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

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.

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Specifications of Standards in Systems and Synthetic Biology

Journal of Integrative Bioinformatics ◽

10.1515/jib-2015-258 ◽

2015 ◽

Vol 12 (2) ◽

pp. 1-3 ◽

Cited By ~ 6

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.

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On the relationship between research parasites and fairness in machine learning: challenges and opportunities

GigaScience ◽

10.1093/gigascience/giab086 ◽

2021 ◽

Vol 10 (12) ◽

Author(s):

Nicolás Nieto ◽

Agostina Larrazabal ◽

Victoria Peterson ◽

Diego H Milone ◽

Enzo Ferrante

Keyword(s):

Machine Learning ◽

Data Model ◽

Learning Systems ◽

Training Data ◽

Model Construction ◽

Daily Lives ◽

The Past ◽

Learning Challenges ◽

Challenges And Opportunities ◽

The Relationship

Abstract Machine learning systems influence our daily lives in many different ways. Hence, it is crucial to ensure that the decisions and recommendations made by these systems are fair, equitable, and free of unintended biases. Over the past few years, the field of fairness in machine learning has grown rapidly, investigating how, when, and why these models capture, and even potentiate, biases that are deeply rooted not only in the training data but also in our society. In this Commentary, we discuss challenges and opportunities for rigorous posterior analyses of publicly available data to build fair and equitable machine learning systems, focusing on the importance of training data, model construction, and diversity in the team of developers. The thoughts presented here have grown out of the work we did, which resulted in our winning the annual Research Parasite Award that GigaSciencesponsors.

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A Qualified Assertion Database for the History of Places

International Journal of Humanities and Arts Computing ◽

10.3366/ijhac.2019.0233 ◽

2019 ◽

Vol 13 (1-2) ◽

pp. 95-115

Author(s):

Brandon Plewe

Keyword(s):

Data Model ◽

Temporal Change ◽

Religious Congregations ◽

Historical Gis ◽

The Past ◽

Model Based ◽

Complex Information ◽

Invaluable Tool ◽

History Of ◽

The Rich

Historical place databases can be an invaluable tool for capturing the rich meaning of past places. However, this richness presents obstacles to success: the daunting need to simultaneously represent complex information such as temporal change, uncertainty, relationships, and thorough sourcing has been an obstacle to historical GIS in the past. The Qualified Assertion Model developed in this paper can represent a variety of historical complexities using a single, simple, flexible data model based on a) documenting assertions of the past world rather than claiming to know the exact truth, and b) qualifying the scope, provenance, quality, and syntactics of those assertions. This model was successfully implemented in a production-strength historical gazetteer of religious congregations, demonstrating its effectiveness and some challenges.

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Brain-eating Amoebae Infection: Challenges and Opportunities in Chemotherapy

Mini-Reviews in Medicinal Chemistry ◽

10.2174/1389557519666190313161854 ◽

2019 ◽

Vol 19 (12) ◽

pp. 980-987 ◽

Cited By ~ 9

Author(s):

Mohammad Ridwane Mungroo ◽

Ayaz Anwar ◽

Naveed Ahmed Khan ◽

Ruqaiyyah Siddiqui

Keyword(s):

Mortality Rate ◽

Free Living ◽

Outdoor Activities ◽

The Past ◽

Free Living Amoeba ◽

Challenges And Opportunities ◽

Life Threatening ◽

The Central Nervous System ◽

Living Nature ◽

Treatment And Diagnosis

Pathogenic free-living amoeba are known to cause a devastating infection of the central nervous system and are often referred to as “brain-eating amoebae”. The mortality rate of more than 90% and free-living nature of these amoebae is a cause for concern. It is distressing that the mortality rate has remained the same over the past few decades, highlighting the lack of interest by the pharmaceutical industry. With the threat of global warming and increased outdoor activities of public, there is a need for renewed interest in identifying potential anti-amoebic compounds for successful prognosis. Here, we discuss the available chemotherapeutic options and opportunities for potential strategies in the treatment and diagnosis of these life-threatening infections.

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LBE for Generalized Hydrodynamics

10.1093/oso/9780199592357.003.0025 ◽

2018 ◽

Author(s):

Sauro Succi

Keyword(s):

Potential Energy ◽

Electric Fields ◽

Chemical Reactions ◽

Soft Matter ◽

Fluid Motion ◽

Life Sciences ◽

Scientific Discipline ◽

The Past ◽

Generalized Hydrodynamics ◽

Internal Forces

This chapter presents the main techniques to incorporate the effects of external and/or internal forces within the LB formalism. This is a very important task, for it permits us to access a wide body of generalized hydrodynamic applications whereby fluid motion couples to a variety of additional physical aspects, such as gravitational and electric fields, potential energy interactions, chemical reactions and many others. It should be emphasized that while hosting a broader and richer phenomenology than “plain” hydrodynamics, generalized hydrodynamics still fits the hydrodynamic picture of weak departure from suitably generalized local equilibria. This class is all but an academic curiosity; for instance, it is central to the fast-growing science of Soft Matter, a scientific discipline which has received an impressive boost in the past decades, under the drive of micro- and nanotechnological developments and major strides in biology and life sciences at large.

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Evoking Issues of Race and Ethnicity in Research on Physiology and Interpersonal Communication

The Oxford Handbook of the Physiology of Interpersonal Communication ◽

10.1093/oxfordhb/9780190679446.013.15 ◽

2020 ◽

pp. 260-287

Author(s):

Shardé M. Davis

Keyword(s):

Interpersonal Communication ◽

Race And Ethnicity ◽

Communication Research ◽

Interpersonal Interactions ◽

The Past ◽

Race Ethnicity ◽

Diverse Groups ◽

Future Work ◽

Area Of Study

Investigating the role of physiology in communication research is a burgeoning area of study that has gained considerable attention by relational scholars in the past decade. Unfortunately, very few published studies on this topic have evoked important questions about the role of race and ethnicity. Exploring issues of ethnicity and race provides a more holistic and inclusive view of interpersonal communication across diverse groups and communities. This chapter addresses the gap in literature by considering the ways in which race and ethnicity matter in work on physiology and interpersonal interactions. More specifically, this chapter will first discuss the conceptual underpinnings of race, ethnicity, and other relevant concepts and then review extant research within and beyond the field of communication on race, ethnicity, interpersonal interactions, and physiology. These discussions set the foundation for this chapter to propose new lines of research that pointedly connect these four concepts and advance key principles that scholars should consider in future work.

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Synthetic biology in biofilms: Tools, challenges, and opportunities

Biotechnology Progress ◽

10.1002/btpr.3123 ◽

2021 ◽

Author(s):

Peter Tran ◽

Arthur Prindle

Keyword(s):

Synthetic Biology ◽

Challenges And Opportunities

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Hearing Loss and Help-Seeking Behavior

Innovation in Aging ◽

10.1093/geroni/igaa057.2889 ◽

2020 ◽

Vol 4 (Supplement_1) ◽

pp. 797-797

Author(s):

Nicholas Reed

Keyword(s):

Health Care ◽

Hearing Loss ◽

Help Seeking ◽

Health Care Quality ◽

Medicare Beneficiary ◽

Care Quality ◽

The Past ◽

Help Seeking Behaviour ◽

Seeking Behavior ◽

Future Work

Abstract Hearing Loss (HL) is common among older adults and is associated with poor health care quality outcomes include 30-day readmissions, length of stay, poorer satisfaction, and increased medical expenditures. These associations may manifest in changes in help-seeking behaviour. In the 2015 Current Medicare Beneficiary Study (MCBS) (n=10848; weighted sample=46.3 million), participants reported whether they knowingly had avoided seeking care in the past year and self-reported HL was measured as degree of trouble (none, a little, or a lot) hearing when using a hearing aid if applicable. In a model adjusted for demographic, socioeconomic, and health factors, those with a little trouble (OR= 1.612; 95% CI= 1.334-1.947; P<0.001) and a lot of trouble hearing (OR= 2.011; 95% CI= 1.443-2.801; P<0.001) had 61.2% and 101.1% higher odds of avoiding health care over the past year relative to participants with no trouble hearing. Future work should examine whether hearing care modifies this association.

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Challenges and Opportunities in Collaborative Vulnerability Research Workflows

Proceedings of the Human Factors and Ergonomics Society Annual Meeting ◽

10.1177/1071181320641094 ◽

2020 ◽

Vol 64 (1) ◽

pp. 420-424

Author(s):

Ryan Mullins ◽

Deirdre Kelliher ◽

Ben Nargi ◽

Mike Keeney ◽

Nathan Schurr

Keyword(s):

Human Performance ◽

Collaborative Work ◽

Research Process ◽

Workflow Model ◽

Human Vulnerability ◽

Research Teams ◽

Reasoning System ◽

Challenges And Opportunities ◽

New Research ◽

Future Work

Recently, cyber reasoning systems demonstrated near-human performance characteristics when they autonomously identified, proved, and mitigated vulnerabilities in software during a competitive event. New research seeks to augment human vulnerability research teams with cyber reasoning system teammates in collaborative work environments. However, the literature lacks a concrete understanding of vulnerability research workflows and practices, limiting designers’, engineers’, and researchers’ ability to successfully integrate these artificially intelligent entities into teams. This paper contributes a general workflow model of the vulnerability research process, and identifies specific collaboration challenges and opportunities anchored in this model. Contributions were derived from a qualitative field study of work habits, behaviors, and practices of human vulnerability research teams. These contributions will inform future work in the vulnerability research domain by establishing an empirically-driven workflow model that can be adapted to specific organizational and functional constraints placed on individual and teams.

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