BioCoRE - Biological Collaborative Research Environment

BioLog is a handy little program written in TCL that lets you easily import text into the BioCoRE notebook. BioLog works best if you are using the Java Web Start version of the Control Panel. When you log into BioCoRE via Java Web Start, a small text file is placed in your home directory that contains the necessary information that BioLog needs to be able to contact the BioCoRE server.

The BioLog TCL script

Requires:

  • TCL version 8.0+
  • TCL version of BioCoRE API - Version 1.15 or higher

    Edit the biolog file to have the correct location of tclsh on the first line, and modify the path listed in the apisource to be correct for your system.

    For biolog to be able to connect to BioCoRE, you need a file: ~/.biocoreProjects.tcl 

    % cat ~/.biocoreProjects.tcl
# map project keys to ids
set Project(firstProj) 12
set Project(secondProj) 3
set Project(thirdProj) 44

# determine ProjectDefault based on current directory
switch -glob [pwd]/ {
  /Projects/proj1/* { set ProjectDefault firstProj }
  /home/yourname/* { set ProjectDefault secondProj }
  default { set ProjectDefault thirdProj }
}
    This information is available from the BioCoRE Control Panel by picking Project->Utilities in the menu and then "API Connection Information" in the web page that pops up. You can define your own short names for your projects; only the numbers are used by the BioCoRE server. The default project is used if you don't specify a project on the command line. 
    % biolog --help
usage: /usr/local/bin/biolog
   [-p ] [-s ] [-k ]... [-f] [-e|-i|]
   -f => do not ask before recording
   -e => input is an email message
   -i => log interactive shell
   -h => display usage information
   /usr/local/bin/biolog -r  => reload from saved backup file
   defined projects: firstProj secondProj thirdProj
    Now try running biolog (use control-D to end your message): 
    % biolog
This is a test.
========
This is a test.
========
PROJECT: default
SUBJECT: comment
DATE: Mon Oct 15 19:00:45 CDT 2001
HOST: your.machine.edu
CWD: /home/yourname/
========
Record this text? ([y]es/[e]dit/[s]ubject/[h]eaders/[a]bort)
y
Recorded successfully.
    Select the 'BioLog Entries' for your project. There should be a message titled "comment" from you. You can use the -p option in biolog to specify the destination project, -s to change the subject, or -k (multiple times) to add keywords. You can edit the text, subject, or headers at the "Record this text?" prompt.

    If you place a command at the end of the biolog command line, the output of this command will be recorded: 

    % biolog ls /Scr
========
despina1
despina2
naiad1
titan
titan2
titan3
========
PROJECT: default
SUBJECT: ls /Scr
DATE: Mon Oct 15 19:08:59 CDT 2001
HOST: your.machine.edu
CWD: /home/yourname/
COMMAND: ls /Scr
========
Record this text? ([y]es/[e]dit/[s]ubject/[h]eaders/[a]bort)
y
Recorded successfully.
    Or, use the -i option to record a shell session: 
    % biolog -i
Script started, file is /tmp/biolog_23328.tmp
% pwd
/home/yourname/
% exit
exit
Script done, file is /tmp/biolog_23328.tmp
========
Script started on Mon 15 Oct 2001 07:09:53 PM CDT
% pwd
/home/yourname/
% exit

exit

script done on Mon 15 Oct 2001 07:09:58 PM CDT
========
PROJECT: default
SUBJECT: interactive
DATE: Mon Oct 15 19:09:53 CDT 2001
HOST: your.machine.edu
CWD: /home/yourname/
INTERACTIVE
========
Record this text? ([y]es/[e]dit/[s]ubject/[h]eaders/[a]bort)
y
Recorded successfully.
    Finally, in the pine mailreader while viewing a message, type "|biolog -f -e" to send the message through biolog in filter (non-interactive) mode and extract the header information from the email. (Can't really show this.)

    This is a great way to dump information into BioCoRE for sharing and later reference. There will certainly be future revisions, but it is currently quite useful.

    BioLog was originally written by Jim Phillips.

    Feedback

    The BioCoRE team welcomes any comments, questions, or suggestions that you might have concerning our software! Please email us or fill out our feedback form.