alyssafrazee

Navigate to the Outlook Web App (mine was mobile.johnshopkins.edu).

Click the little "settings" gear in the upper right corner and click "Options"

Click the "organize email" tab in the left sidebar.

Now you will be in the "inbox rules" tab - stay there! Click the big PLUS (+) button to make a new inbox rule. My rule was:

• apply to all messages
• redirect the message to mygmailaccount@gmail.com
• delete the message

alyssafrazee

Analyzing RNA-seq data with the "Tuxedo" tools

Introduction/tl;dr: I wrote this post as a reference for a few new graduate students in my department that are getting started with RNA-seq data analysis. It begins with an informal, big-picture overview of RNA-seq data analysis, and the general flow of the post outlines one standard RNA-seq workflow, but I wanted to give general audiences a "heads-up" that the post goes into quite a bit of nitty gritty detail that's specific to our department's computing setup.

preliminaries: what's RNA-seq?

RNA-seq is a high-throughput technology used to measure gene expression in cell populations. For a super bare-bones picture of what gene expression is, please enjoy this ASCII art I made to illustrate the process:

[DNA]            ACGTAGGT{CGTATTT}AGCGT{AGCGCCCGA}TTACA
                                    |                   

alyssafrazee

Instructions for Scheduling the Preliminary Oral Examination

The student and his/her Advisor are responsible for initiating arrangements for the preliminary doctoral examination. The departmental academic coordinator will assist with the appropriate forms and other important information.

The Examining Committee must:

1. consist of five voting members. Two members MUST be from the sponsoring department; one of these is the advisor. A third member from the sponsoring department is optional. (LIMIT of 3 members from sponsoring department.)

• The student's advisor of record must serve as a member of the Committee. The senior faculty member without a primary appointment in the student's Department will serve as Chair of the Committee and MUST hold the rank of Associate or Full Professor.
• All faculty members must serve on the Committee representing the department of their primary faculty appointment. The only instance when the faculty member can serve in his/her joint appointment capacity is if he/she i

alyssafrazee

Instructions for the Appointment of Thesis Readers and Final Oral Examination Committee Composition

The student and his/her Thesis Advisor are responsible for initiating arrangements for the appointment of Thesis Readers and Final Oral Examination Committee. The departmental academic coordinator will assist with the appropriate forms and other important information.

The Committee of Thesis Readers and Final Oral Examination Committee must...

1. consist of four voting members. Two members MUST have a primary faculty appointment in the student’s sponsoring department; the other two members must have appointments in two different departments other than the sponsoring department.
   • The student's advisor of record must serve as a Thesis Reader and a member of the Final Oral Examination Committee. Alternates are not permitted to serve in place of the advisor. If the advisor is unable to attend the Final Oral Examination, the examination must be rescheduled. Co-advisors may serve in this role.

alyssafrazee

# do RNA-seq simulation to see if it will work!
# AF 19 december 2013

library(devtools)
##### ADD PASSWORD WHEN RUNNING
install_github('ballgown_paper','alyssafrazee',subdir='simde',password='')
library(simde)

fasta_file = 'chr22.fa'
count_transcripts(fasta_file) #918 transcripts

alyssafrazee

dir()
case0101 = read.csv("CASE0101.csv")
attach(case0101)
names(case0101)
case0101
case0101[1:10,]
case0101[,1]
case0101[,2[
case0101[,2]
case0101[2,]

alyssafrazee

insight, wit, and wisdom

tl;dr

I have unique, original thoughts on various topics! Likely this post will change the way you see the world and probably make you laugh so hard you cry, so you may want to be sitting down and not drinking any beverages while reading.

insight

Most people are pretty unhappy about the cold weather

alyssafrazee

copied directly from the PhD policy and procedure memorandum at JHSPH

PRELIMINARY ORAL EXAM:
The committee shall consist of five voting members. A minimum of three departments of the University, 
at least two being from the School of Public Health, must be represented. Not more than three members 
of the student’s department can serve, and one of these must be the thesis advisor. The primary 
appointment of faculty members determines whether they are considered inside or outside the department. 
Advisors, however, are considered inside examiners even if their appointment is outside of the department 
sponsoring the candidate. The senior faculty member outside the student’s major department will normally 
serve as chair and must hold the rank of Full or Associate Professor and be reviewed and approved by an 

alyssafrazee

faculty = function(name, dept, rank = c("assistant","associate","full","scientist"), sph = TRUE, advisor = FALSE, mydept = TRUE, alt = FALSE, joint = "none"){
  # tell me about your faculty members (make a "faculty" object for each one)
  if(advisor & alt){
    stop("Your advisor cannot be an alternate - he/she must be on the main committee.")
  }
  rank = match.arg(rank)
  return(list(name=name, dept=dept, rank=rank, sph=sph, advisor=advisor, mydept=mydept, alt=alt, joint=joint))
}

# helper function:

alyssafrazee

#!/usr/bin/python

### readlet counting script

### helper functions:
def enum(collection,st):
    #just like "enumerate" but you define your own starting position.
    #this returns indices RELATIVE TO ORIGINAL LIST
    i = st
    while i < len(collection):