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 auction  Mailing list archives

Local Server based tools
   Username and password information
   Request a print queue for a local printer
   Web interface
     Configure your browser to securely connect to this web server
     access: GCG    10.2  via W2H
             EMBOSS 5.0 via W2H EMBOSS-Explorer Pise
             design primers
             process ABI files in home directory
             Process ABI files 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 
             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, Principles of Three-Dimensional Protein Structure
   * Bi/Ch 111, Biochemistry of Gene Expression
   * BMB 178, Fundamentals of Molecular Genetics
   Fundamentals of Sequence Analysis
   EMBOSS tutorial Programming course

Miscellaneous
   Campus servers Internet tools Apache documentation   Saving Power on Idle Computers