scholarly journals Uncovering host-microbiome interactions in global systems with collaborative programming: a novel approach integrating social and data sciences

F1000Research ◽  
2020 ◽  
Vol 9 ◽  
pp. 1478
Author(s):  
Jenna Oberstaller ◽  
Swamy Rakesh Adapa ◽  
Guy W. Dayhoff II ◽  
Justin Gibbons ◽  
Thomas E. Keller ◽  
...  
Keyword(s):  
Data Science ◽  
South Florida ◽  
Technological Advancement ◽  
Real World Data ◽  
Domain Experts ◽  
Novel Approach ◽  
Microbiome Research ◽  
Data Output ◽  
Microbiome Data ◽  
Global Systems

Microbiome data are undergoing exponential growth powered by rapid technological advancement. As the scope and depth of microbiome research increases, cross-disciplinary research is urgently needed for interpreting and harnessing the unprecedented data output. However, conventional research settings pose challenges to much-needed interdisciplinary research efforts due to barriers in scientific terminologies, methodology and research-culture. To breach these barriers, our University of South Florida OneHealth Codeathon was designed to be an interactive, hands-on event that solves real-world data problems. The format brought together students, postdocs, faculty, researchers, and clinicians in a uniquely cross-disciplinary, team-focused setting. Teams were formed to encourage equitable distribution of diverse domain-experts and proficient programmers, with beginners to experts on each team. To unify the intellectual framework, we set the focus on the topics of microbiome interactions at different scales from clinical to environmental sciences, leveraging local expertise in the fields of genetics, genomics, clinical data, and social and geospatial sciences. As a result, teams developed working methods and pipelines to face major challenges in current microbiome research, including data integration, experimental power calculations, geospatial mapping, and machine-learning classifiers. This broad, transdisciplinary and efficient workflow will be an example for future workshops to deliver useful data-science products.

scholarly journals QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science

2018 ◽  
Author(s):  
Evan Bolyen ◽  
Jai Ram Rideout ◽  
Matthew R Dillon ◽  
Nicholas A Bokulich ◽  
Christian Abnet ◽  
...  
Keyword(s):  
Data Science ◽  
Temporal Analysis ◽  
Data Provenance ◽  
Policy Makers ◽  
Shotgun Metagenomics ◽  
Spatial And Temporal Analysis ◽  
Microbiome Research ◽  
Scientists And Engineers ◽  
Visualization Tools ◽  
Microbiome Data

We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the microbiome research ecosystem, from scientists and engineers to clinicians and policy makers. QIIME 2 provides new features that will drive the next generation of microbiome research. These include interactive spatial and temporal analysis and visualization tools, support for metabolomics and shotgun metagenomics analysis, and automated data provenance tracking to ensure reproducible, transparent microbiome data science.

scholarly journals SKIOME Project: a curated collection of skin microbiome datasets enriched with study-related metadata

2021 ◽  
Author(s):  
Giulia Agostinetto ◽  
Davide Bozzi ◽  
Danilo Porro ◽  
Maurizio Casiraghi ◽  
Massimo Labra ◽  
...  
Keyword(s):  
Data Science ◽  
Data Retrieval ◽  
Amplicon Sequencing ◽  
Full Potential ◽  
Skin Microbiome ◽  
Data Accessibility ◽  
16S Rrna Amplicon Sequencing ◽  
Comprehensive Collection ◽  
Microbiome Research ◽  
Microbiome Data

Large amounts of data from microbiome-related studies have been (and are currently being) deposited on international public databases. These datasets represent a valuable resource for the microbiome research community and could serve future researchers interested in integrating multiple datasets into powerful meta-analyses. However, this huge amount of data lacks harmonization and is far from being completely exploited in its full potential to build a foundation that places microbiome research at the nexus of many subdisciplines within and beyond biology. Thus, urges the need for data accessibility and reusability, according to FAIR (Findable, Accessible, Interoperable, and Reusable) principles, as supported by National Microbiome Data Collaborative and FAIR Microbiome. To tackle the challenge of accelerating discovery and advances in skin microbiome research, we collected, integrated and organized existing microbiome data resources from human skin 16S rRNA amplicon sequencing experiments. We generated a comprehensive collection of datasets, enriched in metadata, and organized this information into data frames ready to be integrated into microbiome research projects and advanced post-processing analysis, such as data science applications (e.g. machine learning). Furthermore, we have created a data retrieval and curation framework built on three different stages to maximize the retrieval of datasets and metadata associated with them. Lastly, we highlighted some caveats regarding metadata retrieval and suggested ways to improve future metadata submissions. Overall, our work resulted in a curated skin microbiome datasets collection accompanied by a state-of-the-art analysis of the last 10 years of the skin microbiome field.

scholarly journals QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science

2018 ◽  
Author(s):  
Evan Bolyen ◽  
Jai Ram Rideout ◽  
Matthew R Dillon ◽  
Nicholas A Bokulich ◽  
Christian Abnet ◽  
...  
Keyword(s):  
Data Science ◽  
Temporal Analysis ◽  
Data Provenance ◽  
Policy Makers ◽  
Shotgun Metagenomics ◽  
Spatial And Temporal Analysis ◽  
Microbiome Research ◽  
Scientists And Engineers ◽  
Visualization Tools ◽  
Microbiome Data

We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the microbiome research ecosystem, from scientists and engineers to clinicians and policy makers. QIIME 2 provides new features that will drive the next generation of microbiome research. These include interactive spatial and temporal analysis and visualization tools, support for metabolomics and shotgun metagenomics analysis, and automated data provenance tracking to ensure reproducible, transparent microbiome data science.

scholarly journals Exploring the Microbiome Analysis and Visualization Landscape

2021 ◽  
Vol 1 ◽  
Author(s):  
Jannes Peeters ◽  
Olivier Thas ◽  
Ziv Shkedy ◽  
Leyla Kodalci ◽  
Connie Musisi ◽  
...  
Keyword(s):  
Literature Review ◽  
Visual Analysis ◽  
Visual Representations ◽  
Characterization Methods ◽  
Domain Experts ◽  
Microbiome Analysis ◽  
Wide Range ◽  
Microbiome Research ◽  
Research Questions ◽  
Microbiome Data

Research on the microbiome has boomed recently, which resulted in a wide range of tools, packages, and algorithms to analyze microbiome data. Here we investigate and map currently existing tools that can be used to perform visual analysis on the microbiome, and associate the including methods, visual representations and data features to the research objectives currently of interest in microbiome research. The analysis is based on a combination of a literature review and workshops including a group of domain experts. Both the reviewing process and workshops are based on domain characterization methods to facilitate communication and collaboration between researchers from different disciplines. We identify several research questions related to microbiomes, and describe how different analysis methods and visualizations help in tackling them.

scholarly journals QIIME 2: Reproducible, interactive, scalable, and extensible microbiome data science

2018 ◽  
Author(s):  
Evan Bolyen ◽  
Jai Ram Rideout ◽  
Matthew R Dillon ◽  
Nicholas A Bokulich ◽  
Christian Abnet ◽  
...  
Keyword(s):  
Data Science ◽  
Temporal Analysis ◽  
Data Provenance ◽  
Policy Makers ◽  
Shotgun Metagenomics ◽  
Spatial And Temporal Analysis ◽  
Microbiome Research ◽  
Scientists And Engineers ◽  
Visualization Tools ◽  
Microbiome Data

We present QIIME 2, an open-source microbiome data science platform accessible to users spanning the microbiome research ecosystem, from scientists and engineers to clinicians and policy makers. QIIME 2 provides new features that will drive the next generation of microbiome research. These include interactive spatial and temporal analysis and visualization tools, support for metabolomics and shotgun metagenomics analysis, and automated data provenance tracking to ensure reproducible, transparent microbiome data science.

scholarly journals Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Verónica Lloréns-Rico ◽  
Sara Vieira-Silva ◽  
Pedro J. Gonçalves ◽  
Gwen Falony ◽  
Jeroen Raes
Keyword(s):  
Microbial Communities ◽  
Quantitative Methods ◽  
Microbial Load ◽  
Metagenomic Sequencing ◽  
Sampling Depth ◽  
Microbiome Research ◽  
Microbiome Data ◽  
The Impact ◽  
Analytical Approaches ◽  
Quantitative Approaches

AbstractWhile metagenomic sequencing has become the tool of preference to study host-associated microbial communities, downstream analyses and clinical interpretation of microbiome data remains challenging due to the sparsity and compositionality of sequence matrices. Here, we evaluate both computational and experimental approaches proposed to mitigate the impact of these outstanding issues. Generating fecal metagenomes drawn from simulated microbial communities, we benchmark the performance of thirteen commonly used analytical approaches in terms of diversity estimation, identification of taxon-taxon associations, and assessment of taxon-metadata correlations under the challenge of varying microbial ecosystem loads. We find quantitative approaches including experimental procedures to incorporate microbial load variation in downstream analyses to perform significantly better than computational strategies designed to mitigate data compositionality and sparsity, not only improving the identification of true positive associations, but also reducing false positive detection. When analyzing simulated scenarios of low microbial load dysbiosis as observed in inflammatory pathologies, quantitative methods correcting for sampling depth show higher precision compared to uncorrected scaling. Overall, our findings advocate for a wider adoption of experimental quantitative approaches in microbiome research, yet also suggest preferred transformations for specific cases where determination of microbial load of samples is not feasible.

scholarly journals Streaming histogram sketching for rapid microbiome analytics

2018 ◽  
Author(s):  
Will P. M. Rowe ◽  
Anna Paola Carrieri ◽  
Cristina Alcon-Giner ◽  
Shabhonam Caim ◽  
Alex Shaw ◽  
...  
Keyword(s):  
Locality Sensitive Hashing ◽  
Genomic Research ◽  
Compact Representation ◽  
Sample Type ◽  
Sequencing Data ◽  
Similarity Estimation ◽  
Microbiome Research ◽  
Microbiome Data ◽  
Similarity Searches

AbstractMotivationThe growth in publically available microbiome data in recent years has yielded an invaluable resource for genomic research; allowing for the design of new studies, augmentation of novel datasets and reanalysis of published works. This vast amount of microbiome data, as well as the widespread proliferation of microbiome research and the looming era of clinical metagenomics, means there is an urgent need to develop analytics that can process huge amounts of data in a short amount of time.To address this need, we propose a new method for the compact representation of microbiome sequencing data using similarity-preserving sketches of streaming k-mer spectra. These sketches allow for dissimilarity estimation, rapid microbiome catalogue searching, and classification of microbiome samples in near real-time.ResultsWe apply streaming histogram sketching to microbiome samples as a form of dimensionality reduction, creating a compressed ‘histosketch’ that can be used to efficiently represent microbiome k-mer spectra. Using public microbiome datasets, we show that histosketches can be clustered by sample type using pairwise Jaccard similarity estimation, consequently allowing for rapid microbiome similarity searches via a locality sensitive hashing indexing scheme. Furthermore, we show that histosketches can be used to train machine learning classifiers to accurately label microbiome samples. Specifically, using a collection of 108 novel microbiome samples from a cohort of premature neonates, we trained and tested a Random Forest Classifier that could accurately predict whether the neonate had received antibiotic treatment (95% accuracy, precision 97%) and could subsequently be used to classify microbiome data streams in less than 12 seconds.We provide our implementation, Histosketching Using Little K-mers (HULK), which can histosketch a typical 2GB microbiome in 50 seconds on a standard laptop using 4 cores, with the sketch occupying 3000 bytes of disk space.AvailabilityOur implementation (HULK) is written in Go and is available at: https://github.com/will-rowe/hulk (MIT License)

scholarly journals Optimising Daily Fantasy Sports Teams with Artificial Intelligence

2020 ◽  
Vol 19 (2) ◽  
pp. 21-35
Author(s):  
Ryan Beal ◽  
Timothy J. Norman ◽  
Sarvapali D. Ramchurn
Keyword(s):  
Real World ◽  
National Football League ◽  
Mixed Integer ◽  
Data Sets ◽  
Fantasy Sports ◽  
Real World Data ◽  
Sports Teams ◽  
Novel Approach ◽  
Four Seasons ◽  
Daily Fantasy Sports

AbstractThis paper outlines a novel approach to optimising teams for Daily Fantasy Sports (DFS) contests. To this end, we propose a number of new models and algorithms to solve the team formation problems posed by DFS. Specifically, we focus on the National Football League (NFL) and predict the performance of real-world players to form the optimal fantasy team using mixed-integer programming. We test our solutions using real-world data-sets from across four seasons (2014-2017). We highlight the advantage that can be gained from using our machine-based methods and show that our solutions outperform existing benchmarks, turning a profit in up to 81.3% of DFS game-weeks over a season.

scholarly journals Introduction to the Special Issue: Applications of Internet of Things

Symmetry ◽  
2018 ◽  
Vol 10 (9) ◽  
pp. 374 ◽  
Author(s):  
Chi-Hua Chen ◽  
Eyhab Al-Masri ◽  
Feng-Jang Hwang ◽  
Despo Ktoridou ◽  
Kuen-Rong Lo
Keyword(s):  
Internet Of Things ◽  
Smart Home ◽  
Data Science ◽  
Cooperative Spectrum Sensing ◽  
Smart Homes ◽  
Recognition System ◽  
Special Issue ◽  
Smart Transportation ◽  
User Classification ◽  
Novel Approach

This editorial introduces the special issue, entitled “Applications of Internet of Things”, of Symmetry. The topics covered in this issue fall under four main parts: (I) communication techniques and applications, (II) data science techniques and applications, (III) smart transportation, and (IV) smart homes. Four papers on sensing techniques and applications are included as follows: (1) “Reliability of improved cooperative communication over wireless sensor networks”, by Chen et al.; (2) “User classification in crowdsourcing-based cooperative spectrum sensing”, by Zhai and Wang; (3) “IoT’s tiny steps towards 5G: Telco’s perspective”, by Cero et al.; and (4) “An Internet of things area coverage analyzer (ITHACA) for complex topographical scenarios”, by Parada et al. One paper on data science techniques and applications is as follows: “Internet of things: a scientometric review”, by Ruiz-Rosero et al. Two papers on smart transportation are as follows: (1) “An Internet of things approach for extracting featured data using an AIS database: an application based on the viewpoint of connected ships”, by He et al.; and (2) “The development of key technologies in applications of vessels connected to the Internet”, by Tian et al. Two papers on smart home are as follows: (1) “A novel approach based on time cluster for activity recognition of daily living in smart homes”, by Liu et al.; and (2) “IoT-based image recognition system for smart home-delivered meal services”, by Tseng et al.

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