A Tidy Transcriptomics introduction to RNA-Seq analyses

https://stemangiola.github.io/bioc_2020_tidytranscriptomics/articles/tidytranscriptomics.html

bootcamp useful materials

https://carpentries.github.io/instructor-training/


https://carpentries.org/assessment/

https://www.software.ac.uk/blog/2016-09-26-top-tips-instructors-software-carpentry-workshop?_ga=2.186481833.1056855408.1557515761-1089883757.1557515761

https://carpentries.github.io/instructor-training/

data science workshops

Amit Kaps, data science bootcamp
https://amitkaps.com/dsbootcamp
https://github.com/amitkaps/art-data-science

Jackson lab genomics Day 1

Moring

install anaconda3 on ubuntu virtualbox

#
hqin@rainboxdash:~/anaconda3/bin/$ ./jupter notebook &


https://thejacksonlaboratory.github.io/bd2k-workshop/ 

samtools view example.bam | less

Linux exercises: up and down arrows, tab for file-names autocomplete

bam file

vcf file (variant call file?)

less test.vcf

mkdir tmpdir
cd tmpdir
cd ..
ls

Essential probability and statistics for introduction to big data

• summary stattistics vs empirical statistics
• Common data transformation, Z-scores
• Bayesian inference
• Multiple hypothesis testing

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

Bayes's rule

Introductory Data Mining

=====================
Afternoon

curricula:
 all biology are computational
 computational biology are parasite of biology

Approach:
  research project approach using real datasets
  targeted students: professional and academic oriented?

data carpentry's R for genomcis
http://www.datacarpentry.org/R-genomics/


RStudio projects
https://support.rstudio.com/hc/en-us/articles/200526207-Using-Projects

args(barplot)
?lm
??lm
help.search("kruskal")

==========
Barke Southern Illinois Medical School, longest-living mouse

===========
Brenton Gravely, RNA genomics

Dscam, over 100 exons, an extreme case of alternative splicing
Schmucker 2000 Cell. Mutually exclusive splicing.
Ig Repeats.  Dimerization are isoform specific.
https://www.ncbi.nlm.nih.gov/pubmed/19934230

Dscam variatiosn between species
Gravely 2005, Cell.

Competing RNA base-pairing is a common mechanism for mutually exclusive splicing in anthropods, Yang 2011 Nature Struc Mol Biol
http://www.nature.com/nsmb/journal/v18/n2/abs/nsmb.1959.html

single cell RNA sequencing
Drosophila S2 cells, each cell show the same splicing isoform.

Drop-seq of Drosophila and human cell to control the number of cells in each droplet.

Oxford nanopore sequencing

1500 RNA binding proteins in human genome

Van Nostrand Nature methods, 2016, eCLIP-seq reveqls RBP-specific binding profiles
http://www.nature.com/nmeth/journal/v13/n6/abs/nmeth.3810.html

Eventbrite help pages

Eventbrite, Export attendee information

https://www.eventbrite.com/support/articles/en_US/How_To/how-to-edit-and-export-an-attendee-summary-report?lg=en_US

NSF workshop information

http://www.nsf.gov/pubs/gpg/nsf04_23/2.jsp#IID7


An estimated total budget for the conference, together with an itemized statement of the amount of support requested from NSF (the NSF budget may include participant support for transportation (when appropriate), per diem costs, stipends, publication and other conference-related costs. (Note: participant support costs must be excluded from the indirect cost base.) See Chapter II, Section C.2.g.(v); and


http://www.nsf.gov/bio/mcb/confworkshopguidance.jsp

Allowable costs
http://www.nsf.gov/pubs/manuals/gpm05_131/gpm6.jsp

summer workshop plans, Jamila Canady

Jamila Canady, x5366, summer program.
Called on 2015 Jan 12, Monday. She said sth like that "we will pick up once the proposal is approved".

In Late July or August?
20-30 faculty
computer access
active learning space?
wireless access

Food catering
parking coupons

Software carpentry bootcamp log

Tuesday, June 10, 2014 at 9:00 AM - Wednesday, June 11, 2014 at 4:30 PM (EDT)  

Atlanta, GA | Albro-Falconer-Manely Science Center - Room 232

Spelman College
440 Westview Dr. S.W.
Atlanta 30310

Course site:
http://wltrimbl.github.io/2014-06-10-spelman/

http://continuum.io/downloads

Pre-survey
https://docs.google.com/forms/d/117vOu7siYuixhLM6gkA1fAZgj1opiY4o-Gfy8DYvv6Y/viewform

Post-survey
https://docs.google.com/forms/d/1R21oyG_N2Ov5wnOsQ_VOQn0eIaHz4ijRbhxlG2IF_PI/viewform

Guest wireless, requested through LotusNote.

Ethernet cables, loan request.

Coffee, tea, box lunches, paper cups

Table for the catering, request on lotus note.

Lectures
http://software-carpentry.org/lessons.html


Lessons learned:
-> Forgot to ask for affiliations during registration.
-> Catering ordered has not vegetarian option. One of the instructors is a vegetarian.
I called the catering vendor, and added 6 vegetarian sandwiches, with no additional cost. I replaced the coffee with orange juice.

Volunteers need for a two-day Python programming bootcamp at Spelman College

Experienced Python programmers are needed to work as TAs for a two-day Software Carpentry Bootcamp at Spelman College on June 10-11, 2014.

This two-day bootcamp is scheduled to have 1/2 day on shell programming, 2 half-days on Python programming, 1 half-day on version control using Git. Software Carpentry lesson can be seen at http://software-carpentry.org/lessons.html.  TAs do not have to volunteer for two days.

Please contact hqin at spelman dot edu if you can.

XSEDE workshop, computational thinking

self-paced online tutorials
https://www.xsede.org/web/xup/online-training


https://www.osc.edu/~sgordon/

excel sliding bar

customize ribbon, developer

NameBox

https://www.osc.edu/~sgordon/workshop/materials

http://phet.colorado.edu/

VensimPLE

AgentSheet, shordor

Computational Science Competencies
http://hpcuniversity.org/educators/undergradCompetencies/
http://hpcuniversity.org/trainingMaterials/


inculcate

pictures analysis in R, monroe example

http://www.r-bloggers.com/face-to-face-with-marilyn-monroe/

GitHub for ORAU R tutorial

Create ORAU-R on GitHub website.
https://github.com/hongqin/ORAU-R

Locally,
$ cd  /Users/hongqin/github/ORAU-R
$ git init
Initialized empty Git repository in /Users/hongqin/dropbox/courses.student.research.dp/ORAU-R/.git/
$ git add *


$ git remote add origin https://github.com/hongqin/ORAU-R.git
$ git push --force origin master 


$ git config http.postBuffer 209715200

Username for 'https://github.com': hongqin
Password for 'https://hongqin@github.com': 
Counting objects: 76, done.
Delta compression using up to 2 threads.
Compressing objects: 100% (76/76), done.
Writing objects: 100% (76/76), 11.67 MiB | 4.30 MiB/s, done.
Total 76 (delta 6), reused 0 (delta 0)
To https://github.com/hongqin/ORAU-R.git
 + d602d3b...260adfb master -> master (forced update)

R tutorial for Oak Ridge Science Education

Please note that the entire workshop material can be download from its GitHub repository ORAU-R.

1.What is R? 

Wikipedia entry on R

Why R by Courtney Brown at Emory. 

Why R and beyond.

R blogger that provides recent and often interesting development about R.  

What is R video (Added after the class).

2. Install R to your own computers.

Instructions to download R. 

Install R studio.  RStudio provides a nice GUI to R.

Install packages to R: Video for Windows Version.

3. Introduction to R.

• Stephen J. Eglen's short intro slides. 
•  
•  
•  

Hong Qin's slides: Overview of R;   Basic programming in R; Input & Output in R;

Lydon Walker, getting started with R, an accelerated primer

 4. Simple exercises in R.

Qin's simple.R excises.  Please select 'Raw' and 'save-as' in text format. Unfortunately, web browser seem to automatically add 'txt' to the file name, and Rstudio does not run 'txt' format.  To solve this problem, we can 'create' a new R script, and copy-paste from code from the text file.

(The workshop audience mostly reached this step).

Youtube tutorial converting Excel data to CSV and load into R. 
    The sunflow seed Excel file is here.  

5. Make solution exercise.

Write an R function to calculate how much NaCl needed for X ml of Y mM NaCl solution. 

6. Simple statistical analysis in R.

Simple regression exercise.

7. Advanced training materials.

Multiple regression demo

Hierarchical clustering using cities. Code, Video.

Laddy Gaga and clustering analysis. Code. Video.

Bioconductor workshop materials.

8. Useful R materials.

• Hong Qin's R and computational biology GitHub site

• Stephen J. Eglen's PLOS article. A quick guide to teaching R programming to computational biology students. 

• 
  

http://cran.r-project.org/doc/contrib/Seefeld_StatsRBio.pdf

http://www.rseek.org. 

http://addictedtor.free.fr/graphiques/. 


Newly launched interactive cloud-based R for teaching: http://www.datamind.org/


Google-developers R programming videos


Avril Coghlan's little book of R for bioinformatics.


Github's collection of free R books

R by examples

9. Discussions on programming workshops.

Titus Brown's blog on teaching programming.

10. My reflections

The main workshop is led by Jame Ferguson and Bob Panoff. There were 9 college biology and 2 high-school biology faculty in the workshop.

I was given 90 minutes. My goal was that audience would be able to install R and Rstudio and run R scripts on their own after the workshop.

I spent 30 minutes on introducing R to the audience, my experience of teaching R and computational genomics to undergraduates. I showed them the GEO database and R interface.  I used the examples of make-solution, hclust on cities and Lady Gaga.  For the next 50 minutes, I let the audience to download and install Rstudio.  A few of them needed my help to down and install R and Rstudio. Most of them were able to run to the simple.R exercise (step 4.a). I run out of time after step 6.

I was somewhat stunned that downloading R code directly from GitHub repository is surprisingly cumbersome.

During the exercise time, a few people were clearly ahead and poked around. Some were especially interested in the GEO2R portal.

Bob mentioned that R has been used in a few other liberal art colleges, including Davidson and Pomona.

At the end of the workshop, I was asked "why do 'we' have to teach R to biology students?". I used my own experiences and argued that R is the state-of-the-art tool for data analysis in biology.


For preparation for the workshop

Wireless connection, laptops, power-outlets are recommended. 

Install packages and data on flash-drives in case internet connection is slow. (This can be a problem when all participants are download at the same time.)

A flow-chart on easel can be used for clarity.