Sunday, April 30, 2017

*** sqlite 3 rls.db , result table

sqlite3 on rls.db


.open rls.db
.separator ::
.headers on
.mode column
select distinct experiment from result_experiment limit 20;
.indices set
.width 5
select * from result  limit 1;

/* The following select can take rls and its reference rls */
select experiments,set_name,set_strain,set_background,set_genotype,
 from result  limit 2;

SELECT experiments,set_name,set_strain,set_background,set_genotype,
 FROM result; 

SELECT experiments,set_name,set_strain,set_background,set_genotype,
 set_lifespan_mean,ref_genotype,ref_lifespan_mean, ranksum_p
 FROM result
 WHERE ranksum_p < 0.05

select * from my_RLS_out limit 5;    

select distinct set_genotype from my_RLS_out; 

sqlite> .indices result


#output result table into csv
sqlite> .headers on
sqlite> .mode csv
sqlite> .output qintest.csv
sqlite> select * from result;
sqlite> .quit
emc313b02:data hqin$ ll
total 146712
-rw-r--r--  1 hqin  staff   8.5M Apr 30 23:31 qintest.csv
lrwxr-xr-x  1 hqin  staff    15B Apr 30 20:07 rls.db -> rls_20160802.db
-rw-------  1 hqin  staff   8.3M Aug  9  2016 rls_2016-08-02.csv
-rw-------  1 hqin  staff    55M Aug  9  2016 rls_20160802.db
emc313b02:data hqin$ less qintest.csv 
emc313b02:data hqin$ open qintest.csv 

emc313b02:data hqin$ 

Based on
Sqlite database is not easily convertable to mysql database. 

osX mysql



ants identification key

Tuesday, April 25, 2017

Monday, April 24, 2017

bootstrap of nat-lifespan fitting results

Found out that some MLE fitting results between mac OS and Linux are not the same. Hence, I need to use boostrap again to show the 'consistency' of mle estimates.

Further examination show that avgLS sometimes are also different, indicating file input or output mistakes.

boostrap rls for binomial aging fitting

emc313b02:0.nat.rls.fitting hqin$ pwd
emc313b02:0.nat.rls.fitting hqin$ ll
total 1752
-rw-r--r--    1 hqin  staff   5.9K Apr 24 15:38 0.fit_qinlabrls.Rmd
-rw-r--r--    1 hqin  staff   864K Apr 24 15:38 0.fit_qinlabrls.html
-rw-r--r--    1 hqin  staff   3.1K Apr 24 15:38 1.bootstrap_fit_qinlabrls.Rmd
drwxr-xr-x  102 hqin  staff   3.4K Apr 24 15:38 bootstrap
drwxr-xr-x    5 hqin  staff   170B Apr 24 15:38 sandbox

Saturday, April 22, 2017

Thursday, April 20, 2017

Raspberry Pi NSF awards

Rasper pi, NSF funds
Kirk Cameron (Principal Investigator)
Aditya Johri (Co-Principal Investigator)

Friday, April 14, 2017

deep learning tools

Deep neural networks 

List of potential R packages for deep learning:


Deeplearning libraries in Python, academic use, flexibility. deepSEA
Caffe, developed by the Berkely Vision and Learning Center
Theano, transparent use of GPU.

Keras . (theano + tensorflow)




Wednesday, April 12, 2017

Qin lab brief description

Dr. Hong Qin's group uses computational and mathematical approaches to investigate biomedical and biological questions.  One focus is to develop probabilistic gene network models to infer network changes during cellular aging. We build gene network models from heterogenous genomics data sets, including protein interactions, gene expression data sets, RNAseq data sets, protein mass-spec data sets, high-throuput phenotypic screens, and gene annotations.  We are developing machine-learning methods to automatically estimate cellular lifespan from time-lapsed images. We are also applying engineering principles to study molecular, biological, and ecological networks. We are developing deep-learning methods for better classification and prediction using heterogenous biomedical and biological large data sets. Dr. Hong Qin is a recipient of a NSF CAREER award 2015-2020.

Qin's expertise: Graph reliability modeling; Bioinformatics; Computational genomics; Mathematical modeling; Systems Biology;  Cellular aging; Gene network analysis and modeling. 

Tuesday, April 11, 2017

UTC Research Day

The 2nd annual UTC RESEARCH Dialogues conference, celebrating Scholarship, Engagement, the Arts, Research,Creativity, & the Humanities will take place April 11th & 12th, 2017.  Please take a moment to (1) sign up for one (or more) of the many presentation modes available AND (2) encourage your students to present; the deadline for entry is February 28, 2017Day 1 (April 11) is undergraduate-focused and Day 2 (April 12) spotlights graduate students and faculty.   Faculty are encouraged to participate either or both days!  There is a simple “Application to Present” form available for all presentation types.  You can access details about the event including the schedule, event descriptions, guidelines, and the application form online:

Please block off some time on April 11th and 12th to engage with the RESEARCH Dialogues event as a participant or as an attendee to support your students and colleagues and contribute to the culture of scholarship and creative inquiry on our campus!  If you have any questions or difficulties in registering, please contact

Best regards,

Opportunities to Present
Scholarship and Creative Expression at UTC takes many forms – find the presentation formats that are best for you!
·         Poster & Display Presentations:  Faculty, staff, and students are invited to present posters or tabletop displays related to research, scholarship, or creative activity.  Posters and displays can come in many shapes and sizes!  If your presentation doesn’t work with a traditional poster format, that is no problem.  Models, photos, laptop computers, interactive materials, listening stations, robots – all are welcome and can be accommodated.
·         Podium Presentations:  Faculty, staff, and student presenters are invited to make oral or visual presentations related to research, scholarship, or creative activity.  Podium presentation sessions will be moderated.
·         Panel Discussions / Group Presentations:  Groups of presenters are invited to organize a panel discussion or group presentation.
·         Performance Presentations:  Individuals or groups of faculty, staff, and students are encouraged to participate in performance presentations in the UC Auditorium. 
·         Undergraduate Student Lightning Pitches:  Undergraduate students are invited to compete in the Undergraduate Student Lightning Pitches.  Students will have 2 minutes and can use up to 2 slides to make a pitch for funding for their research, scholarship, outreach, or creative activity.  A panel of community judges will select 1st, 2nd, and 3rd place winners.  1st prize winner gets $100 gift card and a PSRA award (for continuing UTC students). 2nd and 3rd prize winners receive $75 and $50 gift cards respectively.
·         Graduate Student 3 Minute Thesis:  Graduate students are invited to compete in the 3 Minute Thesis (3MT) competition.  Students will have 3 minutes and must follow official 3MT guidelines.  A panel of community judges will select 1st, 2nd, and 3rd place winners.  1st prize winner gets $200 gift card and a PSRA award (for continuing UTC students). 2nd and 3rd prize winners receive $100 and $50 gift cards respectively.
·         Faculty Elevator Speech Competition:  Faculty and staff are invited to participate in the 2nd annual Elevator Speech competition.  Faculty will have 4 minutes to make a pitch for support of their research, scholarship, engagement, or creative activity.  A panel of community judges will select a winner for each topical category (STEM, Health, Arts & Humanities, and Social Sciences) who will receive a $1,500 mini-grant to support their pitch. A grand prize winner will be allocated a part-time graduate assistantship for the 2017-18 academic year.

Other Ways to Participate
There are plenty of ways to be involved!
·         Be a champion for RESEARCH Dialogues in your department, college, unit, or division!  Help spread the word.
·         Moderate a podium presentation session, panel discussion, or performance session. 
·         Encourage your students to attend – consider offering a course or extra credit assignment associated with the event. 
·         Attend the Breakfast Plenary Session on 4/11 and the Lunch Plenary Session on 4/12. 
·         Attend the Reception on 4/12!