ArchiveSpark: Efficient Web Archive Access, Extraction and Derivation

Web archives are a valuable resource for researchers of various disciplines. However, to use them as a scholarly source, researchers require a tool that provides efficient access to Web archive data for extraction and derivation of smaller datasets. Besides efficient access we identify five other objectives based on practical researcher needs such as ease of use, extensibility and reusability. Towards these objectives we propose ArchiveSpark, a framework for efficient, distributed Web archive processing that builds a research corpus by working on existing and standardized data formats commonly held by Web archiving institutions. Performance optimizations in ArchiveSpark, facilitated by the use of a widely available metadata index, result in significant speed-ups of data processing. Our benchmarks show that ArchiveSpark is faster than alternative approaches without depending on any additional data stores while improving usability by seamlessly integrating queries and derivations with external tools.Comment: JCDL 2016, Newark, NJ, US

Research assessment in the humanities: problems and challenges

Research assessment is going to play a new role in the governance of universities and research institutions. Evaluation of results is evolving from a simple tool for resource allocation towards policy design. In this respect "measuring" implies a different approach to quantitative aspects as well as to an estimation of qualitative criteria that are difficult to define. Bibliometrics became so popular, in spite of its limits, just offering a simple solution to complex problems. The theory behind it is not so robust but available results confirm this method as a reasonable trade off between costs and benefits. Indeed there are some fields of science where quantitative indicators are very difficult to apply due to the lack of databases and data, in few words the credibility of existing information. Humanities and social sciences (HSS) need a coherent methodology to assess research outputs but current projects are not very convincing. The possibility of creating a shared ranking of journals by the value of their contents at either institutional, national or European level is not enough as it is raising the same bias as in the hard sciences and it does not solve the problem of the various types of outputs and the different, much longer time of creation and dissemination. The web (and web 2.0) represents a revolution in the communication of research results mainly in the HSS, and also their evaluation has to take into account this change. Furthermore, the increase of open access initiatives (green and gold road) offers a large quantity of transparent, verifiable data structured according to international standards that allow comparability beyond national limits and above all is independent from commercial agents. The pilot scheme carried out at the university of Milan for the Faculty of Humanities demonstrated that it is possible to build quantitative, on average more robust indicators, that could provide a proxy of research production and productiivity even in the HSS

Digital Preservation Services : State of the Art Analysis

Research report funded by the DC-NET project.An overview of the state of the art in service provision for digital preservation and curation. Its focus is on the areas where bridging the gaps is needed between e-Infrastructures and efficient and forward-looking digital preservation services. Based on a desktop study and a rapid analysis of some 190 currently available tools and services for digital preservation, the deliverable provides a high-level view on the range of instruments currently on offer to support various functions within a preservation system.European Commission, FP7peer-reviewe

TmaDB: a repository for tissue microarray data

Background: Tissue microarray (TMA) technology has been developed to facilitate large, genome-scale molecular pathology studies. This technique provides a high-throughput method for analyzing a large cohort of clinical specimens in a single experiment thereby permitting the parallel analysis of molecular alterations ( at the DNA, RNA, or protein level) in thousands of tissue specimens. As a vast quantity of data can be generated in a single TMA experiment a systematic approach is required for the storage and analysis of such data. Description: To analyse TMA output a relational database ( known as TmaDB) has been developed to collate all aspects of information relating to TMAs. These data include the TMA construction protocol, experimental protocol and results from the various immunocytological and histochemical staining experiments including the scanned images for each of the TMA cores. Furthermore the database contains pathological information associated with each of the specimens on the TMA slide, the location of the various TMAs and the individual specimen blocks ( from which cores were taken) in the laboratory and their current status i.e. if they can be sectioned into further slides or if they are exhausted. TmaDB has been designed to incorporate and extend many of the published common data elements and the XML format for TMA experiments and is therefore compatible with the TMA data exchange specifications developed by the Association for Pathology Informatics community. Finally the design of the database is made flexible such that TMA experiments from several types of cancer can be stored in a single database, which incorporates the national minimum data set required for pathology reports supported by the Royal College of Pathologists (UK). Conclusion: TmaDB will provide a comprehensive repository for TMA data such that a large number of results from the numerous immunostaining experiments can be efficiently compared for each of the TMA cores. This will allow a systematic, large-scale comparison of tumour samples to facilitate the identification of gene products of clinical importance such as therapeutic or prognostic markers. In addition this work will contribute to the establishment of a standard for reporting TMA data analogous to MIAME in the description of microarray dat

1st INCF Workshop on Sustainability of Neuroscience Databases

The goal of the workshop was to discuss issues related to the sustainability of neuroscience databases, identify problems and propose solutions, and formulate recommendations to the INCF. The report summarizes the discussions of invited participants from the neuroinformatics community as well as from other disciplines where sustainability issues have already been approached. The recommendations for the INCF involve rating, ranking, and supporting database sustainability

Instant restore after a media failure

Media failures usually leave database systems unavailable for several hours until recovery is complete, especially in applications with large devices and high transaction volume. Previous work introduced a technique called single-pass restore, which increases restore bandwidth and thus substantially decreases time to repair. Instant restore goes further as it permits read/write access to any data on a device undergoing restore--even data not yet restored--by restoring individual data segments on demand. Thus, the restore process is guided primarily by the needs of applications, and the observed mean time to repair is effectively reduced from several hours to a few seconds. This paper presents an implementation and evaluation of instant restore. The technique is incrementally implemented on a system starting with the traditional ARIES design for logging and recovery. Experiments show that the transaction latency perceived after a media failure can be cut down to less than a second and that the overhead imposed by the technique on normal processing is minimal. The net effect is that a few "nines" of availability are added to the system using simple and low-overhead software techniques

Using Links to prototype a Database Wiki

Both relational databases and wikis have strengths that make them attractive for use in collaborative applications. In the last decade, database-backed Web applications have been used extensively to develop valuable shared biological references called curated databases. Databases offer many advantages such as scalability, query optimization and concurrency control, but are not easy to use and lack other features needed for collaboration. Wikis have become very popular for early-stage biocuration projects because they are easy to use, encourage sharing and collaboration, and provide built-in support for archiving, history-tracking and annotation. However, curation projects often outgrow the limited capabilities of wikis for structuring and efficiently querying data at scale, necessitating a painful phase transition to a database-backed Web application. We perceive a need for a new class of general-purpose system, which we call a Database Wiki, that combines flexible wiki-like support for collaboration with robust database-like capabilities for structuring and querying data. This paper presents DBWiki, a design prototype for such a system written in the Web programming language Links. We present the architecture, typical use, and wiki markup language design for DBWiki and discuss features of Links that provided unique advantages for rapid Web/database application prototyping

VXA: A Virtual Architecture for Durable Compressed Archives

Data compression algorithms change frequently, and obsolete decoders do not always run on new hardware and operating systems, threatening the long-term usability of content archived using those algorithms. Re-encoding content into new formats is cumbersome, and highly undesirable when lossy compression is involved. Processor architectures, in contrast, have remained comparatively stable over recent decades. VXA, an archival storage system designed around this observation, archives executable decoders along with the encoded content it stores. VXA decoders run in a specialized virtual machine that implements an OS-independent execution environment based on the standard x86 architecture. The VXA virtual machine strictly limits access to host system services, making decoders safe to run even if an archive contains malicious code. VXA's adoption of a "native" processor architecture instead of type-safe language technology allows reuse of existing "hand-optimized" decoders in C and assembly language, and permits decoders access to performance-enhancing architecture features such as vector processing instructions. The performance cost of VXA's virtualization is typically less than 15% compared with the same decoders running natively. The storage cost of archived decoders, typically 30-130KB each, can be amortized across many archived files sharing the same compression method.Comment: 14 pages, 7 figures, 2 table