Software Issues and Data Formats

2005 ◽  
pp. 131-140
Keyword(s):  
Data Formats

Reproducibility and efficiency in handling complex neurophysiological data

Neuroforum ◽  
2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Michael Denker ◽  
Sonja Grün ◽  
Thomas Wachtler ◽  
Hansjörg Scherberger
Keyword(s):  
Best Practices ◽  
Data Management ◽  
Data Integrity ◽  
Behavioral Neuroscience ◽  
Data Set ◽  
Data Publication ◽  
Electrophysiological Data ◽  
Data Formats ◽  
Neurophysiological Data ◽  
Community Effort

Abstract Preparing a neurophysiological data set with the aim of sharing and publishing is hard. Many of the available tools and services to provide a smooth workflow for data publication are still in their maturing stages and not well integrated. Also, best practices and concrete examples of how to create a rigorous and complete package of an electrophysiology experiment are still lacking. Given the heterogeneity of the field, such unifying guidelines and processes can only be formulated together as a community effort. One of the goals of the NFDI-Neuro consortium initiative is to build such a community for systems and behavioral neuroscience. NFDI-Neuro aims to address the needs of the community to make data management easier and to tackle these challenges in collaboration with various international initiatives (e.g., INCF, EBRAINS). This will give scientists the opportunity to spend more time analyzing the wealth of electrophysiological data they leverage, rather than dealing with data formats and data integrity.

scholarly journals A global view of standards for open image data formats and repositories

2021 ◽  
Author(s):  
Jason R. Swedlow ◽  
Pasi Kankaanpää ◽  
Ugis Sarkans ◽  
Wojtek Goscinski ◽  
Graham Galloway ◽  
...  
Keyword(s):  
Image Data ◽  
Data Formats ◽  
Global View

scholarly journals Mobile Medical Applications and Cloud Federation Challenges

2020 ◽  
Vol 30 (Supplement_5) ◽  
Author(s):  
I Patias ◽  
V Georgiev
Keyword(s):  
Information Systems ◽  
Health Sector ◽  
Added Value ◽  
Data Interoperability ◽  
Layered Architecture ◽  
Data Formats ◽  
Cloud Federation ◽  
Secure Environment ◽  
Internal Operations ◽  
Cloud Users

Abstract Issue Given the importance, of cloud environments for mobile telemedicine information systems, focus is given in this paper on the challenges rising. We discuss the pros of the access to computing services and resources on demand without having own infrastructures, and the need of advanced interoperability data formats and application program interfaces (APIs) to facilitate the usage of the infrastructure. Description of the problem Cloud-Oriented Architecture (COA) describes the architecture, where applications act as services and serve other applications in the cloud environment. The aim is IT infrastructure and software applications to be optimized for their use in cloud computing environments. But what happens in the specific field of health as data interoperability for mobile telemedicine information systems? Results Two architectures were presented using a patient's compliance and engagement solution. A simple Representational State Transfer (REST) based architectural style was implemented in a three-layered architecture first and then compared to a cloud federation model. In the second the interaction goes through the federation via a middleware layer. Internal operations of cloud providers in the federation are still transparent to the cloud users. The middleware layer aims to coordinate the interaction with cloud users and providers in the federation. But, to avoid delays in those interactions interoperability of data formats and APIs. Lessons A Fast Healthcare Interoperability Resources (FHIR) based application was developed. Mobile telemedicine information systems are a strong instrument in patients' compliance. Many systems have proved that the used resources combined can solve clinical and administrative problems in a secure environment. Key messages The use of cloud is wide spread in the health sector. The challenge is to combine this infrastructure into one federated platform and maximize the added value by using advanced interoperability data formats and APIs.

scholarly journals BioCommons: a robust java library for RNA structural bioinformatics

2021 ◽  
Author(s):  
Tomasz Zok
Keyword(s):  
Source Code ◽  
Structural Bioinformatics ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Bioinformatic Tools ◽  
Data Formats ◽  
Central Repository ◽  
Diverse Data ◽  
2D And 3D ◽  
Java Library

Abstract Motivation Biomolecular structures come in multiple representations and diverse data formats. Their incompatibility with the requirements of data analysis programs significantly hinders the analytics and the creation of new structure-oriented bioinformatic tools. Therefore, the need for robust libraries of data processing functions is still growing. Results BioCommons is an open-source, Java library for structural bioinformatics. It contains many functions working with the 2D and 3D structures of biomolecules, with a particular emphasis on RNA. Availability and implementation The library is available in Maven Central Repository and its source code is hosted on GitHub: https://github.com/tzok/BioCommons Supplementary information Supplementary data are available at Bioinformatics online.

484 Bioturing browser: interactively explore public single cell sequencing data

2020 ◽  
Vol 8 (Suppl 3) ◽  
pp. A520-A520
Author(s):  
Son Pham ◽  
Tri Le ◽  
Tan Phan ◽  
Minh Pham ◽  
Huy Nguyen ◽  
...  
Keyword(s):  
Single Cell ◽  
Immune Cell ◽  
Expression Profiles ◽  
Meta Analysis ◽  
Cell Types ◽  
Sequencing Data ◽  
Single Cell Sequencing ◽  
Data Formats ◽  
Cancer Types ◽  
Cell Data

BackgroundSingle-cell sequencing technology has opened an unprecedented ability to interrogate cancer. It reveals significant insights into the intratumoral heterogeneity, metastasis, therapeutic resistance, which facilitates target discovery and validation in cancer treatment. With rapid advancements in throughput and strategies, a particular immuno-oncology study can produce multi-omics profiles for several thousands of individual cells. This overflow of single-cell data poses formidable challenges, including standardizing data formats across studies, performing reanalysis for individual datasets and meta-analysis.MethodsN/AResultsWe present BioTuring Browser, an interactive platform for accessing and reanalyzing published single-cell omics data. The platform is currently hosting a curated database of more than 10 million cells from 247 projects, covering more than 120 immune cell types and subtypes, and 15 different cancer types. All data are processed and annotated with standardized labels of cell types, diseases, therapeutic responses, etc. to be instantly accessed and explored in a uniform visualization and analytics interface. Based on this massive curated database, BioTuring Browser supports searching similar expression profiles, querying a target across datasets and automatic cell type annotation. The platform supports single-cell RNA-seq, CITE-seq and TCR-seq data. BioTuring Browser is now available for download at www.bioturing.com.ConclusionsN/A

UNIFICATION OF DATA FORMATS IN THE IMPLEMENTATION OF THE ANALYTICAL COMPONENT OF INFORMATION SYSTEMS IN THE FIELD OF COMMUNICATIONS AND BROADCASTING

2021 ◽  
Author(s):  
Е.Е. ДЕВЯТКИН ◽  
М.В. ИВАНКОВИЧ ◽  
М.Н. КУПИН
Keyword(s):  
Information Systems ◽  
Research Work ◽  
Automated Systems ◽  
Functional Capabilities ◽  
Data Formats ◽  
Analytical System

Представлены результаты исследовательской работы по унификации форматов данных,которые требуются при реализации аналитической составляющей в структуре информационных систем, предназначенных для решения экспертно-прогностических задач в сфере связи и вещания. По результатам анализа существующих в отрасли основных автоматизированных систем, их функциональных возможностей обоснована необходимость введения в действующие и перспективные системы аналитической составляющей и унификации форматов данных как непременного условия их взаимодействия. Рассматривается набор унифицированных форматов данных, разработанный для перспективного макета аналитической системы развития связи и вещания. The results of research work on unifying the data formats that are required for the implementation of the analytical component in the structure of information systems intended for the solution of expert predictive problems in the sphere of communications and broadcasting are presented. Based on the results of the analysis of the main automated systems and their functional capabilities the necessity of introducing an analytical component into existing and future systems as well as unifying data formats as an indispensable condition for their interaction is substantiated. A set of unified data formats developed for a promising layout of an analytical system for the development of communications and broadcasting is considered.

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