1. Bio 271 Lecture 1

2. Robert Gentleman Office M1B28, Mayer Building at DFCI Phone: 617-632-5250 Email: rgentlem@hsph.harvard.edurgentlem@hsph.harvard.edu Office Hours: TBA It is easiest to contact me by email

3. TA: Beiying Ding email: bding@hsph.harvard.edubding@hsph.harvard.edu Office hours: TBA Office: TBA

4. How do computers work? Memory RAM Harddisk bus peripheral devices

5. Multiusers/multiprocessors Several users sharing one processor job control One user with multiple processors threads, fork Multiple users multiple processors

6. Memory concerns If your job requires more memory than the computer has RAM then swapping/paging occurs This is a relatively slow process Job control uses pretty much the same mechanism Why should you run jobs sequentially rather than concurrently?

7. Some Unix commands Processes on Unix can either run in the foreground (you don’t get the prompt back) or in the background (you can go on while they execute). Processes running in background are sometimes called batch jobs. nice : a Unix command to use for background jobs.

8. Grep grep this searches a file (or several files) for instances of a particular character string you have a number of ways of expressing the character string (regular expressions) grep comes in many flavors (egrep, fgrep) but I don’t believe there is much in it check out the man page….

9. Job control ps : a Unix command to tell you what processes are running. On many machines, but not hsph, top also runs. ps combined with grep can let you see what is going on. Use ssh to go to hsph and then use ps and grep to find all netscape processes that are running.

10. R and Word Find R and start it on your computer. Issue the command plot(rnorm(10), rnorm(10)) Start Word with a new document. Copy the plot to the Word document. You might need to save it as a file and then open the file.

11. Emacs Locate and start emacs on the PC Try starting emacs on hsph…what happens create a file called myfirstday.tex What information do you need?

12. Finding things on Unix find : a useful function, but some think hard to use locate : a much simpler function which : tells you which version of a command will run On Windows, under the start button you should see a tab for Search

13. Try the following on HSPH find /usr1/users/biostat/rgentlem/madman -name ‘*.R’ | xargs grep genefilter what does this command do? what does xargs do? what does grep do?