Open Notebook: March 2020

Tuesday, March 31, 2020

MSI laptop workstation

https://us.msi.com/Workstation/WS72-Workstation-6th-Gen/Specification

Saturday, March 28, 2020

GPUs

I need to purchase a GPU workstation for my lab. Could you share your views on the following two options? I need to pick one for the ordering. Thanks, -- Hong

#1 DELL Precision 5820 Tower Workstation

Intel Xeon W-2145

Nvidia Quadro RTX5000, 16GB, 4DP, VirtualLink (XX20T)

64GB 4x16GB DDR4 2666MHz RDIMM ECC Memory

1^st Hard Drive 1T SATA Class 20 Solid State Drive

2^nd Hard Drive 2T 7200 SATA Hard drive

Price $4,885

https://www.dell.com/en-us/work/shop/desktops-all-in-one-pcs/precision-5820-tower-workstation/spd/precision-5820-workstation/xctopt5820us_2?configurationid=4b81b8ff-2c32-4a20-b6d6-365d32682c07

#2 ALIENWARE AURORA RYZEN™ EDITION GAMING DESKTOP

AMD Ryzen™ 9 3950X (16-Core, 64MB L3 Cache, Max Boost Clock of 4.7GHz)

NVIDIA® GeForce RTX™ 2080 Ti 11GB GDDR6 (OC Ready)

64GB Dual Channel HyperX™ FURY DDR4 XMP at 3200MHz

1TB M.2 PCIe NVMe SSD (Boot) + 2TB 7200RPM SATA 6Gb/s (Storage)

Price $3,937.99

https://www.dell.com/en-us/shop/dell-desktop-computers/new-alienware-aurora-ryzen-edition-gaming-desktop/spd/alienware-aurora-r10-desktop/wdryzr1040?view=configurations&configurationid=52250cfa-fcb4-4187-8bf6-14aa0ae4976c

I did a little bit of investigation.

https://technical.city/en/video/GeForce-RTX-2080-Ti-vs-Quadro-RTX-5000

https://www.notebookcheck.net/Quadro-RTX-5000-Laptop-vs-GeForce-RTX-2080-Ti-Desktop_9852_9526.247598.0.html (performance about representative benchmark problems)

Please see the above links, which compare RTX 5000 with RTX 2080Ti. Seemingly 2080Ti outperforms 5000.

Therefore, I prefer Option 2.

One machine uses Quadro-branded GPU and the other uses GeForce-branded GPU. According to the following wikipedia link:

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

"The GPU chips on Quadro-branded graphics cards are identical to those used on GeForce-branded graphics cards. The Quadro cards differ substantially in their ECC memory and enhanced floating point precision, which tremendously reduce the risks of calculation errors. " So it seems that Quadro has better performance in satisfying high requirement on computation accuracy than GeForce.

Also, on the same page, it says

"A Geforce card focuses more on texture fillrates and high framerates with lighting and sound, but Quadro cards prioritize wireframe rendering and object interactions."

Maybe that's why GeForce is listed more suitable for gaming, as shown in Usage Specific GPU on this page

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

Thursday, March 26, 2020

UTC covid on summer events

sent to UTC info

Greetings from the Office of Research,

Each summer, the UTC campus hosts numerous grant-sponsored residential or group activities – for conferences, academic camps, research experiences, etc. With the ongoing disruptions caused by Covid-19 and uncertainty about the duration of the impact, you may have concerns about whether it will be feasible to hold your planned sponsored group / residential program activities on campus for Summer 2020. Based on initial information from some sponsors, we anticipate that our funders will be understanding if activities are unable to take place. With the situation being so dynamic, many sponsors have not yet formulated or communicated specific guidelines or parameters. However, we wanted to provide this guidance to you, in case it is helpful for purposes of planning and preparation.

· Consider Timing & Scheduling: At present, it seems very unlikely that activities scheduled for April or May will be able to take place on campus. Events scheduled for June or July might be able to take place, but there is significant uncertainty on this.

· Defer to Next Summer: If your grant award or sponsor will allow, our recommendation is to defer your planned summer activity to next summer and seek a no-cost extension to extend your award end-date, as needed. For example, this would be the best option for NSF REU programs.

· Seek Guidance from Sponsor: If you are the PI or PD on a grant with a summer program component, please begin working with your sponsor to determine the next steps which may include some combination of deferring activities into a future year, getting a no-cost extension to extend the end-date, changing the scope of your project, etc.

If you have any questions or need assistance, please contact ORSP staff Angie-Johnson@utc.edu or Tracey-Woodbury@utc.edu.

Tuesday, March 24, 2020

MacOS Jupyternote book pdf feature bug fix

On my new Macbook pro, I cannot generate PDF from JupyterNotebook.

This is old OS.

I added the following line to .bash_profile.

#Texlive 20200323

export PATH=$PATH:/Library/TeX/texbin

I then

source .bash_profile

I then restart JupyterNotebook, and pdf file can be generated.

Qin, data science sample materials

Youtube:
R, convert excel to csv, import to R and plot
https://www.youtube.com/watch?v=-ltUZ6YXwK8&lc=z230dhejioemcfr0nacdp434aqtxwjwrh0ss4h03ujpw03c010c

Sunday, March 22, 2020

data science for biologist, course information

Data Science for Biologists

Both Python and R languages will be taught for data analysis. Students will form team to complete projects of data analysis.

Students will given an academic version of DataCamp account to take data-camp modules.

Sample student projects:
https://youtu.be/-bk-Aj0pTFo. Frog voice analysis
https://youtu.be/9pbCY0zLqr4 Molecular Docking and drug screen
https://youtu.be/y2PiVGrwh5E MD simulation and machine learing
https://youtu.be/1Qv7GiPg-uE R-shiny data analysis

Saturday, March 21, 2020

Stanford web security course materials

https://web.stanford.edu/class/cs253/

Thursday, March 19, 2020

AI image analysis reference

Article Citation:

Famke Aeffner, Kristin Wilson, Nathan T. Martin, Joshua C. Black, Cris L. Luengo Hendriks, Brad Bolon, Daniel G. Rudmann, Roberto Gianani, Sally R. Koegler, Joseph Krueger, and G. Dave Young (2017) The Gold Standard Paradox in Digital Image Analysis: Manual Versus Automated Scoring as Ground Truth. Archives of Pathology & Laboratory Medicine: September 2017, Vol. 141, No. 9, pp. 1267-1275.

Wednesday, March 18, 2020

cyber security with R

https://rud.is/b/r-cyber/ r-cyber

https://isc.sans.edu/forums/diary/ISC+snapshot+rcyber+with+rudis/24996/

data driven cyber security

Students of Concern, online education issues

Faculty & Staff Colleagues,

Students of Concern

As we transition to online instruction, identifying Students of Concern may become more difficult. However, as it has been for each of us, we anticipate this change will be significant for our students during this challenging time. The Office of Student Outreach and Support (SOS) will remain open and available to assist and refer students to University and community resources, in addition to supporting faculty and staff with any student concerns. We encourage faculty and staff to continue submitting Students of Concern via the Community Member of Concern form: www.utc.edu/coc.

Here are some quick tips for things to look for and reasons to submit a referral:

Students not logging into Canvas for period of time and/or not attending Zoom (digital) lectures.
Students not completing work on time or at all.
Students express fear or negative emotions in discussion boards or assignments.
Students reporting mental or physical health concerns (related and unrelated to COVID-19).
Students report being a victim of sexual misconduct, relationship violence, or stalking.

*Faculty are well-placed to spot the warning signs listed above as you will be working closest with our students during this time. That role makes your referrals particularly valuable!

Scrappy’s Cupboard

With the recent changes to the University’s operations related to COVID-19, Scrappy’s Cupboard food pantry will continue to be open for students experiencing food insecurity. Students located in the Chattanooga area may access Scrappy’s Cupboard Monday – Friday from 8:00 am to 5:00 pm by setting up an appointment. To set up an appointment, students should visit our website (https://www.utc.edu/student-outreach/scrappys-cupboard/use.php) or call (423) 425-2299. If students are not located in the Chattanooga area and need assistance, they should contact the Office of Student Outreach & Support (SOS) by e-mailing sos@utc.edu or calling (423) 425-2299. The SOS team will be happy to assist them in accessing resources in their local community.

Most importantly, in order to keep Scrappy’s Cupboard open, we will continue to need donations from our community members. We accept all unexpired, unopened, non-perishable food and personal care items. New this term, we have also begun accepting new and gently used clothing items. All clothing items MUST be clean when donated.

Items currently needed include:

Milk (boxed or canned)
Toilet Paper
Sports Drinks (Powerade/Gatorade)
Pasta
Pasta Sauce
Canned Chicken/Tuna
Cereal
Hand Soap
Canned Fruit
Granola/Breakfast Bars
Gently Used and Clean Jackets/Coats, Hats, Mittens, Pants, Sweaters, Shirts

If you would like to donate to Scrappy’s Cupboard, please call (423) 425-2299 or e-mail scrappyscupboard@utc.edu to set up a time to drop off donations. You can also provide a monetary donations by visiting the UC Foundation Website by clicking on this link. When donating online, please choose "Other" for the "Designation" and enter "Scrappy's Cupboard".

Student Emergency Fund

The Denise and Tim Downey Student Emergency Fund (SEF) will also remain operational during this time. However, available funds are very limited. Please continue to refer students to the SEF application (http://www.utc.edu/sefapply) as additional funding may become available in the coming weeks.

Funds can be used for:

Essential academic needs (e.g. books and supplies).
Replacement of lost personal items due to fire, theft, flood, etc.
Housing needs (e.g. securing short-term housing, security deposits, assistance with utilities, etc.).
One-time / non-recurring medical expenses.
Emergency expenses related to dependents (e.g. childcare).

If you would like to donate to the Student Emergency Fund, please visit the the UC Foundation Website by clicking on this link. When donating online, please choose "Other" for the "Designation" and enter "Student Emergency Fund".

Sincerely,

Office of Student Outreach & Support