scholarly journals Defining File Format Obsolescence: A Risky Journey

2008 ◽  
Vol 3 (1) ◽  
pp. 89-106 ◽  
Author(s):  
David Pearson ◽  
Colin Webb
Keyword(s):  
Risk Factor ◽  
Software Tool ◽  
Digital Information ◽  
File Format ◽  
Sources Of Information ◽  
National Library ◽  
File Formats ◽  
Wide Range ◽  
Information Collections ◽  
Further Development

File format obsolescence is a major risk factor threatening the ongoing usefulness of digital information collections. While the preservation community has become increasingly interested in tools for assessing a wide range of risks, the National Library of Australia is developing mechanisms specifically focused on the risks of format obsolescence. The paper reports on the AONS II Project, undertaken in conjunction with the Australian Partnership for Sustainable Repositories (APSR). The project aimed to refine and develop a software tool that would automatically find and report indicators of obsolescence risks, to help repository managers decide if preservation action is needed. The paper discusses the current mismatch between this objective and the available sources of information on file formats, and emphasises the need to take account of both local and global factors in assessing risk. The paper calls for the preservation community to engage with the further development of thinking about file format obsolescence.

scholarly journals Assessing and assuring interoperability of a genomics file format

2022 ◽  
Author(s):  
Yi Nian Niu ◽  
Eric G. Roberts ◽  
Danielle Denisko ◽  
Michael M. Hoffman
Keyword(s):  
Formal Specification ◽  
Poor Performance ◽  
Multiple Root ◽  
Interval Data ◽  
Test Suite ◽  
File Format ◽  
Software Packages ◽  
File Formats ◽  
Wide Range ◽  
Bioinformatics Software

Background: Bioinformatics software tools operate largely through the use of specialized genomics file formats. Often these formats lack formal specification, and only rarely do the creators of these tools robustly test them for correct handling of input and output. This causes problems in interoperability between different tools that, at best, wastes time and frustrates users. At worst, interoperability issues could lead to undetected errors in scientific results. Methods: We sought (1) to assess the interoperability of a wide range of bioinformatics software using a shared genomics file format and (2) to provide a simple, reproducible method for enhancing interoperability. As a focus, we selected the popular BED file format for genomic interval data. Based on the file format's original documentation, we created a formal specification. We developed a new verification system, Acidbio (https://github.com/hoffmangroup/acidbio), which tests for correct behavior in bioinformatics software packages. We crafted tests to unify correct behavior when tools encounter various edge cases—potentially unexpected inputs that exemplify the limits of the format. To analyze the performance of existing software, we tested the input validation of 80 Bioconda packages that parsed the BED format. We also used a fuzzing approach to automatically perform additional testing. Results: Of 80 software packages examined, 75 achieved less than 70% correctness on our test suite. We categorized multiple root causes for the poor performance of different types of software. Fuzzing detected other errors that the manually designed test suite could not. We also created a badge system that developers can use to indicate more precisely which BED variants their software accepts and to advertise the software's performance on the test suite. Discussion: Acidbio makes it easy to assess interoperability of software using the BED format, and therefore to identify areas for improvement in individual software packages. Applying our approach to other file formats would increase the reliability of bioinformatics software and data.

Evaluating whole-slide imaging viewers used in digital pathology

2020 ◽  
Vol 2020 (9) ◽  
pp. 372-1-372-6
Author(s):  
Wei-Chung Cheng ◽  
Samuel Lam ◽  
Qi Gong ◽  
Paul Lemaillet
Keyword(s):  
Digital Pathology ◽  
Software Tool ◽  
Color Difference ◽  
Third Party ◽  
File Format ◽  
Whole Slide Imaging ◽  
The Past ◽  
Compressed Images ◽  
File Formats ◽  
Color Differences

As a Class II medical device, whole-slide imaging (WSI) systems are emerging to succeed light microscopes used by pathologists in the past decades by digitalizing histological tissue slides into millions of pixels saved in a WSI file. Unlike the standard image file formats such as JPEG or TIFF, a WSI file usually consists of hundreds of compressed images of different magnification levels and focal planes that need to be decompressed, stitched, scaled, and colormanaged to reproduce the view demanded by the user with zooming and panning operations. Currently, most WSI files are stored in proprietary file formats, due to the lack of adopting a standard WSI file format, which hinders the development of third-party WSI viewers by making it difficult to interpret WSI files faithfully. To examine the fidelity of third-party WSI viewers, in this study, three freely available viewers, Sedeen, QuPath, and ASAP, were compared with the factory viewer, NDP, at the pixel level. A software tool was developed to register and calculate the 1976 CIE color difference for each pixel between two viewers. The average color differences were found as 1.30, 18.69, and 18.79 ΔE for Sedeen, QuPath, and ASAP, respectively.

Application of TEM to Deformation, Wear, and Fracture of Ceramics

1974 ◽  
Vol 32 ◽  
pp. 472-473
Author(s):  
B. J. Hockey
Keyword(s):  
Wear Resistance ◽  
High Temperature ◽  
Mechanical Behavior ◽  
Brittle Materials ◽  
High Temperature Strength ◽  
Wide Range ◽  
Corrosive Environments ◽  
Further Development

Ceramics, such as Al2O3 and SiC have numerous current and potential uses in applications where high temperature strength, hardness, and wear resistance are required often in corrosive environments. These materials are, however, highly anisotropic and brittle, so that their mechanical behavior is often unpredictable. The further development of these materials will require a better understanding of the basic mechanisms controlling deformation, wear, and fracture.The purpose of this talk is to describe applications of TEM to the study of the deformation, wear, and fracture of Al2O3. Similar studies are currently being conducted on SiC and the techniques involved should be applicable to a wide range of hard, brittle materials.

scholarly journals Informing the public health response to COVID-19: a systematic review of risk factors for disease, severity, and mortality

2021 ◽  
Vol 21 (1) ◽  
Author(s):  
M. Flook ◽  
C. Jackson ◽  
E. Vasileiou ◽  
C. R. Simpson ◽  
M. D. Muckian ◽  
...  
Keyword(s):  
Public Health ◽  
Risk Factors ◽  
Systematic Review ◽  
At Risk ◽  
Risk Factor ◽  
Disease Severity ◽  
Severe Disease ◽  
Public Health Response ◽  
Wide Range ◽  
Multivariable Analyses

Abstract Background Severe Acute Respiratory Syndrome coronavirus-2 (SARS-CoV-2) has challenged public health agencies globally. In order to effectively target government responses, it is critical to identify the individuals most at risk of coronavirus disease-19 (COVID-19), developing severe clinical signs, and mortality. We undertook a systematic review of the literature to present the current status of scientific knowledge in these areas and describe the need for unified global approaches, moving forwards, as well as lessons learnt for future pandemics. Methods Medline, Embase and Global Health were searched to the end of April 2020, as well as the Web of Science. Search terms were specific to the SARS-CoV-2 virus and COVID-19. Comparative studies of risk factors from any setting, population group and in any language were included. Titles, abstracts and full texts were screened by two reviewers and extracted in duplicate into a standardised form. Data were extracted on risk factors for COVID-19 disease, severe disease, or death and were narratively and descriptively synthesised. Results One thousand two hundred and thirty-eight papers were identified post-deduplication. Thirty-three met our inclusion criteria, of which 26 were from China. Six assessed the risk of contracting the disease, 20 the risk of having severe disease and ten the risk of dying. Age, gender and co-morbidities were commonly assessed as risk factors. The weight of evidence showed increasing age to be associated with severe disease and mortality, and general comorbidities with mortality. Only seven studies presented multivariable analyses and power was generally limited. A wide range of definitions were used for disease severity. Conclusions The volume of literature generated in the short time since the appearance of SARS-CoV-2 has been considerable. Many studies have sought to document the risk factors for COVID-19 disease, disease severity and mortality; age was the only risk factor based on robust studies and with a consistent body of evidence. Mechanistic studies are required to understand why age is such an important risk factor. At the start of pandemics, large, standardised, studies that use multivariable analyses are urgently needed so that the populations most at risk can be rapidly protected. Registration This review was registered on PROSPERO as CRD42020177714.

scholarly journals Biodiversity of Secondary Metabolites Compounds Isolated from Phylum Actinobacteria and Its Therapeutic Applications

Molecules ◽  
2021 ◽  
Vol 26 (15) ◽  
pp. 4504
Author(s):  
Muhanna Al-shaibani ◽  
Radin Maya Saphira Radin Mohamed ◽  
Nik Sidik ◽  
Hesham Enshasy ◽  
Adel Al-Gheethi ◽  
...  
Keyword(s):  
Secondary Metabolites ◽  
Bioactive Compounds ◽  
Extreme Environments ◽  
Software Tool ◽  
Gene Clusters ◽  
Well Being ◽  
Bioactive Substances ◽  
Diverse Range ◽  
Wide Range ◽  
Potential Applications

The current review aims to summarise the biodiversity and biosynthesis of novel secondary metabolites compounds, of the phylum Actinobacteria and the diverse range of secondary metabolites produced that vary depending on its ecological environments they inhabit. Actinobacteria creates a wide range of bioactive substances that can be of great value to public health and the pharmaceutical industry. The literature analysis process for this review was conducted using the VOSviewer software tool to visualise the bibliometric networks of the most relevant databases from the Scopus database in the period between 2010 and 22 March 2021. Screening and exploring the available literature relating to the extreme environments and ecosystems that Actinobacteria inhabit aims to identify new strains of this major microorganism class, producing unique novel bioactive compounds. The knowledge gained from these studies is intended to encourage scientists in the natural product discovery field to identify and characterise novel strains containing various bioactive gene clusters with potential clinical applications. It is evident that Actinobacteria adapted to survive in extreme environments represent an important source of a wide range of bioactive compounds. Actinobacteria have a large number of secondary metabolite biosynthetic gene clusters. They can synthesise thousands of subordinate metabolites with different biological actions such as anti-bacterial, anti-parasitic, anti-fungal, anti-virus, anti-cancer and growth-promoting compounds. These are highly significant economically due to their potential applications in the food, nutrition and health industries and thus support our communities’ well-being.

Research on the Three-Dimensional Displaying of STL ASCII and Binary File

2014 ◽  
Vol 940 ◽  
pp. 433-436 ◽  
Author(s):  
Ying Zhang ◽  
Xin Shi
Keyword(s):  
Detailed Analysis ◽  
Programming Language ◽  
Coordinate Transformation ◽  
Graphical Representation ◽  
Three Dimensional ◽  
File Format ◽  
Binary File ◽  
Stl File ◽  
File Formats ◽  
Three Dimensional Display

Based on the detailed analysis of the STL file format, VC++ 6.0 programming language was used to extract the STL ASCII and binary file information, at the same time, using the OpenGL triangle drawing technology for graphical representation of the STL file, with rendering functions such as material, coordinate transformation, lighting, et al, finally realizing the loading and three-dimensional display of STL ASCII and binary file formats.

The functions and positions of political parties in consociational democracies: theoretical and empirical contexts

2020 ◽  
pp. 28-33
Author(s):  
O. Morhuniuk
Keyword(s):  
Political Parties ◽  
The Netherlands ◽  
Party System ◽  
Party Competition ◽  
European Countries ◽  
The Past ◽  
Democratic Regimes ◽  
Wide Range ◽  
Key Aspects ◽  
Further Development

An article is devoted to the analysis of the functions and formats of political parties in consociational democracies. In particular, it is defined that parties that represent the interests of certain subcultures in society and that reach a consensus among themselves at the level of political agreements are called segmental. At the same time, parties that encapsulate different subgroups of the society that cooperate inside the party within main features of the consociational theory (grand coalition, mutual veto, proportionality in representations, and independence of segments or society subcultures) are called consociational. The theory of consociationalism has received a wide range of theoretical additions and criticism from political scientists over the past fifty years. And while political parties should have been, by definition, one of the key aspects of research within such democratic regimes (parties are part of large coalitions and agents of representation of certain subcultures), there is very scarce number of literature that focuses on this aspect. Therefore, the presented article provides a description of the functions of political parties that could be observed as inside their subcultures as well as in interaction with other segmental parties. Based on the experience of two European countries in the period of “classical” consociationalism (Belgium and the Netherlands), we explain the functions of the parties we have defined in such societies with examples of relevant consociational practices in them. Simultaneously with the analysis of segmental parties, the article also offers the characteristics of consociational parties. The emergence of such parties has its own institutional and historical features. The way of further development of the party system and the level of preservation of consociational practices makes it possible to understand the nature of changes in the societies. Similarly, the analysis of the forms of party competition and interaction between segmental parties makes it possible to outline the forms of those consociational changes that are taking place in the research countries.

Backing up digital preservation practice with empirical research

2017 ◽  
Vol 27 (2) ◽  
pp. 66-82
Author(s):  
Gareth Kay ◽  
Libor Coufal ◽  
Mark Pearson
Keyword(s):  
Knowledge Base ◽  
Empirical Research ◽  
Digital Preservation ◽  
Graph Database ◽  
National Library ◽  
Software Applications ◽  
Functional Relationships ◽  
File Formats ◽  
Digital Objects

This article introduces the National Library of Australia’s Digital Preservation Knowledge Base which helps the Library to manage digital objects from its collections over the long term. The Knowledge Base includes information on file formats, rendering software, operating systems, hardware and, most importantly, the relationships between them. Most of the work on the Knowledge Base over the last few years has been focused on the mapping of functional relationships between file formats, their versions and software applications. The information is gathered through unique empirical research and is initially being recorded in a multiple-worksheet Excel file in a semi-structured format, though development of a prototype graph database is underway.

scholarly journals Digital Curation for Science, Digital Libraries, and Individuals

2008 ◽  
Vol 1 ◽  
pp. 3-16 ◽  
Author(s):  
Neil Beagrie
Keyword(s):  
Digital Libraries ◽  
Digital Information ◽  
Digital Curation ◽  
Wide Range ◽  
Intellectual Assets ◽  
Information Professionals ◽  
Using Data ◽  
Traditional Roles ◽  
Significant Effort ◽  
Digital Assets

The creation, management and use of digital materials are of increasing importance for a wide range of activities. Much of the knowledge base and intellectual assets of institutions and individuals are now in digital form. The term digital curation is increasingly being used for the actions needed to add value to and maintain these digital assets over time for current and future generations of users. The paper explores this emerging field of digital curation as an area of inter-disciplinary research and practice, and the trends which are influencing its development. It analyses the genesis of the term and how traditional roles relating to digital assets are in transition. Finally it explores some of the drivers for curation ranging from trends such as exponential growth in digital information, to "life-caching", digital preservation, the Grid and new opportunities for publishing, sharing, and re-using data. It concludes that significant effort needs to be put into developing a persistent information infrastructure for digital materials and into developing the digital curation skills of researchers and information professionals. Without this, current investment in digitisation and digital content will only secure short-term rather than lasting benefits.

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