Sixth Annual Users' Conference

Conference papers and presentation outlines which address the use of the Transportable Applications Executive (TAE) and its various applications programs are compiled. Emphasis is given to the design of the user interface and image processing workstation in general. Alternate ports of TAE and TAE subsystems are also covered

The space physics environment data analysis system (SPEDAS)

With the advent of the Heliophysics/Geospace System Observatory (H/GSO), a complement of multi-spacecraft missions and ground-based observatories to study the space environment, data retrieval, analysis, and visualization of space physics data can be daunting. The Space Physics Environment Data Analysis System (SPEDAS), a grass-roots software development platform (www.spedas.org), is now officially supported by NASA Heliophysics as part of its data environment infrastructure. It serves more than a dozen space missions and ground observatories and can integrate the full complement of past and upcoming space physics missions with minimal resources, following clear, simple, and well-proven guidelines. Free, modular and configurable to the needs of individual missions, it works in both command-line (ideal for experienced users) and Graphical User Interface (GUI) mode (reducing the learning curve for first-time users). Both options have “crib-sheets,” user-command sequences in ASCII format that can facilitate record-and-repeat actions, especially for complex operations and plotting. Crib-sheets enhance scientific interactions, as users can move rapidly and accurately from exchanges of technical information on data processing to efficient discussions regarding data interpretation and science. SPEDAS can readily query and ingest all International Solar Terrestrial Physics (ISTP)-compatible products from the Space Physics Data Facility (SPDF), enabling access to a vast collection of historic and current mission data. The planned incorporation of Heliophysics Application Programmer’s Interface (HAPI) standards will facilitate data ingestion from distributed datasets that adhere to these standards. Although SPEDAS is currently Interactive Data Language (IDL)-based (and interfaces to Java-based tools such as Autoplot), efforts are under-way to expand it further to work with python (first as an interface tool and potentially even receiving an under-the-hood replacement). We review the SPEDAS development history, goals, and current implementation. We explain its “modes of use” with examples geared for users and outline its technical implementation and requirements with software developers in mind. We also describe SPEDAS personnel and software management, interfaces with other organizations, resources and support structure available to the community, and future development plans.Published versio

An Introduction to Programming for Bioscientists: A Python-based Primer

Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in the biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by fundamental developments in hardware, software, and algorithms. These advances have influenced, and even engendered, a phenomenal array of bioscience fields, including molecular evolution and bioinformatics; genome-, proteome-, transcriptome- and metabolome-wide experimental studies; structural genomics; and atomistic simulations of cellular-scale molecular assemblies as large as ribosomes and intact viruses. In short, much of post-genomic biology is increasingly becoming a form of computational biology. The ability to design and write computer programs is among the most indispensable skills that a modern researcher can cultivate. Python has become a popular programming language in the biosciences, largely because (i) its straightforward semantics and clean syntax make it a readily accessible first language; (ii) it is expressive and well-suited to object-oriented programming, as well as other modern paradigms; and (iii) the many available libraries and third-party toolkits extend the functionality of the core language into virtually every biological domain (sequence and structure analyses, phylogenomics, workflow management systems, etc.). This primer offers a basic introduction to coding, via Python, and it includes concrete examples and exercises to illustrate the language's usage and capabilities; the main text culminates with a final project in structural bioinformatics. A suite of Supplemental Chapters is also provided. Starting with basic concepts, such as that of a 'variable', the Chapters methodically advance the reader to the point of writing a graphical user interface to compute the Hamming distance between two DNA sequences.Comment: 65 pages total, including 45 pages text, 3 figures, 4 tables, numerous exercises, and 19 pages of Supporting Information; currently in press at PLOS Computational Biolog

Second Annual Conference on Astronomical Data Analysis Software and Systems. Abstracts

Abstracts from the conference are presented. The topics covered include the following: next generation software systems and languages; databases, catalogs, and archives; user interfaces/visualization; real-time data acquisition/scheduling; and IRAF/STSDAS/PROS status reports

Software maintenance: generating front ends for cross referencer tools

This thesis surveys the activities performed in software maintenance and identifies some of the software tools which can be utilised by the maintenance programmer. The most expensive phase of software maintenance is surveyed in more detail and tools to support this activity are identified. A new class of cross referencer tool was designed and investigated. The novel aspect of the cross referencer is that it can be used on more than one language, by utihzing grammar driven generators to customize and make maximum re-use of the language independent components, allowing language specific implementations to be generated with minimal effort. The cross referencer also extends an idea of having different levels of detail in cross reference listings by allowing the tool implementor to specify the contents of each level of detail. A proposed experimental toolkit for the automatic construction of these cross referencer front end tools, from non procedural specifications, is designed and investigated

Engineering and Scientific Data Management

The application of data management systems to engineering and scientific data is described

IAC user manual

The User Manual for the Integrated Analysis Capability (IAC) Level 1 system is presented. The IAC system currently supports the thermal, structures, controls and system dynamics technologies, and its development is influenced by the requirements for design/analysis of large space systems. The system has many features which make it applicable to general problems in engineering, and to management of data and software. Information includes basic IAC operation, executive commands, modules, solution paths, data organization and storage, IAC utilities, and module implementation

Interchanging Interactive 3-d Graphics for Astronomy

We demonstrate how interactive, three-dimensional (3-d) scientific visualizations can be efficiently interchanged between a variety of mediums. Through the use of an appropriate interchange format, and a unified interaction interface, we minimize the effort to produce visualizations appropriate for undertaking knowledge discovery at the astronomer's desktop, as part of conference presentations, in digital publications or as Web content. We use examples from cosmological visualization to address some of the issues of interchange, and to describe our approach to adapting S2PLOT desktop visualizations to the Web. Supporting demonstrations are available at http://astronomy.swin.edu.au/s2plot/interchange/Comment: 10 pages, 7 figures, submitted to Publications of the Astronomical Society of Australia. v2. Revised title, revised figure 1, fixed typos, minor additions to future work sectio