The Prickly Pear Archive: a portable hypermedia for scholarly publication

An executable paper is a hypermedia for publishing, reviewing, and reading scholarly papers which include a complete HPC software development or scientific code. A hypermedia is an integrated interface to multimedia including text, figures, video, and executables, on a subject of interest. Results within the executable paper include numeric output, graphs, charts, tables, equations and the underlying codes which generated such results. These results are dynamically regenerated and included in the paper upon recompilation and re-execution of the code. This enables a scientifically enriched environment which functions not only as a journal but as a laboratory in itself, in which readers and reviewers may interact with and validate the results.

The Prickly Pear Archive (PPA) is such a system [2]. One distinguishing feature of the PPA is the inclusion of an underlying component-based simulation framework, Cactus [8], which simplifies the process of composing, compiling, and executing simulation codes. Code creation is simplified using common bits of infrastructure; each paper augments to the functionality of the framework. New distinguishing features include the (1) portability and (2) reproducibility of the archive, which allow researchers to move and re-create the software environment in which the simulation code was created. Further, the (3) Piraha parser is now used to match complex multi-line expressions inside parameter and LaTEX files. Finally, (4) an altogether new web interface has been created. The new interface options closely mirror the directory structure within the paper itself, which gives the reader a transparent view of the paper. Thus, once accustomed to reading from the archive, assembling a paper package becomes a straightforward and intuitive process.

A PPA production system hosted on HPC resources (e.g. an XSEDE machine) unifies the computational scientific process with the publication process. A researcher may use the production archive to test simulations; and upon arriving at a scientifically meaningful result, the user may then incorporate the result in an executable paper on the very same resource the simulation was conducted. Housed within a virtual machine, the PPA allows multiple accounts within the same production archive, enabling users across campuses to bridge their efforts in developing scientific codes.