Spatial and temporal tools for building a human cell atlas

Jonah Cool; Richard S. Conroy; Sean E. Hanlon; Shannon K. Hughes; Ananda L. Roy

doi:10.1091/mbc.e18-10-0667

Spatial and temporal tools for building a human cell atlas

Molecular Biology of the Cell ◽

10.1091/mbc.e18-10-0667 ◽

2019 ◽

Vol 30 (19) ◽

pp. 2435-2438 ◽

Cited By ~ 2

Author(s):

Jonah Cool ◽

Richard S. Conroy ◽

Sean E. Hanlon ◽

Shannon K. Hughes ◽

Ananda L. Roy

Keyword(s):

Scientific Community ◽

Large Data ◽

Large Data Sets ◽

Data Sets ◽

Experimental Conditions ◽

Modeling Tools ◽

Holistic View ◽

Multiple Timescales ◽

Single Cell Sequencing ◽

Coordination And Collaboration

Improvements in the sensitivity, content, and throughput of microscopy, in the depth and throughput of single-cell sequencing approaches, and in computational and modeling tools for data integration have created a portfolio of methods for building spatiotemporal cell atlases. Challenges in this fast-moving field include optimizing experimental conditions to allow a holistic view of tissues, extending molecular analysis across multiple timescales, and developing new tools for 1) managing large data sets, 2) extracting patterns and correlation from these data, and 3) integrating and visualizing data and derived results in an informative way. The utility of these tools and atlases for the broader scientific community will be accelerated through a commitment to findable, accessible, interoperable, and reusable data and tool sharing principles that can be facilitated through coordination and collaboration between programs working in this space.

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Compartment and hub definitions tune metabolic networks for metabolomic interpretations

GigaScience ◽

10.1093/gigascience/giz137 ◽

2020 ◽

Vol 9 (1) ◽

Cited By ~ 3

Author(s):

T Cameron Waller ◽

Jordan A Berg ◽

Alexander Lex ◽

Brian E Chapman ◽

Jared Rutter

Keyword(s):

Large Scale ◽

Metabolic Networks ◽

Shortest Paths ◽

Large Data ◽

Differential Regulation ◽

Large Data Sets ◽

Data Sets ◽

Human Metabolism ◽

Experimental Conditions ◽

Systemic Model

Abstract Background Metabolic networks represent all chemical reactions that occur between molecular metabolites in an organism’s cells. They offer biological context in which to integrate, analyze, and interpret omic measurements, but their large scale and extensive connectivity present unique challenges. While it is practical to simplify these networks by placing constraints on compartments and hubs, it is unclear how these simplifications alter the structure of metabolic networks and the interpretation of metabolomic experiments. Results We curated and adapted the latest systemic model of human metabolism and developed customizable tools to define metabolic networks with and without compartmentalization in subcellular organelles and with or without inclusion of prolific metabolite hubs. Compartmentalization made networks larger, less dense, and more modular, whereas hubs made networks larger, more dense, and less modular. When present, these hubs also dominated shortest paths in the network, yet their exclusion exposed the subtler prominence of other metabolites that are typically more relevant to metabolomic experiments. We applied the non-compartmental network without metabolite hubs in a retrospective, exploratory analysis of metabolomic measurements from 5 studies on human tissues. Network clusters identified individual reactions that might experience differential regulation between experimental conditions, several of which were not apparent in the original publications. Conclusions Exclusion of specific metabolite hubs exposes modularity in both compartmental and non-compartmental metabolic networks, improving detection of relevant clusters in omic measurements. Better computational detection of metabolic network clusters in large data sets has potential to identify differential regulation of individual genes, transcripts, and proteins.

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Measuring the Information Obtained from a Single-Cell Sequencing Experiment

10.1101/2020.10.01.322255 ◽

2020 ◽

Author(s):

Michael J. Casey ◽

Rubén J. Sánchez-García ◽

Ben D. MacArthur

Keyword(s):

Single Cell ◽

Expression Patterns ◽

Large Data ◽

Large Data Sets ◽

Data Sets ◽

Sequencing Data ◽

Data Set ◽

Single Cell Sequencing ◽

Amount Of Information ◽

Formal Framework

ABSTRACTSingle-cell sequencing (sc-Seq) experiments are producing increasingly large data sets. However, large data sets do not necessarily contain large amounts of information. Here, we introduce a formal framework for assessing the amount of information obtained from a sc-Seq experiment, which can be used throughout the sc-Seq analysis pipeline, including for quality control, feature selection and cluster evaluation. We illustrate this framework with some simple examples, including using it to quantify the amount of information in a single-cell sequencing data set that is explained by a proposed clustering, and thereby to determine cluster quality. Our information-theoretic framework provides a formal way to assess the quality of data obtained from sc-Seq experiments and the effectiveness of analyses performed, with wide implications for our understanding of variability in gene expression patterns within heterogeneous cell populations.

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An example of spectrum imaging used for comparison of EELS quantitative analysis techniques on Al-Li

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010008794x ◽

1991 ◽

Vol 49 ◽

pp. 726-727

Author(s):

John A. Hunt

Keyword(s):

Quantitative Analysis ◽

Large Data ◽

Difference Spectrum ◽

Large Data Sets ◽

Foil Thickness ◽

Data Sets ◽

Analysis Techniques ◽

Spectrum Imaging ◽

Normal Spectrum ◽

Electron Energy Loss

Spectrum-imaging is a useful technique for comparing different processing methods on very large data sets which are identical for each method. This paper is concerned with comparing methods of electron energy-loss spectroscopy (EELS) quantitative analysis on the Al-Li system. The spectrum-image analyzed here was obtained from an Al-10at%Li foil aged to produce δ' precipitates that can span the foil thickness. Two 1024 channel EELS spectra offset in energy by 1 eV were recorded and stored at each pixel in the 80x80 spectrum-image (25 Mbytes). An energy range of 39-89eV (20 channels/eV) are represented. During processing the spectra are either subtracted to create an artifact corrected difference spectrum, or the energy offset is numerically removed and the spectra are added to create a normal spectrum. The spectrum-images are processed into 2D floating-point images using methods and software described in [1].

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Cluster analysis for large data sets: applications to individual aerosol particles from the mid-pacific

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100132078 ◽

1992 ◽

Vol 50 (2) ◽

pp. 1488-1489

Author(s):

Thomas W. Shattuck ◽

James R. Anderson ◽

Neil W. Tindale ◽

Peter R. Buseck

Keyword(s):

Cluster Analysis ◽

Chemical Reactivity ◽

Large Data ◽

Large Data Sets ◽

Particle Analysis ◽

Data Sets ◽

Halogen Chemistry ◽

Complete Study ◽

Components Analysis ◽

Automated Scanning

Individual particle analysis involves the study of tens of thousands of particles using automated scanning electron microscopy and elemental analysis by energy-dispersive, x-ray emission spectroscopy (EDS). EDS produces large data sets that must be analyzed using multi-variate statistical techniques. A complete study uses cluster analysis, discriminant analysis, and factor or principal components analysis (PCA). The three techniques are used in the study of particles sampled during the FeLine cruise to the mid-Pacific ocean in the summer of 1990. The mid-Pacific aerosol provides information on long range particle transport, iron deposition, sea salt ageing, and halogen chemistry.Aerosol particle data sets suffer from a number of difficulties for pattern recognition using cluster analysis. There is a great disparity in the number of observations per cluster and the range of the variables in each cluster. The variables are not normally distributed, they are subject to considerable experimental error, and many values are zero, because of finite detection limits. Many of the clusters show considerable overlap, because of natural variability, agglomeration, and chemical reactivity.

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Faculty Opinions recommendation of Detecting novel associations in large data sets.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.13805958.793484294 ◽

2014 ◽

Author(s):

Daniel Lee

Keyword(s):

Large Data ◽

Large Data Sets ◽

Data Sets ◽

Novel Associations

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NVESTIGATION OF THE EFFICIENCY OF DISTRIBUTED INFORMATION SYSTEMS BASED ON THE PROCESSING OF LARGE AMOUNTS OF DATA

Visnyk Universytetu “Ukraina” ◽

10.36994/2707-4110-2019-2-23-03 ◽

2019 ◽

Author(s):

Mykhajlo Klymash ◽

Olena Hordiichuk — Bublivska ◽

Ihor Tchaikovskyi ◽

Oksana Urikova

Keyword(s):

Distributed Systems ◽

Large Data ◽

Large Data Sets ◽

Data Sets ◽

Data Decomposition ◽

Distributed Information ◽

Software Model ◽

Computing Performance ◽

Mapreduce Model ◽

Singular Data

In this article investigated the features of processing large arrays of information for distributed systems. A method of singular data decomposition is used to reduce the amount of data processed, eliminating redundancy. Dependencies of computational efficiency on distributed systems were obtained using the MPI messaging protocol and MapReduce node interaction software model. Were analyzed the efficiency of the application of each technology for the processing of different sizes of data: Non — distributed systems are inefficient for large volumes of information due to low computing performance. It is proposed to use distributed systems that use the method of singular data decomposition, which will reduce the amount of information processed. The study of systems using the MPI protocol and MapReduce model obtained the dependence of the duration calculations time on the number of processes, which testify to the expediency of using distributed computing when processing large data sets. It is also found that distributed systems using MapReduce model work much more efficiently than MPI, especially with large amounts of data. MPI makes it possible to perform calculations more efficiently for small amounts of information. When increased the data sets, advisable to use the Map Reduce model.

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Using Large Data Sets and Statistical Tools to Define “Failure” and Demonstrate the Safety of DPR

Proceedings of the Water Environment Federation ◽

10.2175/193864718824828128 ◽

2018 ◽

Vol 2018 (6) ◽

pp. 38-39

Author(s):

Austa Parker ◽

Yan Qu ◽

David Hokanson ◽

Jeff Soller ◽

Eric Dickenson ◽

...

Keyword(s):

Large Data ◽

Large Data Sets ◽

Data Sets ◽

Statistical Tools

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Online Judging Platform Utilizing Dynamic Plagiarism Detection Facilities

Computers ◽

10.3390/computers10040047 ◽

2021 ◽

Vol 10 (4) ◽

pp. 47

Author(s):

Fariha Iffath ◽

A. S. M. Kayes ◽

Md. Tahsin Rahman ◽

Jannatul Ferdows ◽

Mohammad Shamsul Arefin ◽

...

Keyword(s):

Source Code ◽

Large Data ◽

Large Data Sets ◽

Detection Technique ◽

Data Sets ◽

Plagiarism Detection ◽

Source Codes ◽

Efficient Detection ◽

Mathematical Problems ◽

Automatic Scoring

A programming contest generally involves the host presenting a set of logical and mathematical problems to the contestants. The contestants are required to write computer programs that are capable of solving these problems. An online judge system is used to automate the judging procedure of the programs that are submitted by the users. Online judges are systems designed for the reliable evaluation of the source codes submitted by the users. Traditional online judging platforms are not ideally suitable for programming labs, as they do not support partial scoring and efficient detection of plagiarized codes. When considering this fact, in this paper, we present an online judging framework that is capable of automatic scoring of codes by detecting plagiarized contents and the level of accuracy of codes efficiently. Our system performs the detection of plagiarism by detecting fingerprints of programs and using the fingerprints to compare them instead of using the whole file. We used winnowing to select fingerprints among k-gram hash values of a source code, which was generated by the Rabin–Karp Algorithm. The proposed system is compared with the existing online judging platforms to show the superiority in terms of time efficiency, correctness, and feature availability. In addition, we evaluated our system by using large data sets and comparing the run time with MOSS, which is the widely used plagiarism detection technique.

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