https://www.causeweb.org/cause/uscots/uscots21
Wednesday, June 30, 2021
Tuesday, June 29, 2021
Saturday, June 26, 2021
quantum speed up on alignment or alignment sequence analysis
alignment is a score matrix, so matrix method might speed the best alignment?
https://www.youtube.com/watch?v=p2hZL38tqAs
quantum solution on the maximum unique match might be a good starting point.
https://en.wikipedia.org/wiki/Sequence_alignment#Maximal_unique_match
alignment - free sequence
https://bioinformaticsreview.com/20170704/role-of-information-theory-chaos-theory-and-linear-algebra-and-statistics-in-the-development-of-alignment-free-sequence-analysis/
Square of Ajacency matrice give estimation of path
Quantum Walk and Graph search.
Qin: sequence alignment can be conerted all-2-all adjacent matrix. So, sequence alignment then might become a quantum walk and graph search problem.
Friday, June 25, 2021
GTEx factorization tissue specific regulation
sn-spMF: matrix factorization informs tissue-specific genetic regulation of gene expression
https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02129-6
UTC DUO VPN instructions
Starting 7/1/2021 access to UTC using the VPN will require the use of your UTCID, password, and Duo 2FA client. If you are using your UTCID and already have 2FA setup, the only change should be a prompt for you to send a Duo push to your Duo client.
If you are using your simcenter account to login, you will need to use your UTCID and password instead. We have tried to ensure that affiliates w/o UTCIDs have them generated by Central IT and sent to the user.
LINUX COMMAND LINE USERS will no longer BE ABLE TO USE THE COMMAND LINE to connect to the VPN. You will need to install the "UI" version of the package for your operating system and use it to connect. See Central IT's link below for more details.
Duo Setup
VPN Setup
Thursday, June 24, 2021
gtex aspera command line, ts117
reference:
https://www.ibm.com/support/pages/downloading-data-ncbi-command-line
conda create --name aspera
conda active aspera
-bash-4.2$ wget https://d3gcli72yxqn2z.cloudfront.net/connect_latest/v4/bin/ibm-aspera-connect-3.11.2.63-linux-g2.12-64.tar.gz
--2021-06-24 12:32:34-- https://d3gcli72yxqn2z.cloudfront.net/connect_latest/v4/bin/ibm-aspera-connect-3.11.2.63-linux-g2.12-64.tar.gz
Resolving d3gcli72yxqn2z.cloudfront.net (d3gcli72yxqn2z.cloudfront.net)... 13.249.125.124, 13.249.125.227, 13.249.125.202, ...
Connecting to d3gcli72yxqn2z.cloudfront.net (d3gcli72yxqn2z.cloudfront.net)|13.249.125.124|:443... connected.
HTTP request sent, awaiting response... 200 OK
Length: 38715569 (37M) [application/gzip]
Saving to: ‘ibm-aspera-connect-3.11.2.63-linux-g2.12-64.tar.gz’
100%[===========================================================================================================================>] 38,715,569 80.1MB/s in 0.5s
2021-06-24 12:32:35 (80.1 MB/s) - ‘ibm-aspera-connect-3.11.2.63-linux-g2.12-64.tar.gz’ saved [38715569/38715569]
-bash-4.2$ ll
(aspera) -bash-4.2$ sh ibm-aspera-connect-3.11.2.63-linux-g2.12-64.sh
Installing IBM Aspera Connect
Deploying IBM Aspera Connect (/home/hqin/.aspera/connect) for the current user only.
Install complete.
(aspera) -bash-4.2$ cd /scr/hqin/gtex/
(aspera) -bash-4.2$ ls
(aspera) -bash-4.2$ /home/hqin/.aspera/connect/bin/ascp -QTr -l 300M -k 1 -i /home/hqin/.aspera/connect/etc/asperaweb_id_dsa.openssh -W private-key-here dbtest@gap-upload.ncbi.nlm.nih.gov:data/instant/hongqin/82927 .
Release_Notes.phs000424.GTEx.v8.p2.MULTI.pdf. 100% 432KB 5.0Mb/s 00:00
Study_Report.phs000424.GTEx.v8.p2.MULTI.pdf.n 100% 94KB 5.0Mb/s 00:00
manifest_phs000424.GTEx.v8.p2.c1.GRU.pdf.ncbi 100% 43KB 5.0Mb/s 00:00
phs000424.v8.pht002740.v8.GTEx_Subject.data_d 100% 1200 5.0Mb/s 00:00
phs000424.v8.pht002740.v8.p2.GTEx_Subject.MUL 100% 6000 5.0Mb/s 00:00
phs000424.v8.pht002740.v8.p2.GTEx_Subject.var 100% 3264 5.0Mb/s 00:00
phs000424.v8.pht002741.v8.GTEx_Sample.data_di 100% 992 5.0Mb/s 00:00
phs000424.v8.pht002741.v8.p2.GTEx_Sample.MULT 100% 271KB 5.0Mb/s 00:01
phs000424.v8.pht002741.v8.p2.GTEx_Sample.var_ 100% 2032 5.0Mb/s 00:01
phs000424.v8.pht002742.v8.GTEx_Subject_Phenot 100% 89KB 5.0Mb/s 00:01
phs000424.v8.pht002742.v8.p2.GTEx_Subject_Phe 100% 293KB 11.2Mb/s 00:01
phs000424.v8.pht002742.v8.p2.c1.GTEx_Subject_ 100% 197KB 11.2Mb/s 00:01
phs000424.v8.pht002743.v8.GTEx_Sample_Attribu 100% 26KB 11.2Mb/s 00:01
phs000424.v8.pht002743.v8.p2.GTEx_Sample_Attr 100% 124KB 11.2Mb/s 00:01
phs000424.v8.pht002743.v8.p2.c1.GTEx_Sample_A 100% 3617KB 23.6Mb/s 00:02
phg000219.v4.GTEx_Pilot_Illumina5M.genotype-c 100% 698MB 292Mb/s 00:24
phg000219.v4.GTEx_Pilot_Illumina5M.genotype-o 14% 5337MB 290Mb/s 15:44 ETAc
......
(aspera) -bash-4.2$ Completed: 1448373288K bytes transferred in 40722 seconds
(291366K bits/sec), in 59 files, 7 directories; 16 files skipped or empty.
fine grained or not,
Your "Flamingo" is My "Bird": Fine-Grained, or Not
https://github.com/PRIS-CV/Fine-Grained-or-Not
https://arxiv.org/abs/2011.09040
Sunday, June 20, 2021
research.gov margin and line space problems
lines problem can be fixed by setting exact point, or at least 12 points.
margin problems are often due to auto-formating in special cases, such as ending, bulleting points.
https://www.galoisrepresentations.com/2019/09/06/nsf-application-tips-latex-edition/
make line at least 12 pt in WORD generally solve this problem.
It turns out that Adobe File Reduce can change the line space which will lead to warnings in resaerch.gov. Interestingly, WORD-saved pdf can pass the line-space check. Because the WORD file has a size limit of 10M, so I have to use small sized figures (save png as jpg, and then re-upload the figure to WORD). I used Photoshop to convert png to jpg to reduce WORD file size.
Saturday, June 19, 2021
‘invariant rate of ageing’ hypothesis
invariant rate of ageing
https://www.nature.com/articles/s41467-021-23894-3
https://github.com/fercol/ColcheroEtal2021NatComm
CVPR meeting notes
morphing attack detection
https://www.christoph-busch.de/projects-mad.html
https://ieeexplore.ieee.org/document/9246583
https://biolab.csr.unibo.it/FVCOnGoing/UI/Form/BenchmarkAreas/BenchmarkAreaDMAD.aspx
intel analytics zoo
https://github.com/intel-analytics/analytics-zoo
normalization method in dnn
https://normalization-dnn.github.io/
https://github.com/QinLab/network-controllability
https://www.youtube.com/watch?v=bwIgpxmWnWM
https://sites.google.com/view/fgvc8
https://fadetrcv.github.io/2021/
neural network architecture search: https://cvpr21-nas.com/
https://www.es.ele.tue.nl/cvpm21/program.pdf
microscopic image: https://cvmi2021.github.io/
The Cell Tracking and Mitosis Challenge
https://github.com/JonathonLuiten/TrackEval/blob/master/docs/MOTChallenge-Official/Readme.md
Friday, June 18, 2021
Thursday, June 17, 2021
facebook deepfake detection
https://www.theregister.com/2021/06/17/facebook_deepfake_identification/
https://github.com/vishal3477/Reverse_Engineering_GMs
Tweetable mathematical art with R
https://fronkonstin.com/2018/09/06/tweetable-mathematical-art-with-r/
Wednesday, June 16, 2021
Towards Deep Interpretable Predictions for Multi-Scope Temporal Events
https://www.nsf.gov/awardsearch/showAward?AWD_ID=2047843
Monday, June 14, 2021
aging clock
Royal society medicine webinar
sheep clock, universal mammalian clock
ribosomal DNA is a good clock, but not conserved among species
tortoise and lizard?
in human, female aging advantage is more pronounced in liver tissues. So far, epi aging clock is not related to fertility in human.
Shiqing Cai
https://www.nature.com/articles/s41586-020-2037-y
Sunday, June 13, 2021
tweet sentiment pytorch
https://github.com/BinaryBlackhole/Pytorch-implementation-twitter-sentiment-analysis-using-RNN
linear regression, MLE versus Bayesian MAP
https://towardsdatascience.com/frequentist-vs-bayesian-approaches-in-machine-learning-86ece21e820e
Thursday, June 10, 2021
de bivort lab, fly neural biology
http://debivort.org/contact.html
De Bivort agrees to my Q that stochastic gene regulation may contribute to the individuality.
Monday, June 7, 2021
biological network across scales
https://reintegratingbiology.org/wp-content/uploads/2019/12/Netwoks-Across-Scales-Gustavo-Caetano-Anolles.pdf
Friday, June 4, 2021
Baez, category data, permutation
https://math.ucr.edu/home/baez/
https://twitter.com/johncarlosbaez
permutations: https://math.ucr.edu/home/baez/permutations/
NSF Computational Data-Enabled Science and Engineering
NSF has released a new version of its Computational Data-Enabled Science and Engineering program. The CDS&E program encourages research that pushes the envelope of science and engineering through computation and data, welcoming proposals in any area of research supported by the participating divisions. A proposal may address topics that develop or enable interactions among theory, computing, experiment, and observation to achieve progress on hitherto intractable science and engineering problems.
The participating divisions and their deadlines are below. Each division has specific emphasis areas. See the solicitation for details: https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=505920. I strongly encourage everyone whose work falls under one of these divisions to explore the solicitation and see if it would make sense to prepare a proposal!
Directorate | Division and Program | Submission Window or Target Date |
ENG | Division of Chemical, Bioengineering, Environmental, and Transport Systems | September 01, 2021 - September 15, 2021 September 01- September 15, Annually Thereafter |
ENG | Division of Civil, Mechanical and Manufacturing Innovation | September 01, 2021 - September 15, 2021 September 01- September 15, Annually Thereafter |
MPS | Division of Mathematical Sciences | September 01, 2021 - September 15, 2021 September 01- September 15, Annually Thereafter |
MPS | Division of Chemistry - Chemical Catalysis (CAT), Chemical Structure, Dynamics and Mechanisms-A (CSDM-A), Chemical Structure Dynamics and Mechanisms-B (CSDM-B), Chemical Synthesis (SYN), Chemical Theory, Models and Computational Methods (CTMC) | September 01, 2021 - September 30, 2021 September 01 - September 30, Annually Thereafter |
MPS | Division of Materials Research | October 15, 2021 October 15, Annually Thereafter |
MPS | Division of Astronomical Sciences - Advanced Technologies and Instrumentation | October 01, 2021 - November 15, 2021 October 01 - November 15, Annually Thereafter |
CISE | Office of Advanced Cyberinfrastructure | October 01, 2021 - November 01, 2021 October 01 - October 31, Annually Thereafter |
ENG | Division of Electrical, Communications and Cyber Systems | October 01, 2021 - November 01, 2021 October 01 - October 31, Annually Thereafter |
MPS | Division of Chemistry - Chemical Measurement and Imaging (CMI), Chemistry of Life Processes (CLP), Environmental Chemical Sciences (ECS), and Macromolecular, Supramolecular and Nanochemistry (MSN) | October 01, 2021 - November 01, 2021 October 1 - October 31, Annually Thereafter |
MPS | Division of Astronomical Sciences - Astronomy and Astrophysics Research Grants | October 01, 2021 - November 15, 2021 October 01 - November 15, Annually Thereafter |
MPS | Division of Physics: Investigator-Initiated Research Projects | Per specific program |
gtex
Your request #29078: "Develop a multi-view knowledge-based neural network model to integrate heterogeneous genomics data and detect conserved mechanisms for cellular lifespan regulation" for access to NCBI dbGaP Program datasets has been authorized by your institutional Signing Official (Meredith Perry) and forwarded to the responsible Data Access Committee(s) (DAC) for review.
The result of DAC review will be communicated by email. If access is approved, that communication also will contain instructions for access to the datasets.
The DAC(s) responsible for reviewing your request can be contacted by email to
- Genotype-Tissue Expression (GTEx): nhgridac@mail.nih.gov
Thursday, June 3, 2021
student research work hours at UTC
during semester, 20 hours maximal
during summer, 30 hours maximal, more than this need to be classified as full-time employee.
Wednesday, June 2, 2021
UTC PhD require 72 credit hours
UTC PhD course Requirements:
Doctoral students must complete a minimum of 72 hours beyond the bachelor’s degree, exclusive of credit for the master’s thesis. These hours must include a minimum of 24 semester hours in Doctoral Research and Dissertation and a minimum of 48 semester hours in other courses. At least 12 of the required 24 research and dissertation hours must be in Dissertation from an established concentration area.
UTC faculty website
I wanted to provide you with an update concerning your faculty web profile (http://www.utc.edu/faculty/hong-qin/). Communication and Marketing were able to migrate your content over to the following pages:
Events: https://blog.utc.edu/hong-qin/events/
ICompBio: https://blog.utc.edu/hong-qin/icompbio/
CyberCorps: https://blog.utc.edu/hong-qin/cybercorps/
I went ahead and hyperlinked these pages for you on your faculty web profile (http://www.utc.edu/faculty/hong-qin/), which will update in the next few hours to display the links. Edits in Digital Measures are pushed to your webpage on a 12-hour cycle. By the time you get this email, the changes may be reflected. If you wish to edit the list of links on your faculty web profile, you can do so by logging into digital measures and clicking on “Biography.” (Guide here: https://utc.teamdynamix.com/TDClient/2717/Portal/KB/ArticleDet?ID=131677#Topic3)
To edit any of the pages on the blog (such as https://blog.utc.edu/hong-qin/cybercorps/) you can do so by going to https://blog.utc.edu/ and clicking “Log In” at the bottom of the page. Here is a direct link to the blog log-in page: https://blog.utc.edu/wp-login.php.
Hebbian, Oja learning
14:16:01 From Hong Qin to Everyone:
https://en.wikipedia.org/wiki/Lasso_(statistics)
14:24:48 From Trevor Peyton to Everyone:
https://en.wikipedia.org/wiki/Hebbian_theory
14:25:25 From Trevor Peyton to Everyone:
https://en.wikipedia.org/wiki/Generalized_Hebbian_algorithm
14:26:08 From Trevor Peyton to Everyone:
https://en.wikipedia.org/wiki/Oja%27s_rule
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