scholarly journals Modeling Biological Systems Using Crowdsourcing

2018 ◽  
Vol 43 (3) ◽  
pp. 219-243 ◽  
Author(s):  
Szymon Wasik
Keyword(s):  
Systems Biology ◽  
Serious Games ◽  
Domain Knowledge ◽  
Biological Systems ◽  
Effective Technique ◽  
Design Models ◽  
Modeling Systems ◽  
Vast Network

Abstract Crowdsourcing is a very effective technique for outsourcing work to a vast network usually comprising anonymous people. In this study, we review the application of crowdsourcing to modeling systems originating from systems biology. We consider a variety of verified approaches, including well-known projects such as EyeWire, FoldIt, and DREAM Challenges, as well as novel projects conducted at the European Center for Bioinformatics and Genomics. The latter projects utilized crowdsourced serious games to design models of dynamic biological systems, and it was demonstrated that these models could be used successfully to involve players without domain knowledge. We conclude the review of these systems by providing 10 guidelines to facilitate the efficient use of crowdsourcing.

GAME-BASED LEARNING IN INTEGRATED DOMAINS WITH AN APPLICATION FOR STEAM CENTERS

2021 ◽  
Vol 12 (1) ◽  
pp. 209-214
Author(s):  
Stefani Paunova ◽  
◽  
Vilyana Doychevska ◽  
Valentin Yordanov ◽  
Stanimir Stoyanov ◽  
...  
Keyword(s):  
Artificial Intelligence ◽  
Logic Programming ◽  
Programming Language ◽  
Research Program ◽  
Serious Games ◽  
Game Based Learning ◽  
Modeling Systems ◽  
National Research Program ◽  
Integrated Domains ◽  
The University

The article presents a game-based learning environment that is being deeloped as a component of the ATOS platform (the platform is an article described for the same conference). The proposed environment is an adaptation of a component for serious games, developed within two projects – the National Research Program „Intelligent Agriculture (2021-2024)“ and the university project „ViSCoD – environment for modeling systems for intelligent agriculture“. The opportunities for game-based learning in integrated domains (in this case intelligent agriculture – STEAM center) are demonstrated with a version of the well-known game „Twenty question game“, adapted for the Bulgarian flora. The system is fully implemented in the logic programming language Prolog and thus can also be used to teach students in the discipline „Artificial Intelligence“.

Systems Approach to Understanding Oral Diseases

2010 ◽  
pp. 29-45
Author(s):  
Amit Chattopadhyay
Keyword(s):  
Systems Biology ◽  
Molecular Modeling ◽  
Molecular Biology ◽  
Structure Prediction ◽  
Systems Approach ◽  
Human Microbiome ◽  
Oral Diseases ◽  
Computational Biophysics ◽  
Prognostic Information ◽  
Modeling Systems

This chapter reviews the principles of systems biology and their application through computational methods (bioinformatics, computational biomodeling, genomics, proteomics, oral human microbiome, molecular modeling, systems biology, protein structure prediction, structural genomics, computational biochemistry and computational biophysics methods and projects) that have been applied to oral diseases research. The emphasis of the chapter is on concepts from molecular biology, genetics, and traditional pathology to provide new insights into oral diseases, and the associated technologies to provide new diagnostic, therapeutic and prognostic information. Another goal of the manuscript will be to serve as a central reference to access of information about systems biology resources for research into oral diseases.

7. The lawless pursuit of biological systems

2020 ◽  
pp. 108-122
Author(s):  
Eberhard O. Voit
Keyword(s):  
Systems Biology ◽  
Biological Systems ◽  
Large Classes ◽  
The Future

The laws of physics are a prerequisite for us to make reliable predictions regarding our surroundings. By extension, making reliable predictions in biology requires laws of biology. The problem is that such laws are almost non-existent, because biological systems are hugely complex and diverse. As a consequence, it is difficult to make true statements covering all organisms on Earth—or even large classes of organisms. This difficulty translates directly into the challenge of identifying rules that govern biological systems. What would such biological rules or laws even look like? ‘The lawless pursuit of biological systems’ considers the future of systems biology and discusses how it might evolve as it matures as a field of investigation.

Crowdfunding Serious Games

2021 ◽  
pp. 112-129
Author(s):  
Christopher Buckingham ◽  
Vanissa Wanick
Keyword(s):  
Game Design ◽  
Serious Games ◽  
Business Case ◽  
Serious Game ◽  
Design Models ◽  
Robust Approach ◽  
Early Stages ◽  
Depth Analysis ◽  
Target Markets

In serious game design, addressing issues related to the value and opportunity of the development of a game is vital in the early stages, creating a more structured and robust approach by exploring the business case. Present frameworks provide an in-depth analysis of game design models but often fail to state the case of predetermined target markets and new funding options for serious game design. Crowdfunding is an emerging funding path for these games and one that leads the vanguard in breaking with traditional forms of raising funding. This chapter aims to help in addressing an existing limitation in the literature by reviewing an existing framework on game design and blending this with the concept of crowdfunding. This chapter proposes the extension of a framework that reflects the possibility for early crowdfunding of a serious game.

scholarly journals Systems Biology and Multi-Omics Integration: Viewpoints from the Metabolomics Research Community

Metabolites ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 76 ◽  
Author(s):  
Farhana R. Pinu ◽  
David J. Beale ◽  
Amy M. Paten ◽  
Konstantinos Kouremenos ◽  
Sanjay Swarup ◽  
...  
Keyword(s):  
New Zealand ◽  
Systems Biology ◽  
Life Science ◽  
Biological Systems ◽  
Research Community ◽  
Data Sets ◽  
Omics Data ◽  
Omics Integration ◽  
Traditional Approaches ◽  
Multiple Interactions

The use of multiple omics techniques (i.e., genomics, transcriptomics, proteomics, and metabolomics) is becoming increasingly popular in all facets of life science. Omics techniques provide a more holistic molecular perspective of studied biological systems compared to traditional approaches. However, due to their inherent data differences, integrating multiple omics platforms remains an ongoing challenge for many researchers. As metabolites represent the downstream products of multiple interactions between genes, transcripts, and proteins, metabolomics, the tools and approaches routinely used in this field could assist with the integration of these complex multi-omics data sets. The question is, how? Here we provide some answers (in terms of methods, software tools and databases) along with a variety of recommendations and a list of continuing challenges as identified during a peer session on multi-omics integration that was held at the recent ‘Australian and New Zealand Metabolomics Conference’ (ANZMET 2018) in Auckland, New Zealand (Sept. 2018). We envisage that this document will serve as a guide to metabolomics researchers and other members of the community wishing to perform multi-omics studies. We also believe that these ideas may allow the full promise of integrated multi-omics research and, ultimately, of systems biology to be realized.

scholarly journals Systems Biology and Design of Biological Systems

2006 ◽  
Vol 46 (5) ◽  
pp. 244-250
Author(s):  
Hiroyuki KURATA
Keyword(s):  
Systems Biology ◽  
Biological Systems

scholarly journals Differences and implications in biogeochemistry from maximizing entropy production locally versus globally

2011 ◽  
Vol 2 (1) ◽  
pp. 69-85 ◽  
Author(s):  
J. J. Vallino
Keyword(s):  
Entropy Production ◽  
Biological Systems ◽  
Biogeochemical Processes ◽  
Biological Structure ◽  
Transient Conditions ◽  
Entropy Maximization ◽  
Planetary Scale ◽  
Modeling Systems ◽  
Spatial Dimensions ◽  
Multiple Levels

Abstract. In this manuscript we investigate the use of the maximum entropy production (MEP) principle for modeling biogeochemical processes that are catalyzed by living systems. Because of novelties introduced by the MEP approach, many questions need to be answered and techniques developed in the application of MEP to describe biological systems that are responsible for energy and mass transformations on a planetary scale. In previous work we introduce the importance of integrating entropy production over time to distinguish abiotic from biotic processes under transient conditions. Here we investigate the ramifications of modeling biological systems involving one or more spatial dimensions. When modeling systems over space, entropy production can be maximized either locally at each point in space asynchronously or globally over the system domain synchronously. We use a simple two-box model inspired by two-layer ocean models to illustrate the differences in local versus global entropy maximization. Synthesis and oxidation of biological structure is modeled using two autocatalytic reactions that account for changes in community kinetics using a single parameter each. Our results show that entropy production can be increased if maximized over the system domain rather than locally, which has important implications regarding how biological systems organize and supports the hypothesis for multiple levels of selection and cooperation in biology for the dissipation of free energy.

scholarly journals Current systems biology approaches in hazard assessment of nanoparticles

2015 ◽  
Author(s):  
Friederike Ehrhart ◽  
Chris Evelo ◽  
Egon Willighagen
Keyword(s):  
Systems Biology ◽  
Hazard Assessment ◽  
Low Dose ◽  
Bulk Material ◽  
Common Knowledge ◽  
Biological Systems ◽  
Consumer Products ◽  
Human Environment ◽  
Current Systems ◽  
Nano Size

The amount of nanoparticles (NPs) in human environment is increasing. The main sources are the increased introduction in consumer products and air pollution (diesel exhaust). It is meanwhile common knowledge that NPs behave differently as bulk material because of their nano-size. This leads in general to a higher reactivity and some other changed properties, e.g. solubility, surface potential, conductivity, and, to different effects on biological systems. The main impacts of NPs on a cellular and organism level are meanwhile well known: release of toxic ions, increased oxidative stress, and inflammation. Beside these, there is increasing evidence that NPs, especially in low dose/long exposure scenarios, affect biological systems in a broader way, interact with drugs, and exacerbate the effects of diseases. To investigate these effects systems biology approaches are the method of choice. This review summarizes the state of the art of nanoparticle effects on cells and organisms and demonstrate the add value of systems biology investigations to NP hazard assessment.

Conceptual models for automatic generation of knowledge-acquisition tools

1993 ◽  
Vol 8 (1) ◽  
pp. 27-47 ◽  
Author(s):  
Henrik Eriksson ◽  
Mark A. Musen
Keyword(s):  
Knowledge Acquisition ◽  
Domain Knowledge ◽  
Conceptual Models ◽  
Automatic Generation ◽  
Design Models ◽  
Domain Specific ◽  
Generic Design ◽  
Relevant Domain

AbstractInteractive knowledge-acquisition (KA) programs allow users to enter relevant domain knowledge according to a model predefined by the tool developers. KA tools are designed to provide conceptual models of the knowledge to their users. Many different classes of models are possible, resulting in different categories of tools. Whenever it is possible to describe KA tools according to explicit conceptual models, it is also possible to edit the models and to instantiate new KA tools automatically for specialized purposes. Several meta-tools that address this task have been implemented. Meta-tools provide developers of domain-specific KA tools with generic design models, or meta-views, of the emerging KA tools. The same KA tool can be specified according to several alternative meta-views.

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