ActivePapers is a software infrastructure for creating and working with
electronic documents that contain scientific data, executable code
working on this data, as well as visualization code and human-readable
documentation. For more information, see

   http://dirac.cnrs-orleans.fr/plone/software/activepapers/


Working with a development snapshot
===================================

The following instructions should work on any Unix-like operating
system; they have been tested with Linux (Ubuntu 10.04) and
MacOS X (10.5 and 10.6).

Prerequisites:
- Java 6 or higher (Java 5 should work, but hasn't been tested)

No installation is required. After unpacking the downlaoded file
(which you presumably already did if you are reading this file), you
can run the command line tool with ./bin/a-paper.  If you wish to copy
this script to some other location on your computer, you need to
change the three lines that identify the installation directory; see
the comment in the script.

For your first steps with ActivePapers, see doc/tutorial.txt.


Building from source code
=========================

The following instructions should work on any Unix-like operating
system; they have been tested with Linux (Ubuntu 10.04) and
MacOS X (10.5 and 10.6). The ActivePapers system should work
under Windows as well, but the installation procedure and the
script in bin/a-paper need to be adapted.

Prerequisites:
- Java 6 or higher (Java 5 should work, but hasn't been tested)
- Gradle 1.0 (http://www.gradle.org/)
- wget for downloading the dependencies

Steps:

1) Go to the active_papers directory
2) ./bin/initialize
3) gradle build

After that, you can run the command line tool with ./bin/a-paper.
If you wish to copy this script to some other location on your computer,
you need to change the three lines that identify the installation
directory; see the comment in the script.

For your first steps with ActivePapers, see doc/tutorial.txt.


Acknowledgements
================

The following freely available JVM libraries are included in this
distribution:

- Clojure 1.2.1
- Clojure-contrib 1.2.0
- JHDF 11.05 (which includes the HDF5 library)
- clj-hdf5 0.1
- swank-clojure 1.3.0
- clojure-jsr223
- Jython 2.5.2
- JFreeChart 1.3.0
- JCommon 1.0
- Incanter 1.2
- Clojuresque 1.4.1

I would like to thank the Clojure, Jython, and HDF5 communities as
well as the author of the JHDF5 library for having answered many
questions.

This work was supported by the Agence Nationale de la Recherche
(Contract No. ANR-2010-COSI-001-01).


Konrad Hinsen
Centre de Biophysique Moleculaire (CNRS)
research@khinsen.fastmail.net