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

SAF
   What and who is it?
   Software documentation
   Accounts (Caltech personnel only) search apply
   Anonymous FTP directory via: ftp, http
   closed 3/1/07 DNA Sequencing Core Facility  instructions dna_pickup
   Productivity Tools (Hardware and Software information, stockroom forms, calendars ) 
   Biology Division Surplus  Mailing list archives

Local Server based tools
   Username and password information
   Request a print queue for a local printer
   Web interface SAF certificates for secure browsing
     GCG    10.2  via W2H (on oldSAF)
     EMBOSS 6.0.1 via W2H EMBOSS-Explorer 
     Design primers with Primer3
     Process ABI files in home directory from Laragen or wherever
     Cloneit!  (Determine cloning strategies)
     SAF multiple sequence alignment server
     SAF parallel BLAST server  faster than the NCBI!!! 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:
     drag and drop  Windows Macintosh
     scp or sftp    Windows Macintosh

Programs for PC and/or Macintosh
   Site licensed programs

Biology Resources
   Databases: by Organism Others
   Assorted services and resources
   Celera information

Courses (* = campus access only)
   BMB/Bi/Ch 170, Biochemistry and Biophysics of Macromolecules and Molecular Assemblies
   * Bi/Ch 111, Biochemistry of Gene Expression
   BMB 178, Enzyme kinetics 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
Updated 9/21/2012