CS 459 - Topics in CS, Bioinformatics Programming

Spring 2019


This is the website for CS 459 - Topics in CS, Bioinformatics Programming offered in Spring 2019 and taught by Jeff Kinne. This class will be held Tuesdays and Fridays 4-4:50pm in Root Hall A-017.

Muhammad Hashmi, mhashmi@sycamores.indstate.edu is a GA supporting this class.

Jeff's Office hours are: MWF 9am-noon in Root Hall A-140D.

Muhammad's office hours are: M 9:30-11am and 4-5pm, W 9:30am-noon and 4-5pm in Root Hall A-015.

Click on the links on the left for information about the course.


  • Here I'll keep notes on announcements for the course.
    Skip to the latest

    Things to look at down the line at some point (I'll add to this list as things come up that I hadn't thought of before) - ggnet2

  • Jan 15 plan ...
    • Administrivia - anyone still need to register, does everyone here have this course in your blackboard list
    • Course overview
  • Jan 18 plan ...
    • See Muhammad's office hours above.
    • CS class accounts - username and password are in blackboard, get logged in
    • Getting started with linux/unix. See Links for some resources on this.
    • Getting started with R. See Links for some resources. Maybe play with weather data.
  • Jan 22 plan ...
    • Jeff's R programming slides - I'll focus on adding to those. Look through them before each class/lecture.
    • Case studies - starting to play with case studies, that will drive what we need to learn. First up - weather data; that pushes us to get comfortable dealing with data frames (subsetting rows, columns, etc.)
    • Assignments - try before class/lecture, let us help you fix things in class/lecture. If you don't do anything with them, you won't get full benefit from our time together.
    • R tutorial - spend some time reading through them. With programming, you need to get to a certain threshold of "brain dump" before it really sinks in and you become better at it (and enjoy it more).
  • Jan 25 plan ...
    • Review everything from last time and start looking at weather data.
    • Also, we will attend the seminar presentations for the bioinformatics faculty candidates. Those presentations are scheduled for 4-5pm in Science 0012 on Jan 29, February 5, February 12, and February 14.
  • Feb 1 plan ...
    • HW 3 with the weather data - Jeff's solution, and you all finishing yours
    • Something new - with the weather data or some other data
    • Note - we'll keep track of what we need from R that isn't Jeff's slides, to update the slides
    • New R things - summary, table, tapply, plot, points, legend, lm,
    • Linux commands - head, tail, wc, ls -lh, man
  • Feb 8 plan ...
    • BD4ISU students - requirement to see Muhammad in his lab hours to show him what you have for the HW assignments so far. If none of his office hours work, you need to set an appointment. Do that right now...
    • HW 4 - more with weather data. Go through Jeff's solution. You should get as much of it done as possible before class.
    • Updates on R slides - summary, table, tapply, plot, points, legend, lm, anything else from weather.R
    • Coming soon - basic types of plots in R - plot, hist, boxplot
    • Coming soon - R functions and classes (it is too annoying to do so much copy/pasting...)
    • By popular demand - slides of useful linux commands?
  • Feb 15 plan ...
    • Remember - open invitation, if you have some data for us to work with, let me know.
    • HW 5. Also review of HW 4. See Jeff's weather_new.R in the code directory.
    • Note on exporting figures - dev.copy(pdf,"name.pdf");dev.off()
    • Check the R programming slides again. I keep adding a few slides per week. Try out the code as you go through the slides. Try making little changes to the code.
    • Take a look at R cheat sheets at - https://www.rstudio.com/resources/cheatsheets/, in particular "R Studio IDE" and "Base R" (that is towards the bottom)
  • Feb 19 plan ...
    • Another work day.
    • Quickest start guide to R Markdown - in the R programming slides. So go ahead and create a new Rmarkdown file, make sure you can knit it, and change some of the formatting, etc. Then take whatever R file you have been working on, and get it into an Rmd file instead.
    • Reminder - BD4ISU students, you should have a regular time each week that you meet Muhammad in the unix lab to go through what you're working on with R.
  • Feb 23 plan ...
    • Note the fitting examples in the R slides
    • New dataset to look at GSE69618 csv file and Rmd file in the in class code.
    • Coming soon - dataset/project from Guy Brock's visit to ISU last summer.
    • Coming soon - statistics.
  • Mar 1 plan ...
    • More with dataset GSE69618 csv file and Rmd file.
    • Getting started with statistics, doing some simulations in R.
    • Your data and project?
  • Mar 12 plan ...
    • Note - Muhammad has led you through some activities the past few meetings.
    • New assignment based on the gene expression data. See the assignments page...
  • Apr 5
    • BD4ISU and poster students - setup an appointment this coming week to come show me your results of your HW assignments in this class. Check in with Muhammad first if you need to.
    • Tuesday 4pm biology seminars - 4/9 Hugo Gante, 4/16 Kris Schwab.
    • Ending the year for us - statistics, project from Guy Brock of OSU
    • Note - updated version of GSE*.Rmd in the code directory
  • Apr 16
    • Have a look at - https://www.nature.com/articles/srep19083. Questions - is their raw data somewhere to download, things you don't understand (terms, etc.), claims you don't agree with / possible objections to their results / what follow up research would you think of.
    • More statistics
  • Apr 19
    • Quiz over Jeff's R slides, R and Rmd files we have used for this course. Please take it seriously and do some studying/reviewing.
    • Part of the quiz will be turning in a 1/2 - 3 page review of the Nature paper.
  • Apr 23
    • Biology Seminar in Science 0012 - Dr. Schwab presents on his current research project(s).
  • Apr 26
    • Discussion of the Nature paper.
    • Review of HW9 quiz
  • Apr 30
    • Biology Seminar in Science - Tim Divoll presents on his current research project(s).
  • May 2
    • Fun from one of the OSU visitors from last summer.
    • No exam in this class. Good luck with exams!
    • Today's examples...
      cd ~
      mkdir may3
      cd /u1/junk/bd4isu/Guy_Brock_Examples/
      cp *.* ~/may3
      ssh -Y cs
      limit maxproc 100
      cd ~/may3
      rstudio &
      and then open up either of the .Rmd files, skip past the code chunks with knitr::opts and install.packages, then start running the code chunks and looking at the plots and variables and such. Note - do not use the limit maxproc command for any other reason, and make sure to close rstudio when you are done, don't leave it running. Please do not break cs!
Note: course website layout/code/template from Steve Baker. Anything horrible is not his fault.