES DRIVING DISEASE ASSOCIATIONAwardee 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:1R21LM012744-01Contact PI / Project Leader:CHU, HAITAO
Title:JOINT META-REGRESSION METHODS ACCOUNTING FOR POSTRANDOMIZATION VARIABLESAwardee 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:1R21LM012763-01A1Contact PI / Project Leader:GRANT, GREGORY R
Title:THE NEXT GENERATION OF RNA-SEQ SIMULATORS FOR BENCHMARKING ANALYSESAwardee 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:1R21LM012578-01Contact 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 YMSMAwardee 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:1R21LM012772-01A1Contact PI / Project Leader:KORKIN, DMITRY
Title:FUNCTIONAL CHARACTERIZATION OF GENETIC AND POST-TRANSCRIPTIONAL VARIATION USING MACHINE LEARNING METHODSAwardee Organization:WORCESTER POLYTECHNIC INSTITUTE

Thursday, August 9, 2018

UTC grade change







Download DAVID Knowledge base for S cerevisae taxid 4392

https://david.ncifcrf.gov/knowledgebase/DAVID_knowledgebase.html


NCBI Saccharomyces cerevisiae taxid 4932



Saccharomyces cerevisiae

Taxonomy ID: 4932 (for references in articles please use NCBI:txid4932)
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/


Tuesday, August 7, 2018

Monday, August 6, 2018