scholarly journals A comprehensive, FAIR file format for neuroanatomical structure modeling

2020 ◽  
Author(s):  
A. E. Sullivan ◽  
S. J. Tappan ◽  
P. J. Angstman ◽  
A. Rodriguez ◽  
G. C. Thomas ◽  
...  
Keyword(s):  
Biological Research ◽  
File Format ◽  
Data Types ◽  
Alternative Analysis ◽  
Data Format ◽  
Digital Reconstruction ◽  
Data Files ◽  
Rich Data ◽  
Scientific Questions ◽  
Neuroscience Community

AbstractWith advances in microscopy and computer science, the technique of digitally reconstructing, modeling, and quantifying microscopic anatomies has become central to many fields of biological research. MBF Bioscience has chosen to openly document their digital reconstruction file format, Neuromorphological File Specification (4.0), available at www.mbfbioscience.com/filespecification (Angstman et al. 2020). One of such technologies, the format created and maintained by MBF Bioscience is broadly utilized by the neuroscience community. The data format’s structure and capabilities have evolved since its inception, with modifications made to keep pace with advancements in microscopy and the scientific questions raised by worldwide experts in the field. More recent modifications to the neuromorphological data format ensure it abides by the Findable, Accessible, Interoperable, and Reusable (FAIR) data standards promoted by the International Neuroinformatics Coordinating Facility (INCF; Wilkinson et al. 2016). The incorporated metadata make it easy to identify and repurpose these data types for downstream application and investigation. This publication describes key elements of the file format and details their relevant structural advantages in an effort to encourage the reuse of these rich data files for alternative analysis or reproduction of derived conclusions.

scholarly journals A Comprehensive, FAIR File Format for Neuroanatomical Structure Modeling

2021 ◽  
Author(s):  
A. E. Sullivan ◽  
S. J. Tappan ◽  
P. J. Angstman ◽  
A. Rodriguez ◽  
G. C. Thomas ◽  
...  
Keyword(s):  
Scientific Data ◽  
Biological Research ◽  
File Format ◽  
Data Types ◽  
Alternative Analysis ◽  
Digital Reconstruction ◽  
Data Files ◽  
Rich Data ◽  
Scientific Questions ◽  
Neuroscience Community

AbstractWith advances in microscopy and computer science, the technique of digitally reconstructing, modeling, and quantifying microscopic anatomies has become central to many fields of biological research. MBF Bioscience has chosen to openly document their digital reconstruction file format, the Neuromorphological File Specification, available at www.mbfbioscience.com/filespecification (Angstman et al., 2020). The format, created and maintained by MBF Bioscience, is broadly utilized by the neuroscience community. The data format’s structure and capabilities have evolved since its inception, with modifications made to keep pace with advancements in microscopy and the scientific questions raised by worldwide experts in the field. More recent modifications to the neuromorphological file format ensure it abides by the Findable, Accessible, Interoperable, and Reusable (FAIR) data principles promoted by the International Neuroinformatics Coordinating Facility (INCF; Wilkinson et al., Scientific Data, 3, 160018,, 2016). The incorporated metadata make it easy to identify and repurpose these data types for downstream applications and investigation. This publication describes key elements of the file format and details their relevant structural advantages in an effort to encourage the reuse of these rich data files for alternative analysis or reproduction of derived conclusions.

scholarly journals Recommendations for an Open Science approach to welding process research data

2021 ◽  
Author(s):  
Cagtay Fabry ◽  
Andreas Pittner ◽  
Volker Hirthammer ◽  
Michael Rethmeier
Keyword(s):  
Domain Knowledge ◽  
Knowledge Exchange ◽  
Welding Process ◽  
Open Science ◽  
Research Data ◽  
Fusion Welding ◽  
File Format ◽  
Data Format ◽  
Science Practices ◽  
Science Community

AbstractThe increasing adoption of Open Science principles has been a prevalent topic in the welding science community over the last years. Providing access to welding knowledge in the form of complex and complete datasets in addition to peer-reviewed publications can be identified as an important step to promote knowledge exchange and cooperation. There exist previous efforts on building data models specifically for fusion welding applications; however, a common agreed upon implementation that is used by the community is still lacking. One proven approach in other domains has been the use of an openly accessible and agreed upon file and data format used for archiving and sharing domain knowledge in the form of experimental data. Going into a similar direction, the welding community faces particular practical, technical, and also ideological challenges that are discussed in this paper. Collaboratively building upon previous work with modern tools and platforms, the authors motivate, propose, and outline the use of a common file format specifically tailored to the needs of the welding research community as a complement to other already established Open Science practices. Successfully establishing a culture of openly accessible research data has the potential to significantly stimulate progress in welding research.

scholarly journals LandScape: a web application for interactive genomic summary visualization

2019 ◽  
Author(s):  
Wenlong Jia ◽  
Hechen Li ◽  
Shiying Li ◽  
Shuaicheng Li
Keyword(s):  
Genetic Information ◽  
Web Application ◽  
Genomic Research ◽  
File Format ◽  
Data Types ◽  
Web Based ◽  
Link Type ◽  
Level Data ◽  
Real Time Visualization ◽  
Information Landscape

ABSTRACTSummaryVisualizing integrated-level data from genomic research remains a challenge, as it requires sufficient coding skills and experience. Here, we present LandScapeoviz, a web-based application for interactive and real-time visualization of summarized genetic information. LandScape utilizes a well-designed file format that is capable of handling various data types, and offers a series of built-in functions to customize the appearance, explore results, and export high-quality diagrams that are available for publication.Availability and implementationLandScape is deployed at bio.oviz.org/demo-project/analyses/landscape for online use. Documentation and demo data are freely available on this website and GitHub (github.com/Nobel-Justin/Oviz-Bio-demo)[email protected]

scholarly journals The Association of Religion Data Archives (ARDA): Online Research Data, Tools and References

2008 ◽  
Vol 1 (3) ◽  
pp. 456-470 ◽  
Author(s):  
Roger Finke ◽  
Amy Adamczyk
Keyword(s):  
State University ◽  
Pennsylvania State University ◽  
Research And Teaching ◽  
Data Archives ◽  
Wide Range ◽  
International Data ◽  
Data Files ◽  
The Rich ◽  
Rich Data ◽  
Website Features

AbstractThe Association of Religion Data Archives (ARDA) currently archives over 500 local, national, and international data files, and offers a wide range of research tools to build surveys, preview data online, develop customized maps and reports of United States church membership, and examine religion differences across nations and regions of the world. The ARDA also supports reference and teaching tools that draw on the rich data archive. This research article offers a brief introduction to the quantitative data available for exploration or download, and a few of the website features most useful for research and teaching. Supported by the Lilly Endowment, the John Templeton Foundation, the Pennsylvania State University, and the Baylor Institute for Studies of Religion, all data downloads and online services are free of charge.

Electronic Charts for Oceangoing Vessels

1993 ◽  
Vol 46 (3) ◽  
pp. 406-411 ◽  
Author(s):  
Colin G. Weeks
Keyword(s):  
Information System ◽  
New Orleans ◽  
Software Package ◽  
Current Data ◽  
Differential Gps ◽  
Data Format ◽  
Blind Navigation ◽  
The Us ◽  
Electronic Chart ◽  
Data Files

It is probable that Congress will require oceangoing ships in US ports to use Differential GPS (DGPS) and electronic charts once DGPS is available on all coasts of the US, which is currently scheduled for completion by the end of 1996. The type of electronic chart currently envisaged, the Electronic Chart Display and Information System (ECDIS) under development by the IMO & IHO, is unsuitable for those ports which are entered through long dredged channels – a category that includes Houston, Gramercy and New Orleans, the three ports which handled the most foreign tonnage in 1991. A different type of electronic chart has been in daily use in such channels, with microwave positioning, since 1984; the combination of DGPS with such a software package has been called an Electronic Navigation System (ENS) and differs from ECDIS in that the ENS is designed to supplement the published chart, not replace it. The paper suggests that the utility of ECDIS would be enhanced if its specifications were modified to allow the entry of the data files used by the ENS, thus giving ECDIS a similar capability for blind navigation in confined waters. Standardization of the current data format would also permit alternative versions of ENS to be developed.

scholarly journals New features and improvements in the NEA nuclear data tool suite

2020 ◽  
Vol 239 ◽  
pp. 19003
Author(s):  
M. Fleming ◽  
I. Hill ◽  
J. Dyrda ◽  
L. Fiorito ◽  
N. Soppera ◽  
...  
Keyword(s):  
Relational Databases ◽  
Uncertainty Propagation ◽  
Nuclear Data ◽  
Data Types ◽  
Reactor Physics ◽  
Energy Agency ◽  
Order Of Magnitude ◽  
Data Files ◽  
Improved Performance ◽  
Data Libraries

The OECD Nuclear Energy Agency (NEA) has developed and maintains several products that are used in the verification and validation of nuclear data, including the Java-based Nuclear Data Information System (JANIS) and the Nuclear Data Sensitivity Tool (NDaST). These integrate other collections of the NEA, including the International Handbooks of benchmark experiments on Criticality Safety and Reactor Physics (ICSBEP and IRPhEP) and their supporting relational databases (DICE and IDAT). Recent development of the JANIS, DICE and NDaST systems have resulted in the ability to perform uncertainty propagation utilising Legendre polynomial sensitivities, calculation of case-to-case covariances and correlations, use of spectrum weighting in perturbations, calculation of statistical results with suites of randomly sampled nuclear data files and new command-line interfaces to automate analyses and generate XML outputs. All of the most recent, major nuclear data libraries have been fully processed and incorporated, along with new visualisation features for covariances and sensitivities, an expanded set of reaction channel definitions, and new EXFOR data types defined by the NRDC. Optimisation of numerical methods has also improved performance, with over order-of-magnitude speed-up in the case of sensitivity-uncertainty calculations.

Dynamic Metadata Management System for Digital Archives

2005 ◽  
pp. 55-75
Author(s):  
Shien-chiang Yu ◽  
Hsueh-hua Chen ◽  
Chao-chen Chen
Keyword(s):  
Management System ◽  
Metadata Management ◽  
Digital Archives ◽  
Data Types ◽  
Data Format ◽  
Digital Museum ◽  
National Science ◽  
National Science Council

This chapter describes metalogy, an XML/metadata framework that can handle several different metadata formats. Metalogy was developed under the Digital Museum Project funded by the National Science Council of Taiwan. It is common to have different data types and catalog formats even within one organization. In order to accommodate a variety of objects, it is often necessary to adopt several metadata formats. Thus, when designing a metadata management system, one needs to be able to handle heterogeneous metadata formats. XML, being a standard gaining increasing popularity, is also often used as data format so that exchange between data can be done in a uniform way.

The BioDynaMo Project

2021 ◽  
pp. 1785-1791
Author(s):  
Roman Bauer ◽  
Lukas Breitwieser ◽  
Alberto Di Meglio ◽  
Leonard Johard ◽  
Marcus Kaiser ◽  
...  
Keyword(s):  
Computer Simulations ◽  
Lessons Learned ◽  
Biological Research ◽  
Computing Systems ◽  
Spatial And Temporal Scales ◽  
Scientific Investigations ◽  
Complex Organization ◽  
Computer Resources ◽  
Scientific Questions ◽  
Heterogeneous Interactions

Computer simulations have become a very powerful tool for scientific research. Given the vast complexity that comes with many open scientific questions, a purely analytical or experimental approach is often not viable. For example, biological systems comprise an extremely complex organization and heterogeneous interactions across different spatial and temporal scales. In order to facilitate research on such problems, the BioDynaMo project aims at a general platform for computer simulations for biological research. Since scientific investigations require extensive computer resources, this platform should be executable on hybrid cloud computing systems, allowing for the efficient use of state-of-the-art computing technology. This chapter describes challenges during the early stages of the software development process. In particular, we describe issues regarding the implementation and the highly interdisciplinary as well as international nature of the collaboration. Moreover, we explain the methodologies, the approach, and the lessons learned by the team during these first stages.

Recommended standard for seismic (/radar) data files in the personal computer environment

Geophysics ◽  
1990 ◽  
Vol 55 (9) ◽  
pp. 1260-1271 ◽  
Author(s):  
S. E. Pullan
Keyword(s):  
Personal Computer ◽  
Data File ◽  
Radar Data ◽  
Small Computer ◽  
File Format ◽  
Shallow Seismic ◽  
Computer Environment ◽  
Data Files

This paper is the result of the work of a subcommittee of SEG’s Engineering and Groundwater Geophysics Committee. It recommends a data file format for raw or processed shallow seismic or digital radar data in the small computer environment. It is recommended that this format be known as the SEG-2 format.

AN ONTOLOGY FOR SEMANTIC INTEGRATION OF LIFE SCIENCE WEB DATABASES

2003 ◽  
Vol 12 (02) ◽  
pp. 275-294 ◽  
Author(s):  
ZINA BEN MILED ◽  
YUE W. WEBSTER ◽  
YANG LIU ◽  
NIANHUA LI
Keyword(s):  
Semantic Integration ◽  
Biological Data ◽  
Biological Research ◽  
Complex Data ◽  
Biological Databases ◽  
Web Databases ◽  
Data Format ◽  
Data Formats ◽  
Other Information ◽  
Biological Ontology

The incompatibilities among complex data formats and various schema used by biological databases that house these data are becoming a bottleneck in biological research. For example, biological data format varies from simple words (e.g. gene name), numbers (e.g. molecular weight) to sequence strings (e.g. nucleic acid sequence), to even more complex data formats such as taxonomy trees. Some information is embedded in narrative text, such as expert comments and publications. Some other information is expressed as graphs or images (e.g. pathways networks). The confederation of heterogeneous web databases has become a crucial issue in today's biological research. In other words, interoperability has to be archieved among the biological web databases and the heterogeneity of the web databases has to be resolved. This paper presents a biological ontology, BAO, and discusses its advantages in supporting the semantic integration of biological web databases are discussed.

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