Fedora - An Open Source Digital Preservation Solution

Fedora is an open source, digital preservation focused digital repository platform used for the management and dissemination of digital content. Used by a wide variety of institution types and scientific research centers, Fedora provides the flexibility and extensibility to store and provide access to large and complex collections of digital objects. Agnostic of the file formats it can accept, Fedora is well suited to handle a variety of use cases with a focus on providing robust digital preservation. Fedora 6.2 is the most current version of the application and is being well-received in the community. This version is a major rewrite of the popular, widely-used digital repository and was guided by three themes: enhanced digital preservation sensibilities, migration support from all previous versions going back to version 3, and improved performance and scalability. With an emphasis on digital preservation standards, Fedora 6 enhances these capabilities by incorporating the Oxford Common File Layout (OCFL). The OCFL specifies a transparent, well-structured and application-independent storage layer for digital objects. This presentation will highlight features available in Fedora 6.x and outline their importance for providing enhanced digital preservation within your repository. Features of interest include OCFL-based persistence for long-term storage, simple search, and real-time repository performance monitoring through the use of Grafana and Prometheus

Using pattern languages in participatory design

In this paper, we examine the contribution that pattern languages could make to user participation in the design of interactive systems, and we report on our experiences of using pattern languages in this way. In recent years, there has been a growing interest in the use of patterns and pattern languages in the design of interactive systems. Pattern languages were originally developed by the architect, Christopher Alexander, both as a way of understanding the nature of building designs that promote a ‘humane’ or living built environment; and as a practical tool to aid in participatory design of buildings. Our experience suggests that pattern languages do have considerable potential to support participatory design in HCI, but that many pragmatic issues remain to be resolved.</p

The architectures of media power: editing, the newsroom, and urban public space

This paper considers the relation of the newsroom and the city as a lens into the more general relation of production spaces and mediated publics. Leading theoretically from Lee and LiPuma’s (2002) notion of ‘cultures of circulation’, and drawing on an ethnography of the Toronto Star, the paper focuses on how media forms circulate and are enacted through particular practices and material settings. With its attention to the urban milieus and orientations of media organizations, this paper exhibits both affinities with but also differences to current interests in the urban architectures of media, which describe and theorize how media get ‘built into’ the urban experience more generally. In looking at editing practices situated in the newsroom, an emphasis is placed on the phenomenological appearance of media forms both as objects for material assembly as well as more abstracted subjects of reflexivity, anticipation and purposiveness. Although this is explored with detailed attention to the settings of the newsroom and the city, the paper seeks to also provide insight into the more general question of how publicness is material shaped and sited

Scaffolder - Software for Reproducible Genome Scaffolding.

Background: Assembly of short-read sequencing data can result in a fragmented non-contiguous series of genomic sequences. Therefore a common step in a genome project is to join neighboring sequence regions together and fill gaps in the assembly using additional sequences. This scaffolding step, however, is non-trivial and requires manually editing large blocks of nucleotide sequence. Joining these sequences together also hides the source of each region in the final genome sequence. Taken together, these considerations may make reproducing or editing an existing genome build difficult.&#xd;&#xa;&#xd;&#xa;Methods: The software outlined here, &#x201c;Scaffolder,&#x201d; is implemented in the Ruby programming language and can be installed via the RubyGems software management system. Genome scaffolds are defined using YAML - a data format, which is both human and machine-readable. Command line binaries and extensive documentation are available.&#xd;&#xa;&#xd;&#xa;Results: This software allows a genome build to be defined in terms of the constituent sequences using a relatively simple syntax to define the scaffold. This syntax further allows unknown regions to be defined, and adds additional sequences to fill gaps in the scaffold. Defining the genome construction in a file makes the scaffolding process reproducible and easier to edit compared with FASTA nucleotide sequence.&#xd;&#xa;&#xd;&#xa;Conclusions: Scaffolder is easy-to-use genome scaffolding software. This tool promotes reproducibility and continuous development in a genome project. Scaffolder can be found at http://next.gs

Adapting SAM for CDF

The CDF and D0 experiments probe the high-energy frontier and as they do so have accumulated hundreds of Terabytes of data on the way to petabytes of data over the next two years. The experiments have made a commitment to use the developing Grid based on the SAM system to handle these data. The D0 SAM has been extended for use in CDF as common patterns of design emerged to meet the similar requirements of these experiments. The process by which the merger was achieved is explained with particular emphasis on lessons learned concerning the database design patterns plus realization of the use cases.Comment: Talk from the 2003 Computing in High Energy and Nuclear Physics (CHEP03), La Jolla, Ca, USA, March 2003, 4 pages, pdf format, TUAT00