UTC travel reimbursment

Before travel, fill a T18 form

http://finance.tennessee.edu/wp-content/uploads/forms/T-18.pdf


After the travel

1. Complete  and sign a T3 form  http://finance.tennessee.edu/wp-content/uploads/forms/T-3.doc
2. Receipts of hotel, parking
3. Meeting program,
4. Your presentations
5. A cover letter to explain the reasons for your travel, your activities, explain your actual travel arrangement.
6. If mileage, print out round trip between home and meeting location

Python deep learning bootcamp, Github

https://mmeysenburg.github.io/image-processing/

duplicate genes identification:

https://media.nature.com/original/nature-assets/ng/journal/v36/n6/extref/ng1355-S2.pdf

Identification of duplicate genes and singletons After database cleaning, we conducted an all-against-all FASTA3 self-search for the entire proteome of Drosophila melanogaster (http://www.ensembl.org/Drosophila_melanogaster/) and that of Saccharomyces cerevisiae (http://genome-www.stanford.edu/Saccharomyces/). A single copy gene (i.e., a singleton) was defined as a protein that did not hit any other proteins in the FASTA search with E = 0.1; this loose similarity search criterion was used to make sure that a singleton is indeed a singleton. Two genes were regarded as duplicate genes if they meet the following three criteria during FASTA all-against-all search (modified after Ref 4): (1) E = 10-10; (2) their similarity is ≥ I (I= 30% if L ≥ 150 a.a. and I = 0.01n + 4.8L -0.32(1 + exp(-L/1000)) if L <150 a.a., where n = 6 and L is the length of the alignable region); and (3) the length of the alignable region between the two sequences is >50% of the longer protein. Since we wanted to detect the differences in expression change between real duplicate genes and singletons, we

pandas append dataframe

https://pandas.pydata.org/pandas-docs/stable/reference/api/pandas.DataFrame.append.html#pandas.DataFrame.append

ipad zoom meeting sharing bug fixed

Zoom cannot share screen on ipad.

Removed and reinstalled Zoom, fixed this problem.

UTC summer housing support
https://www.utc.edu/housing/summerservices/summercampconferencespacerequest.php

porcupoine problem

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

power of good stories

Qin, Fall 2019 course schedule

bibtex, pdflatex

applejack:bmc_netwk_aging_manuscript hqin$ bibtex bmc_networkaging

This is BibTeX, Version 0.99d (TeX Live 2016)

The top-level auxiliary file: bmc_networkaging.aux

The style file: bmc-mathphys.bst

Database file #1: qin_networkaging.bib

pdflatex bmc_networkaging

pdflatex bmc_networkaging

Bibtex from PubMed, TexMed

https://www.bioinformatics.org/texmed/

minIon yeast sequence data . SRA

SRA
https://www.ncbi.nlm.nih.gov/sra/?term=MinION+yeast

https://www.ncbi.nlm.nih.gov/sra/SRX5004466[accn]
https://trace.ncbi.nlm.nih.gov/Traces/sra/?run=SRR8184500

https://www.ncbi.nlm.nih.gov/sra/SRX1285790[accn]

**** cpsc4999 plan

Key topics
Linux
RNAseq
R/Rstudio Rmd

Online:
Regular expression online exercise

RNAseq
biological network


Potential student projects: 
time lapsed image analysis
rDNA reads in yeast genomes ~ lifespan
chemical compounds
network controllability
yeast RLS ~ genomics features
prediction of essential and non-essential genes.
ecology network analysis
aging data comparison
RNN reverse engineering of gene interactions


Reference:
data visualization book
https://serialmentor.com/dataviz/

http://hongqinlab.blogspot.com/2015/06/ngs-tutorials.html
http://www-personal.une.edu.au/~cgondro2/Rcourse.htm
Jackson lab workshop
Data Carpentry,
https://github.com/data-lessons/genomics-workshop
https://data-lessons.github.io/genomics-workshop/ 

EdX genomics course

how to read a scientific paper

https://violentmetaphors.com/2013/08/25/how-to-read-and-understand-a-scientific-paper-2/?fbclid=IwAR0p8P5EAi8Mir_rDyH-TLY6uUsn9ZVa2YvLMgjoEj3H6lxQdYqUvAKTnHU

Spearman footrule distance

Spearman footrule distance, a meaningful way to combine value and ranks

https://people.revoledu.com/kardi/tutorial/Similarity/FootruleDistance.html

UTC photo gallaries

https://utc.photoshelter.com/galleries/C0000g3KyZC5vIX0/G0000C1.scZCezc8/Downtown-and-North-Shore

https://utc.photoshelter.com/image?&_bqG=47&_bqH=eJwdi70OgjAYRd.mc2tiTEk6fG2xkFBQ2jiwNPxGBtQUBPHpBYd7hnNyqW_4xUwD76p5_fRNSnkx0HQ6QxycDgHBeN9G7aQRzPdz6zv_fExIO5PllkmwIfpHB6lku89y5WLJsv13E4q0UowVjrciEqEgicBE7PqFRUu.lvil6.FYmJC8G6wX5EBYNralr.8_.vMwkg--&GM_ID=