Pound Shell (lbsh):

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"lbsh" (also called Pound-Shell) is a shell monitor. It stands for lab-book shell. It is designed to act as an automated lab-book for people that conduct experiments in their standard shell environments. The high-level goal of Pound-Shell is to allow users to log data processing experiments (with little/no manual effort or interference) in such a way that they can later go back and recall (or rediscover) and reproduce their steps. Basically, it's designed to help us determine our own data's provenance. Further, Pound-Shell allows users to almost automatically re-run old experiments with new data. This type of work includes processing files with R, using gnuplot, interactive perl/python, standard data processing with shell commands (awk, sort, join, etc.), etc. Pound-Shell does not attempt to trace commands if it detects that a program has "captured the screen". Examples include Vim, emacs, etc. In such cases, Pound-Shell waits for the sub-process to end and then resumes recording.

With Pound-Shell, you can send a colleague your data-set(s) and your lbsh lab-book, and they can understand/reproduce/verify your results with Pound-Shell's automated tools.

In essence, you simply run "lbsh" and it automatically creates a new shell (the same type [bash | tcsh | etc.] that you already use) in a child process. Figure 1 shows how your session goes through Pound-Shell to the real shell underneath. When you decide you want to start logging commands for an experiment, you tell Pound-Shell to start logging. Then Pound-Shell simply records your commands (and also traces into the above mentioned tools). It does not record passwords, or anything else that is not output the screen. You can use tab-completes, issue commands that span multiple lines, use shell history, etc. When you are done, you tell Pound-Shell to stop logging. Then you may do whatever and Pound-Shell will quietly wait. You may repeat as needed without having to restart Pound-Shell each time.
Figure 1

Pound-Shell is intended to provide the same utility as a scientist's lab-book. After processing and analyzing and producing data, it is often very desirable to know ``exactly'' what one did to arrive at their current state. Sometimes we would like to recreate an old graph with newer data, but it's been so long we're not sure how we got it the first time. In other fields (such as the natural sciences) scientists will take notes, but we often type very fast and pursue numerous fruitless avenues. Pound-Shell allows users to log each of their sessions (even as they enter into other programs listed above) and recreate an entire session to arrive at the same results.

The advances that Pound-Shell offers are:

  • it is able to provide its utility without requiring the user to behave any differently. In a sense, users are free from needing to learn the diligence practiced by other scientists in their labs. In other words, it should make people's lives easy w/o being painful.
  • it has processing scripts (file-provenance.pl, exeggutor.pl, etc.) that allow one to specify a file name (such as a graph) and see all of the experiments that were needed to derive its data. The history (or provenance) of files can be seen as an ordered list of experiment IDs or as a Dataset Derivation Graph (or DDG), like this one.
  • it can be used to re-run experiments with new or old data to update findings or reproduce prior results using a file's provenance.

Other detailed information is available in the README file.


Downloads:

Pound-Shell is available under the BSD-license and has been tested in Mac OS X, FreeBSD, and Linux (and should be compatible with most major Unix flavors).

There is a Debian package for Pound-Shell which is available from the sourceforge site. Instructions for installing it are described here.

In order to build lbsh you must install the libncurses and the boost_regex library. Instructions on how to use apt-get or emerge to do this can be found here. Alternately, for FreeBSD go to /usr/ports/devel/boost and run make install or on OS X use darwinports and run sudo port install boost.

lbsh can be downloaded from SourceForge.net Logo


Documentation:


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Known Issues:

Please submit any bugs or problems via SourceForge's bug tracker
here
For comments or questions, please contact: Eric Osterweil (eoster@cs.ucla.edu)