Bio 271

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Bio 271

• Lecture 1

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Robert Gentleman

• Office M1B20, Mayer Building at DFCI
• Phone [phone]
• Email rgentlem_at_hsph.harvard.edu
• Office Hours TBA
• It is easiest to contact me by email

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TA Jarek Harezlak

• email jharezla_at_hsph.harvard.edu
• Office hours TBA
• Office TBA

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The course

• Approximately 14 two hour lectures that will
  introduce various concepts (computational)
• Homework weekly assignments
• you should spend approximately 3-4 hours on these
• if it looks like it will take longer get help
  from either Jarek or me

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Expectations

• different students have different backgrounds
• I dont expect all of you to turn in exactly the
  same thing those that have stronger backgrounds
  may in some cases do more
• I will try to make sure that the grading is
  handled fairly

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Evaluation

• I want you to learn something
• hopefully the homework assignments will provide
  enough information
• if not (and if you decide not to come to class)
  then we will have a final exam

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Main Part of Lecture 1

• in this lecture we will go over some of the basic
  functional aspects of computers and how they work
• some of the basic ideas are included in the
  handout (based on The Way Things Work).

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How do computers work

• Basic tasks
• making bits
• storing bits
• processing bits
• sending bits

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Making bits

• keyboard input
• mouse
• others?

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Storing bits

• types of storage
• ram
• hard-disk
• tape/cdrom/dvd
• memory card

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Processing bits

• the processor
• how does it work?
• where does the data come from and where does it
  go?
• whats a bus?

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Sending bits

• what happens to the bits after we process them?
• how do we send email?
• how do computers communicate?

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User Interactions

• the operating system is a layer of abstraction
  that is applied to the basic computer
  architecture
• users interact with the operating system and it
  handles most of the low level details
• but, it isnt that smart, so we need to
  understand enough so that we dont tell it to do
  silly things

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How do computers work?

• cpu
• memory
• RAM
• other (hard disk, cdrom, floppy)
• peripheral devices
• input devices

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Multiusers/multiprocessors

• Several users sharing one processor
• job control
• One user with multiple processors
• threads, fork
• Multiple users multiple processors

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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?

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User interfaces

• on Unix systems (and old Msoft) the primary user
  interface is the shell
• on Macintosh (and new Msoft) the primary user
  interface is a window system
• Unix also supports window systems (and there are
  many different ones)

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Window Systems

• a window UI is generally intended to be intuitive
  and to allow users to point and click their way
  through complex tasks
• generally it works pretty well (but can be hard
  to repeat what you just did)

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The Shell

• the shell is an interface that interprets a set
  of commands (which ones and what they mean
  depends on the shell being used)
• modern shells can be programmed and provide a
  rich set of tools for interacting with the
  computer
• they are not very intuitive for some definition
  of intuitive

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Unix shells

• there are many
• shell-differences
• you can find out your shell by typing
• echo SHELL
• the default on hsph is tcsh
• you dont seem to be able to change it ?

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Unix Shells

• finding out about things
• man xxx
• apropos xxx
• use google or other search engine
• bash common on Linux and among the younger
  generation
• you can change shells by typing the name of the
  new shell (not permanent)

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Some Unix commands

• Processes on Unix can either run in the
  foreground (you dont 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.

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Grep

• grep this searches its input (which may be a
  file) 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
  dont believe there is much in it
• check out the man page.

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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 (using a pipe)
• Use ssh to go to hsph and then use ps and grep to
  find all netscape processes that are running.

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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.

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Emacs

• Locate and start emacs on the PC
• Try starting emacs on hsphwhat happens
• create a file called myfirstday.tex
• What information do you need?

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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

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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?