scholarly journals Specifications of Standards in Systems and Synthetic Biology

2015 ◽  
Vol 12 (2) ◽  
pp. 1-3 ◽  
Author(s):  
Falk Schreiber ◽  
Gary D. Bader ◽  
Martin Golebiewski ◽  
Michael Hucka ◽  
Benjamin Kormeier ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Information Exchange ◽  
Computational Models ◽  
Access Point ◽  
Economic Benefits ◽  
Special Issue ◽  
Community Initiative ◽  
Central Access ◽  
Oral Presentations ◽  
Modeling In Biology

Summary Standards shape our everyday life. From nuts and bolts to electronic devices and technological processes, standardised products and processes are all around us. Standards have technological and economic benefits, such as making information exchange, production, and services more efficient. However, novel, innovative areas often either lack proper standards, or documents about standards in these areas are not available from a centralised platform or formal body (such as the International Standardisation Organisation).Systems and synthetic biology is a relatively novel area, and it is only in the last decade that the standardisation of data, information, and models related to systems and synthetic biology has become a community-wide effort. Several open standards have been established and are under continuous development as a community initiative. COMBINE, the ‘COmputational Modeling in BIology’ NEtwork [1] has been established as an umbrella initiative to coordinate and promote the development of the various community standards and formats for computational models. There are yearly two meeting, HARMONY (Hackathons on Resources for Modeling in Biology), Hackathon-type meetings with a focus on development of the support for standards, and COMBINE forums, workshop-style events with oral presentations, discussion, poster, and breakout sessions for further developing the standards. For more information see http://co.mbine.org/.So far the different standards were published and made accessible through the standards’ web-pages or preprint services. The aim of this special issue is to provide a single, easily accessible and citable platform for the publication of standards in systems and synthetic biology. This special issue is intended to serve as a central access point to standards and related initiatives in systems and synthetic biology, it will be published annually to provide an opportunity for standard development groups to communicate updated specifications.

scholarly journals The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE)

2020 ◽  
Vol 17 (2-3) ◽  
Author(s):  
Dagmar Waltemath ◽  
Martin Golebiewski ◽  
Michael L Blinov ◽  
Padraig Gleeson ◽  
Henning Hermjakob ◽  
...  
Keyword(s):  
Synthetic Biology ◽  
Data Model ◽  
Computational Models ◽  
Life Sciences ◽  
The Past ◽  
Challenges And Opportunities ◽  
Stakeholder Workshop ◽  
Software Engineers ◽  
Future Work ◽  
Modeling In Biology

AbstractThis paper presents a report on outcomes of the 10th Computational Modeling in Biology Network (COMBINE) meeting that was held in Heidelberg, Germany, in July of 2019. The annual event brings together researchers, biocurators and software engineers to present recent results and discuss future work in the area of standards for systems and synthetic biology. The COMBINE initiative coordinates the development of various community standards and formats for computational models in the life sciences. Over the past 10 years, COMBINE has brought together standard communities that have further developed and harmonized their standards for better interoperability of models and data. COMBINE 2019 was co-located with a stakeholder workshop of the European EU-STANDS4PM initiative that aims at harmonized data and model standardization for in silico models in the field of personalized medicine, as well as with the FAIRDOM PALs meeting to discuss findable, accessible, interoperable and reusable (FAIR) data sharing. This report briefly describes the work discussed in invited and contributed talks as well as during breakout sessions. It also highlights recent advancements in data, model, and annotation standardization efforts. Finally, this report concludes with some challenges and opportunities that this community will face during the next 10 years.

scholarly journals Special Issue “Metabolic Engineering and Synthetic Biology Volume 2”

Metabolites ◽  
2021 ◽  
Vol 11 (1) ◽  
pp. 35
Author(s):  
An N. T. Phan ◽  
Lars M. Blank
Keyword(s):  
Metabolic Engineering ◽  
Synthetic Biology ◽  
Special Issue ◽  
Subsequent Increase ◽  
Increasing Demand

In times of ever-increasing demand for chemicals and the subsequent increase in CO2 in the atmosphere, we have to intensify our efforts to establish a circular (bio) economy [...]

scholarly journals COVID-19 preVIEW: Semantic Search to Explore COVID-19 Research Preprints

2021 ◽  
Author(s):  
Lisa Langnickel ◽  
Roman Baum ◽  
Johannes Darms ◽  
Sumit Madan ◽  
Juliane Fluck
Keyword(s):  
Search Engine ◽  
Access Point ◽  
Semantic Search ◽  
Web Interface ◽  
Disease Trajectory ◽  
Human Genes ◽  
Central Access ◽  
Semantic Information Retrieval ◽  
User Friendly ◽  
Semantic Search Engine

During the current COVID-19 pandemic, the rapid availability of profound information is crucial in order to derive information about diagnosis, disease trajectory, treatment or to adapt the rules of conduct in public. The increased importance of preprints for COVID-19 research initiated the design of the preprint search engine preVIEW. Conceptually, it is a lightweight semantic search engine focusing on easy inclusion of specialized COVID-19 textual collections and provides a user friendly web interface for semantic information retrieval. In order to support semantic search functionality, we integrated a text mining workflow for indexing with relevant terminologies. Currently, diseases, human genes and SARS-CoV-2 proteins are annotated, and more will be added in future. The system integrates collections from several different preprint servers that are used in the biomedical domain to publish non-peer-reviewed work, thereby enabling one central access point for the users. In addition, our service offers facet searching, export functionality and an API access. COVID-19 preVIEW is publicly available at https://preview.zbmed.de.

scholarly journals Spending Time in the Nineteenth Century

2021 ◽  
Author(s):  
Rieke Jordan
Keyword(s):  
Nineteenth Century ◽  
American Literature ◽  
Literary History ◽  
Access Point ◽  
Analytical Framework ◽  
Free Time ◽  
Special Issue ◽  
Nineteenth Century American Literature ◽  
Cultural Aspects ◽  
American Literary History

This special issue of New American Studies Journal: A Forum looks at nineteenth-century American literature and culture through the analytical lens of free time and leisure. This analytical framework affords a novel access point to American literary history—free time, as this special issue will explore, is a highly contested and politicized concept and resource of the nineteenth century, one that restructures temporalities and spaces. Nineteenth-century American culture and literature can be understood as an archive to explore free time as a significant social and economic innovation into the texture of individual life. The contributions to this special issue explore the rise of free time in the nineteenth century with particular attention toward temporal and spatial reconfigurations that free time afforded. Furthermore they explore the societal and cultural aspects of free time that grew around the logics and logistics of nineteenth-century capitalism—a social formation that made leisure, time off work, not merely possible, but that created entire industries and spaces for leisure and repose.

Introduction to the Special Issue on Computational Synthetic Biology

2014 ◽  
Vol 11 (3) ◽  
pp. 1-5
Author(s):  
Chris J. Myers ◽  
Herbert Sauro ◽  
Anil Wipat
Keyword(s):  
Synthetic Biology ◽  
Special Issue

scholarly journals The economic benefits of health information exchange interoperability for Australia

2007 ◽  
Vol 31 (4) ◽  
pp. 531 ◽  
Author(s):  
Peter Sprivulis ◽  
Jan Walker ◽  
Douglas Johnston ◽  
Eric Pan ◽  
Julia Adler-Milstein ◽  
...  
Keyword(s):  
Health Care ◽  
Steady State ◽  
Health Information ◽  
Information Exchange ◽  
Health Information Exchange ◽  
Semantic Content ◽  
Economic Benefits ◽  
Policy Position ◽  
Care Providers ◽  
Level 3

Objective: To estimate costs and benefits for Australia of implementing health information exchange interoperability among health care providers and other health care stakeholders. Design: A cost?benefit model considering four levels of interoperability (Level 1, paper based; Level 2, machine transportable; Level 3, machine readable; and Level 4, machine interpretable) was developed for Government-funded health services, then validated by expert review. Results: Roll-out costs for Level 3 and Level 4 interoperability were projected to be $21.5 billion and $14.2 billion, respectively, and steady-state costs, $1470 million and $933 million per annum, respectively. Level 3 interoperability would achieve steadystate savings of $1820 million, and Level 4 interoperability, $2990 million, comprising transactions of: laboratory $1180 million (39%); other providers, $893 million (30%); imaging centre, $680 million (23%); pharmacy, $213 million (7%) and public health, $27 million (1%). Net steady-state Level 4 benefits are projected to be $2050 million: $1710 million more than Level 3 benefits of $348 million, reflecting reduced interface costs for Level 4 interoperability due to standardisation of the semantic content of Level 4 messages. Conclusions: Benefits to both providers and society will accrue from the implementation of interoperability. Standards are needed for the semantic content of clinical messages, in addition to message exchange standards, for the full benefits of interoperability to be realised. An Australian Government policy position supporting such standards is recommended.

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