neutron scattering and HPC

F. Bao, math depart

HPC, neutro scattering

I(Q,omega), Q is the 3D neutron wave vector transfer
omega is the energy transfer between neutron and material sample.

I = S*R (convolution).

S is modeled scattering function, interest from material science.

Partition all parameters into several subvectors.

Model: silicon crystal structure with first to fourth nearest neighbor interactions

hierarchical parameter space

latin hypertube sampling

Eric Lingerfelt, Yawei Hui, CS
Richard Archibald, math
Oliveier Delaire, materials

UTC web training

webtrain.utc.edu

ZSpacve, 3D virtual reality learning

Virtual reality

http://zspace.com/

bio3250 genetics, review exam2 on linkage, ch6 chromosome

review exam2,

review ch6 exercise

prepare for ch6 exam

Sample videos, Developing YouTube video to enhance education and training in bioinformatics and genomics

Selected Bioinformatics Videos

• Annotate ORF using APE
• Design PCR primers to amply a fragment that contains the mutation on msh2
• Analyzing PCR primer using ApE
• Protein structure visualization using SWISS PDB Viewer
• Translation from DNA to protein, Python
• Find Restriction Enzyme recognition sites, Python demo

Seletec Computing with R Videos

• A quick introduction to basic R usage (in RStudio)
• Serial dilution data analysis using R
• Standard curve analysis using R
• Flow cytometry data analysis, clustering, using R
• Convert Excel file to csv format, read into R and plot. 
• Hierarchical Clustering by hclust in R on a distance matrix between four cities.
• Hierarchical clustering illustrated by Lady Gaga using hclust() in R.
• Retrieve and analyze a gene expression data set from NCBI GEO in R
• How to change R working directory in Windows
• How to use 'match' function in R, and How to use R match() function to merge different data sets
• Multiple regression and causal factor identification using R
• Introduction to epidemiology using the London Cholera example (simulation needs improvement)
• Make solution demo in Rstudio, BIO125, spring 2015

Other tutorial videos

• Serial dilution demo, paper and coloring exercises

Animation on herd immunity
https://imgur.com/gallery/8M7q8#J7LANQ4

cancer bad luck controversies

cancer bad luck controversies
http://science.sciencemag.org/content/347/6217/78

http://erlichya.tumblr.com/post/108802484899/cancer-bad-luck-the-first-law-of-holes


http://www.vox.com/science-and-health/2017/3/3/14792174/half-scientific-studies-news-are-wrong

Carl Zimmer, personal genome

60G raw data

http://scopeblog.stanford.edu/2017/03/09/what-can-you-learn-from-your-own-genome-science-writer-carl-zimmer-found-out/

todo: lectin hemoglobin modeling

lectinhemoglobin, optimal oxygen concentration, respiratory, o

*** Qin Fall 2017 course schedule

Fall 2018,
8/21 Mon, classes begin
October 2-13 (Monday-Friday)

October 16-17 (Monday-Tuesday)

Fall Break - no classes

December 4 (Monday)	Last day of classes for Fall semester
December 5 (Tuesday)	Reading Day
December 6-12 (Wednesday-Tuesday)	Final Examinations

• FA17.BIOL.4999.48263: Computational Genomics (not currently available)
• FA17.CPSC.4999.48778: Computational Genomics (not currently available)
• FA17.CPSC.5910.48779: Computational Genomics (not currently available)

48263, 48778, 48779

*** Alzheimer's Disease NIH, data resources

Limited Competition for the Renewal of the National Cell Repository of Alzheimer's Disease (NCRAD) (U24)

https://grants.nih.gov/grants/guide/pa-files/PAR-17-214.html

• The NIA Genetics of Alzheimer's Disease Data Storage Site (NIAGADS)
• The NIA Genomic Center for Alzheimer's Disease (GCAD)
• The National Cell Repository for Alzheimer's Disease (NCRAD)
• The National Alzheimer's Coordinating Center (NACC)
• The Database of Genotypes and Phenotypes (dbGaP)
• The Alzheimer's Disease Genetics Consortium (ADGC)
• The Alzheimer's Disease Centers (ADCs)
• Cohorts for Heart and Aging Research in Genomic Epidemiology (CHARGE)
• The Alzheimer's Disease Neuroimaging Initiative (ADNI)
• The National Alzheimer’s Project Act (NAPA) and the related milestones  
• Information relevant to Alzheimer's Disease Related Dementias (ADRD)
• Other websites designed to store and distribute data related to AD

drug database of aging

Aging Cell. 2017 Mar 16. doi: 10.1111/acel.12585. [Epub ahead of print]

The DrugAge database of aging-related drugs.

https://www.ncbi.nlm.nih.gov/pubmed/28299908

GPU server

---------- Forwarded message ----------
From: Thinkmate <tmsales@thinkmate.com>
Date: 2017-02-13 1:54 GMT-05:00

Toll Free: 1-800-371-1212 Fax: 781-688-2260 www.thinkmate.com

This product email has been sent from Thinkmate at the request of LD

	GPX XT24-2460V4-10GPU My System February 13th, 1:35 am EST Configured Price: $35,656.00
Selection Summary
Barebone	Intel C612 Chipset - Dual 1-Gigabit Ethernet - 4U GPU Server - 2000W (2+2) Redundant Power Supply
Processor	2 x Eight-Core Intel Xeon Processor E5-2620 v4 2.10GHz 20MB Cache (85W)
Memory	24 x 64GB PC4-19200 2400MHz DDR4 ECC Registered Load-Reduced DIMM
Boot Drive	No SATA Disk on Module for boot
Hard Drive	2 x 2.0TB SATA 6.0Gb/s 7200RPM - 2.5" - Seagate Enterprise Capacity (512e)
Optical Drive	No Optical Drive Support
Video Card	Integrated Video (Included with Motherboard)
Co-Processors	8 x PNY NVIDIA GeForce GTX 1070 Founders Edition 8GB GDDR5 (1xDVI, 1xHDMI, 3xDP)
Network Card	Intel Ethernet Server Adapter I350-T2V2 Dual Port (2x RJ-45)
Accessories	Replacement Chassis Top Cover (required for NVIDIA GeForce GTX graphics card support)
Power Protection	APC Smart-UPS 3000VA LCD 208V - 2U Rackmount
Operating System	No Operating System (Hardware Warranty Only, No Software Support)
Warranty	3 Year Advanced Parts Replacement Warranty
Tech Specs
Barebone
Memory Technology	DDR4 ECC Reg
North Bridge	Intel C612
Form Factor	4U
Color	Black
Memory Slots	24x 288-pin DIMM Sockets
Graphics	ASPEED AST2400 BMC
Ethernet	Dual Gigabit Ethernet Ports with Intel i350
Power	2000W Redundant Power Supplies with PMBus
External Bays	24x 2.5" Hard drive bays
Expansion Slots	11x PCI-E 3.0 x16 (FH, FL) slots 1x PCI-E 3.0 x8 (in x16) slots Single Root Complex
Back Panel	4x USB 3.0 ports 2x RJ45 Gigabit Ethernet LAN ports 1x RJ45 Dedicated IPMI LAN port 1x VGA Connector
Dimensions (WxHxD)	17.2" (437mm) x 7.0" (178mm) x 29" (737mm)
SATA 6Gbps AHCI Controller	Intel C612
SATA 6Gbps AHCI Ports	6
SATA 6Gbps SCU Controller	sSATA
SATA 6Gbps SCU Ports	4
Processor
Product Line	Xeon E5-2600 v4
Socket	LGA2011-v3 Socket
Clock Speed	2.10 GHz
QuickPath Interconnect	8.0 GT/s
Smart Cache	20MB
Cores/Threads	8C / 16T
Intel Virtualization Technology	Yes
Intel Hyper-Threading	Yes
Wattage	85W
Memory
Technology	DDR4 Load-Reduced
Type	288-pin LRDIMM
Capacity	24 x 64 GB
Speed	2400 MHz
Error Checking	ECC
Signal Processing	Registered
Hard Drive
Storage Capacity	2 x 2.0TB
Interface	6.0Gb/s Serial ATA
Rotational Speed	7200RPM
Cache	128MB
Format	512e
Co-Processors
Memory Capacity	8 GB
Processor	GeForce GTX 1070 (GP104)
Core Clock Speed	1506 MHz (1683 MHz Boost Clock)
Multi-GPU Technology	NVIDIA SLI Ready
DisplayPort Output	3x DisplayPort 1.4
DVI Output	1x Dual-Link DVI
HDMI Output	1x HDMI 2.0b
Network Card
Transmission Speed	1-Gbps Ethernet
Port Interface	RJ-45
Host Interface	PCI Express 2.1 x4
Cable Medium	Copper
VT for Directed I/O (VT-d)	No

Product Page:
http://www.thinkmate.com/system/gpx-xt24-2460v4-10gpu/189938
Thinkmate's Homepage:
http://www.thinkmate.com/

All prices subject to change.

ch5 exam review

2 points cross
3 point cross
fruit fly genetic map
chi-sq
contingency table

blackboard, creast test with random blocks

http://edtech.mst.edu/media/informationtechnology/edtech/documents/blackboard91/Random_Question_Pool.pdf

negative crossover interference

Negative Crossover Interference in Maize Translocation Heterozygotes

http://www.genetics.org/content/159/4/1717

Can negative crossover interference be predicted from DNA sequences? 

bio3250 three point cross, ch5, part 4

Zoom video
Socrative
three point cross.

Exam 2a on Friday and Saturday.

quantum experience, IBM

quantum experience, IBM

quantum Q,

github customized domain name setup

https://help.github.com/articles/troubleshooting-custom-domains/#github-repository-setup-errors

applejack:_s hqin$ dig compmodelmatch.github.io

; <<>> DiG 9.8.3-P1 <<>> compmodelmatch.github.io

;; global options: +cmd

;; Got answer:

;; ->>HEADER<<- opcode: QUERY, status: NOERROR, id: 12824

;; flags: qr rd ra; QUERY: 1, ANSWER: 2, AUTHORITY: 4, ADDITIONAL: 4

;; QUESTION SECTION:

;compmodelmatch.github.io. IN A

;; ANSWER SECTION:

compmodelmatch.github.io. 3600 IN CNAME github.map.fastly.net.

github.map.fastly.net. 27 IN A 151.101.56.133

bigdata visualization

https://alistapart.com/article/big-data-visualization-with-meaning?utm_content=bufferc6739&utm_medium=social&utm_source=twitter.com&utm_campaign=buffer

transfer bigdata

http://moo.nac.uci.edu/~hjm/HOWTO_move_data.html

respondus lockdown broswer add password to blackboard tests

These password are lockdown browser to ensure the test canonly taken through lockdown browser. These password should be not be removed. Once removed, "error" occur in exam and have to be fixed.

rasperry pi,

4273 pi

https://4273pi.org/loan-boxes/