• To install biopython on the NSLC machines:
  1. Open the NSLC-Server icon from your desktop and navigate to BioCSCourse.
  2. Double-click one of the numpy..stuff..dmg files, and follow its instructions for the installation of numpy.

     • Choose the one whose name includes 10.6 if you have 10.6 (Snow Leopard)
     • Choose the one whose name includes 10.3 if you have 10.5 (Leopard) or earlier
     • When prompted for the password, use the one shown on the whiteboard.

  3. Launch Terminal

     It's the black and white rectangular icon on our Dock. You can also launch it from spotlight by typing terminal.

  4. Enter (copy from here and paste into the Terminal window) the following, stopping and asking questions if anything seems sketchy:

     1. cd /Volumes/NSLC-Server/BioCSCourse/biopython-1.57

     2. Hit enter (return)

     3. sudo python setup.py install

        You will need the password from the whiteboard for this.

     4. Hit enter (return)
     5. Close Terminal
  5. Go to your eclipse repository and let's get python to find the new biopython software:
     1. On your main project name, right- (control-) click and drag down to Properties
     2. Choose Pydev - Interpreter/Grammar
     3. Click on Click here to configure an interpreter not listed
     4. Click Apply
     5. Click (check-mark) the only interpreter you should see in the box that pops up
     6. Click OK
     7. Wait while the sparks fly
     8. OK your way back to the main eclipse screen
  6. Update your repo
  7. Locate the bio package
  8. Run the SwissProtTest python program (taken from the biopython tutorial) and you should see:

     O23729
     CHS3_BROFI
     RecName: Full=Chalcone synthase 3; EC=2.3.1.74; AltName: Full=Naringenin-chalcone synthase 3;
     Seq('MAPAMEEIRQAQRAEGPAAVLAIGTSTPPNALYQADYPDYYFRITKSEHLTELK...GAE', ProteinAlphabet())
     Length 394
     ['Acyltransferase', 'Flavonoid biosynthesis', 'Transferase']
     

  9. Rejoice in the fact that you just retrived an amino acid sequence from the SwissProt database. You printed the sequence, its length, and its annotations.

  ---

• For instructions on how to install PIL on Snow Leopard, follow this link
• If you have the red flag in your eclipse workspace showing that the interpreter is not configured properly, then follow the following procedure:

  1. Get somebody to read these instructions to you as you act upon them.
  2. Right- (control-) click on the top level repository name in the package explorer.
  3. Drag down to Properties
  4. Click in the left column on PyDev–Interpreter/Grammar
  5. Be sure the Grammar version is 2.7
  6. Click on the Click here to configure an interpreter not listed
  7. If a Python interpreter shows in the top window, click on it and Remove it.
  8. Click New..
  9. Click Browse...
  10. If you are in the bin directory and see python2.7, them skip to the next numbered step.
      • Otherwise, click on the hard drive icon in the left column
      • Click on Library
      • Click on Frameworks
      • Click on Python.framework
      • Click on Versions
      • Click on 2.7
      • Click on bin
  11. Click on python2.7
  12. Click on Open and click OK to apply changes and get the interpreter configured.

• Welcome! Click on the calendar (syllabus) to see what's up.

About the course: CSE 131 provides an introduction to fundamental software concepts. It is ideal for students considering a major or minor in computer science, as well as for students who want to learn about computing for use in another discipline. See the CSE 131 Course Description for an overview and the links at the left for details.

Instructor:

• Ron K. Cytron
• Office in Bryan 509
• Office hours: TBA

TA

• Doug Shook

Times and Places:

• The course calendar shows the schedule for this course.
• All meetings are in the Natural Sciences Learning Center NSLC

Textbook:

No textbook is required for CSE131. Everything you need is either discussed in class or accesible from this web site. If you'd like a book to supplement the material covered in class, you're welcome to stop by during office hours and ask for a recommendation.