biomedical data science

PH525x series - Biomedical Data Science

http://genomicsclass.github.io/book/

PSORT WWW Server

PSORT is a computer program for the prediction of protein localization sites in cells. It receives the information of an amino acid sequence and its source orgin, e.g., Gram-negative bacteria, as inputs. Then, it analyzes the input sequence by applying the stored rules for various sequence features of known protein sorting signals. Finally, it reports the possiblity for the input protein to be localized at each candidate site with additional information.

https://psort.hgc.jp/

big data meetings

http://www.kdnuggets.com/meetings/

https://www.cvent.com/events/2017-ieee-international-conference-on-big-data-big-data-/registration-727b98832f12467d92cab7855ec03080.aspx?fqp=true

https://theinnovationenterprise.com/summits/big-data-innovation-summit-boston-2017

ebird

Ebird

https://confluence.cornell.edu/display/CLOISAPI/eBird+API+1.1 

https://pypi.python.org/pypi/ebird-api/2.0.0 

https://github.com/ropensci/rebird 

hubzero

The Hub Concept for Scientific Collaboration

https://hubzero.org/resources/12

dynamical equilibrium

I was challenged today to provide examples of dynamical equilibrium

I mentioned that riding a bicycle is an example.

Later, it occurred to me that the Red Queen theory is another example.

A UCLA math prof seem to argue that dynamical equilibrium is a oxymoronic word, 'homeostasis' implies stationary.  To his critique on stationary interpretation of homeostasis, I disagreed. I offered the predator-prey model as an example of dynamical equilibrium.

23andMe, open data set

Reposivie 23andMe open collection

https://discover.repositive.io/collections/f3f50a6c-a27c-431a-93dc-95587b013a14

Tennessee GDP by industry

Tennessee GDP by industry

http://cber.haslam.utk.edu/bea/gspdata.htm

CAR (chimeric antigene receptor)

https://en.wikipedia.org/wiki/Chimeric_antigen_receptor

big data resources

https://nysci.org/event/big-data-fest/

https://welikia.org/download/scientific-data/

skin deg

EG:

asymmetry ratio, mother-daughter, and image evaluation

Cytosim.org

Nedelec lab, EMBL
http://www.cytosim.org/

Mogilner lab codes

https://cims.nyu.edu/~mogilner/codes.html

Sean Davis, github, computational genomics

Sean Davis, NCI, github provides many tutorials using R for comp genomics
https://github.com/seandavi

change disk size of VirtualBox, in osX

http://osxdaily.com/2015/04/07/how-to-resize-a-virtualbox-vdi-or-vhd-file-on-mac-os-x/

applejack:MacOS hqin$ VBoxManage modifyhd /Users/hqin/VirtualBox\ VMs/windows10/

Logs/                windows10.vbox       windows10.vbox-prev  windows10.vdi        

applejack:MacOS hqin$ VBoxManage modifyhd --resize 40000 /Users/hqin/VirtualBox\ VMs/windows10/windows10.vdi 

0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%

applejack:MacOS hqin$ VBoxManage showhdinfo  /Users/hqin/VirtualBox\ VMs/windows10/windows10.vdi 

UUID:           3a38dc04-987c-46be-9dda-1ded6cece216

Parent UUID:    base

State:          created

Type:           normal (base)

Location:       /Users/hqin/VirtualBox VMs/windows10/windows10.vdi

Storage format: VDI

Format variant: dynamic default

Capacity:       40000 MBytes

Size on disk:   20154 MBytes

Encryption:     disabled

In use by VMs:  windows10 (UUID: 46645298-3095-4fa0-8b95-f625b89c4b24)

UTC syllabus tempalte 2017-2018

https://www.utc.edu/walker-center-teaching-learning/information-services/syllabus-resources.php

As you may know, UTC adopted Quality Matters (QM) in 2015. QM provides a set of standards for course design based on  practices proven to enhance student persistence and increase faculty content focus time by reducing focus on course management issues, for example, with course and program alignment as the central principle guiding the standards. Having our course outcomes aligned with course content, activities, and assessment is very important for demonstrating authentic student learning and institutional effectiveness. Many of our courses at UTC have been designed with QM standards and we are moving forward to include QM standard alignment in every UTC course syllabus. As a result, the syllabus template has been updated to include additional required items to address QM standards. These additions to the syllabus will improve student learning and support our continued efforts of curriculum mapping.

I am pleased that the updated syllabus template includes alignments to 13 QM standards. The syllabus checklist has also been updated and explains each of the items in the syllabus template; please use both of these documents when developing your syllabi. An additional benefit to using the syllabus template is that it is in an accessible format. Accessibility is a major initiative on campus and it is our goal that all instructional materials be accessible. The syllabus template also includes a new standardized statement about course evaluations that is required for every syllabus. This statement will assist us in communicating with students about the availability of course evaluations and the importance of completing them. As always, syllabi that contain the required components assist us with SACS COC accreditation.

 If you have questions about the updated syllabus template, please contact the Walker Center for Teaching and Learning at 425-4188 or wctl@utc.edu.

openflow, wireless communication network simulation

http://archive.openflow.org/wp/getstarted/

wireless communication simulation

kinetic modeling

https://github.com/Kinetic

BLENDER GIS

blender +  GIS

https://en.wikipedia.org/wiki/Blender_(software) . 3D computer graphics

open computer vision openCV

http://opencv.org/

iTEST

18 pairs of students, Saturday labs.

AI and machine learning

Hologram on smart phone, tablets.


TODO:
 Statement on Saturdays
 Cost for Saturdays, raspberry pi

autism, ADHD, neural diverse

Neurodiversity: autism and ADHD. Autism is an expensive diagnosis, many kids from poor family are only diagnosed with ADHD.

Hispanic family expect kids to generate income after high-schools.

school bus

Cancer research grand challenge

Grand Challenge Awards

Opp ID: 161829 | Collaboration or Cooperative Agreement Research | Last edited on 26 Jun 2017

• Full Details

Website

https://www.cancerresearchuk.org/funding-for-researchers/how-we-deliver-research/grand-challenge-award?wssl=1

Sponsor

Cancer Research UK (CRUK)

Amount

Upper  £20,000,000GBP

Each shortlisted team will be awarded up to £30,000 seed funding.

Winning teams will receive an award of up to £20 million, typically over five years.

Applicant Type

Individuals: Early Career and Emerging in Field

Individuals: Mid-Career to Established in Field

Citizenship or Residency

Unrestricted

Activity location

Unrestricted

Abstract

Grand Challenge awards are the most ambitious cancer research grants in the world. They're intended to catalyse a revolution in how we prevent, diagnose, and treat cancer by bringing together the brightest minds around the globe, providing the freedom to undertake innovative, game-changing research.

CRUK are looking for applications from interdisciplinary teams with novel, exciting ways of solving one of seven Grand Challenges, which together encompass some of the most important unanswered questions in cancer research. If applicants can convince CRUK they're on to something extraordinary, CRUK will give the team up to £20m to prove it. Cancer Research UK is seeking scientific adventurers who are willing to take risks in exchange for the ultimate reward - making cancer a disease that no longer inspires fear.

An independent advisory panel have now set 8 new Grand Challenges and are inviting the world's top scientists to come together proposing novel ways to tackle them.

- Tissue Specificity
Devise approaches to prevent or treat cancer based on mechanisms that determine tissue specificity of some cancer genes.

- Tumour Vaccinology
Create novel tumour vaccinology approaches that establish or enhance successful immune responses beyond what is revealed by current checkpoint therapy.

- Treatment Regimens
Define mechanistic rules for combinatorial treatments to overcome resistance and avoid toxicity.

- Dormancy
Identify and target tumour cells that remain dormant for many years after seemingly effective treatment.

- Lethal vs non-lethal
Distinguish between lethal cancers which need treating, and non-lethal cancers that don't.

- Artificial Intelligence
Detect cancer earlier by interrogating medical and non-medical data sets using machine and deep-learning.

- Microbiota
Improve treatment responses by manipulating the composition and status of the microbiota.

- Cancer Causes
Determine the mechanisms that cause cancer without known mutagenesis, such as obesity, in order to devise novel interventions. 
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Eligibility

CRUK will support the best scientists from around the world and enable the optimal mix of disciplines and approaches. Teams are expected to be international in nature, with roughly 25% of the team being based in a different country from the rest of the consortium. There is no requirement for any of the team members to be based in the UK.

Academic-commercial collaboration is encouraged within individual Co-Investigator-led work packages.

Applicants are encouraged to consider the balance of gender and career-stage within their teams.

Teams are encouraged to look for opportunities to build patient involvement into their research. At a minimum, each team is expected to have a patient representative with a clearly defined role and remit. 
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download all file from Docscan

Turn on webserver of DocScan

This is an open access to anyone on the network.

Failed to work on osX

wget -r -np -l 1 -A zip http://example.com/download/

wget -r -l1 -H -t1 -nd -N -np -A.mp3 -erobots=off [url of website]

In virtualbox windows, use flastget3 to download all files from 192.168.1.10*

Alternatively, iTunes can import all the PDFs

wget to osX

install wget to applejack mac osX

sudo port install wget