Sequence
---------  Analysis Facility (SAF), Biology Division, Caltech
Structure

SAF
   What and who is it?
   Software documentation
   Caltech only:
      Computing Resources accounts:  search apply
   Anonymous FTP directory via: ftp, https
   Miscellaneous (printer and monitor testing, old stockroom forms, PS/PDF calendars ) 
   Biology Division Surplus  Mailing list archives

Local Server based tools
   Username and password information
   Web interface SAF certificates for secure browsing
     GCG    10.2  via W2H (on oldSAF)
     EMBOSS 6.4.0 via W2H EMBOSS-Explorer 
     Design primers with Primer3
     Process ABI files from any source (call bases, plot, compare to reference)
     Cloneit!  (Determine cloning strategies)
     SAF multiple sequence alignment server
     SAF parallel BLAST server  how it works
     SAF parallel HMMER server  All HMMER programs plus hmmsearch of (translated) BLAST databases 
     Miscellaneous:  TMHMM 
     Mail 
   command line interface
     Using secure connections Quick instructions: Windows, Macintosh
     Using command line programs
   Xwindows interface
     Launch X11 applications
   Transferring files:
     scp or sftp    Windows Macintosh

Programs for PC and/or Macintosh
   Site licensed programs

Biology Resources
   Databases


Courses (* = campus access only)
   BMB/Bi/Ch 170, Biochemistry and Biophysics of Macromolecules and Molecular Assemblies
   BMB/Bi/Ch 173, Biophysical/Structural Methods
   BMB/Bi/Ch 174, Molecular Machines in the Cell
   * Bi/Ch 111, Biochemistry of Gene Expression
   BMB 178, Macromolecular Function: Kinetics, Energetics, and Mechanisms
   Fundamentals of Sequence Analysis
   EMBOSS tutorial Programming course

Miscellaneous
   Apache web server documentation
   Campus servers
   CrystalEyes repair
   Stereo techniques using LCD monitors
   PDF files for classes - factors to consider
   PowerPoint Graphics Portability Issues
   Saving Power on Idle Computers

Historical interest only
   closed 3/1/07 DNA Sequencing Core Facility  instructions dna_pickup
   Celera information