Foundations of Computational Biology and Bioinformatics II Lab

• Attendance
  
  The computer section of Foundations of Computational Biology and Bioinformatics II Spring 2009 will take place in Jenkins 122. Attendance will be mandatory and will count towards the participation component of your grade for the course. A sign in sheet will be passed around each Friday. There are a limited number of workstations available, so please be prepared to share or bring your laptop.
  
  Location of Jenkins Hall (#34): Map of Homewood Campus
  
  
  
• Programming Assignments
  
  Programming homework assingments may be submitted via e-mail to the course gmail acount. Students are welcome to use various text editors or IDEs to write their code, but please ensure that your code will run on the workstations in Jenkins 122 before submitting or you may lose points.
  
  Follow the coding guidelines laid out in this document: Programming Guidelines
  
  
  
• Jenkins 122 Computer Accounts and Building Access
  
  All students will need to submit a request for a computer account and building access. Please fill out the form at http://biophysics.jhu.edu/122.html.
  
  
  
• Hopkins Wireless Access
  
  Step-by-step instructions available at: http://it.jhu.edu/networking/wireless/.
  
  
  
• Schedule
  
  http://mct.aacrjournals.org/cgi/content/full/7/5/1013
  

  Date	Topics	Materials	Additional Information
  Jan 30 (Fri)	Intro to Python Programming	Python exercises Python exercise solutions 2isb.pdb famDgpcr.fa famDgpcr.fa.masked famEgpcr.fa famEgpcr.fa.masked glycer3_phos_dehydrog.fa glycer3_phos_dehydrog.fa.masked olfactoryGPCRs.fa olfactoryGPCRs.fa.masked 2bb2.1.t99.a2m 2bb2.1.t99.a2m.masked other.0.a2m other.0.a2m.masked	Official Emacs Documentation Simple Emacs Tutorial Emacs Quick Reference Intro_to_Python.ppt Python Tutorial Dive into Python Programming Python in Emacs
  Feb 06 (Fri)	Intro to R	R exercises R exercises solution Wine Dataset Wine Dataset Description	R Homepage R Manuals R Basics R Wiki Tutorials Tips by Task
  Feb 13 (Fri)	Calling R from python Sravanti will present at 3:30 in CSEB 209	R from Python PPT	Rpy Homepage Rpy Manuals Fitting Distributions with R
  Feb 20 (Fri)	Open Lab
  Feb 27 (Fri)	Open Lab
  March 6 (Fri)	Open Lab
  March 13 (Fri)	Open Lab
  March 20 (Fri)	Spring Break
  March 27 (Fri)	Object Oriented Programming in Python	Object Oriented Programming in Python ppt Simple matrix class	Dive into Python: Objects
  April 3 (Fri)	Machine Learning Overview	Machine Learning ppt	Machine Learning - Useful Links Example: prediction of tumor subtype from microarray data
  April 10 (Fri)	TBA		Python Tips for Efficient Coding Ptyhon Idioms and Efficiency (practical tips)

  
  
  
• Other
  
  Emacs built in tutorial: To run the tutorial, start Emacs, then type ctrl-h t