emiRIT: A text-mining based resource for microRNA information

AbstractMotivationmicroRNAs (miRNAs) are essential gene regulators and their dysregulation often leads to diseases. Easy access to miRNA information is crucial for interpreting generated experimental data, connecting facts across publications, and developing new hypotheses built on previous knowledge. Here, we present emiRIT, a text mining-based resource, which presents miRNA information mined from the literature through a user-friendly interface.ResultsWe collected 149,233 miRNA-PubMed ID pairs from Medline between January 1997 to May 2020. emiRIT currently contains miRNA-gene regulation (60,491 relations); miRNA-disease (cancer) (12,300 relations); miRNA-biological process and pathways (23,390 relations); and circulatory miRNAs in extracellular locations (3,782 relations). Biological entities and their relation to miRNAs were extracted from Medline abstracts using publicly available and in-house developed text mining tools, and the entities were normalized to facilitate querying and integration. We built a database and an interface to store and access the integrated data, respectively.ConclusionWe provide an up-to-date and user-friendly resource to facilitate access to comprehensive miRNA information from the literature on a large-scale, enabling users to navigate through different roles of miRNA and examine them in a context specific to their information needs. To assess our resource’s information coverage, in the absence of gold standards, we have conducted two case studies focusing on the target and differential expression information of miRNAs in the context of diseases. Database URL: https://research.bioinformatics.udel.edu/emirit/

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A Universal, Genomewide GuideFinder for CRISPR/Cas9 Targeting in Microbial Genomes

mSphere ◽

10.1128/msphere.00086-20 ◽

2020 ◽

Vol 5 (1) ◽

Author(s):

Michelle Spoto ◽

Changhui Guan ◽

Elizabeth Fleming ◽

Julia Oh

Keyword(s):

Gene Function ◽

Large Scale ◽

Essential Gene ◽

Bacterial Species ◽

Bacterial Genome ◽

Model Organisms ◽

Design Parameters ◽

Bacterial Genomes ◽

Wide Range ◽

User Friendly

ABSTRACT The CRISPR/Cas system has significant potential to facilitate gene editing in a variety of bacterial species. CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) represent modifications of the CRISPR/Cas9 system utilizing a catalytically inactive Cas9 protein for transcription repression and activation, respectively. While CRISPRi and CRISPRa have tremendous potential to systematically investigate gene function in bacteria, few programs are specifically tailored to identify guides in draft bacterial genomes genomewide. Furthermore, few programs offer open-source code with flexible design parameters for bacterial targeting. To address these limitations, we created GuideFinder, a customizable, user-friendly program that can design guides for any annotated bacterial genome. GuideFinder designs guides from NGG protospacer-adjacent motif (PAM) sites for any number of genes by the use of an annotated genome and FASTA file input by the user. Guides are filtered according to user-defined design parameters and removed if they contain any off-target matches. Iteration with lowered parameter thresholds allows the program to design guides for genes that did not produce guides with the more stringent parameters, one of several features unique to GuideFinder. GuideFinder can also identify paired guides for targeting multiplicity, whose validity we tested experimentally. GuideFinder has been tested on a variety of diverse bacterial genomes, finding guides for 95% of genes on average. Moreover, guides designed by the program are functionally useful—focusing on CRISPRi as a potential application—as demonstrated by essential gene knockdown in two staphylococcal species. Through the large-scale generation of guides, this open-access software will improve accessibility to CRISPR/Cas studies of a variety of bacterial species. IMPORTANCE With the explosion in our understanding of human and environmental microbial diversity, corresponding efforts to understand gene function in these organisms are strongly needed. CRISPR/Cas9 technology has revolutionized interrogation of gene function in a wide variety of model organisms. Efficient CRISPR guide design is required for systematic gene targeting. However, existing tools are not adapted for the broad needs of microbial targeting, which include extraordinary species and subspecies genetic diversity, the overwhelming majority of which is characterized by draft genomes. In addition, flexibility in guide design parameters is important to consider the wide range of factors that can affect guide efficacy, many of which can be species and strain specific. We designed GuideFinder, a customizable, user-friendly program that addresses the limitations of existing software and that can design guides for any annotated bacterial genome with numerous features that facilitate guide design in a wide variety of microorganisms.

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lncRNATargets: A platform for lncRNA target prediction based on nucleic acid thermodynamics

Journal of Bioinformatics and Computational Biology ◽

10.1142/s0219720016500165 ◽

2016 ◽

Vol 14 (04) ◽

pp. 1650016 ◽

Cited By ~ 17

Author(s):

Ruifeng Hu ◽

Xiaobo Sun

Keyword(s):

Free Energy ◽

Nucleic Acid ◽

Large Scale ◽

Nearest Neighbor ◽

Binding Free Energy ◽

Target Prediction ◽

Easy Access ◽

Web Based ◽

Size Limitation ◽

User Friendly

Many studies have supported that long noncoding RNAs (lncRNAs) perform various functions in various critical biological processes. Advanced experimental and computational technologies allow access to more information on lncRNAs. Determining the functions and action mechanisms of these RNAs on a large scale is urgently needed. We provided lncRNATargets, which is a web-based platform for lncRNA target prediction based on nucleic acid thermodynamics. The nearest-neighbor (NN) model was used to calculate binging-free energy. The main principle of NN model for nucleic acid assumes that identity and orientation of neighbor base pairs determine stability of a given base pair. lncRNATargets features the following options: setting of a specific temperature that allow use not only for human but also for other animals or plants; processing all lncRNAs in high throughput without RNA size limitation that is superior to any other existing tool; and web-based, user-friendly interface, and colored result displays that allow easy access for nonskilled computer operators and provide better understanding of results. This technique could provide accurate calculation on the binding-free energy of lncRNA-target dimers to predict if these structures are well targeted together. lncRNATargets provides high accuracy calculations, and this user-friendly program is available for free at http://www.herbbol.org:8001/lrt/ .

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Innovative management of accelerometry, inertial, acoustic, and satellite data using netCDF and Postgres

10.7287/peerj.preprints.26731 ◽

2018 ◽

Author(s):

Alex Nunes ◽

Damian Lidgard ◽

Franziska Broell

Keyword(s):

High Resolution ◽

Satellite Data ◽

Large Scale ◽

Cluster Computing ◽

Movement Ecology ◽

Application Programming Interface ◽

Easy Access ◽

Application Programming ◽

Original Size ◽

User Friendly

In 2015, as part of the Ocean Tracking Network’s bioprobe initiative, 20 grey seals (Halichoerus grypus) were tagged with a high-resolution (> 30 Hz) inertial tags (> 30 Hz), a depth-temperature satellite tag (0.1 Hz), and an acoustic transceiver on Sable Island for 6 months. Comparable to similar large-scale studies in movement ecology, the unprecedented size of the data (gigabytes for a single seal) collected by these instruments raises new challenges in efficient database management. Here we propose the utility of Postgres and netCDF for storing the biotelemetry data and associated metadata. While it was possible to write the lower-resolution (acoustic and satellite) data to a Postgres database, netCDF was chosen as the format for the high-resolution movement (acceleration and inertial) records. Even without access to cluster computing, data could be efficiently (CPU time) recorded, as 920 million records were written in < 3 hours. ERDDAP was used to access and link the different datastreams with a user-friendly Application Programming Interface. This approach compresses the data to a fifth of its original size, and storing the data in a tree-like structure enables easy access and visualization for the end user.

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Innovative management of accelerometry, inertial, acoustic, and satellite data using netCDF and Postgres

10.7287/peerj.preprints.26731v1 ◽

2018 ◽

Author(s):

Alex Nunes ◽

Damian Lidgard ◽

Franziska Broell

Keyword(s):

High Resolution ◽

Satellite Data ◽

Large Scale ◽

Cluster Computing ◽

Movement Ecology ◽

Application Programming Interface ◽

Easy Access ◽

Application Programming ◽

Original Size ◽

User Friendly

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A universal, genome-wide guide finder for CRISPR/Cas9 targeting in microbial genomes

10.1101/194241 ◽

2017 ◽

Author(s):

Michelle Spoto ◽

Elizabeth Fleming ◽

Julia Oh

Keyword(s):

Large Scale ◽

Essential Gene ◽

Bacterial Species ◽

Bacterial Genome ◽

Design Parameters ◽

Bacterial Genomes ◽

Microbial Genomes ◽

Genome Wide ◽

Cas9 Protein ◽

User Friendly

AbstractBackgroundThe CRISPR/Cas system has significant potential to facilitate gene editing in a variety of bacterial species. CRISPR interference (CRISPRi) and CRISPR activation (CRISPRa) represent modifications of the CRISPR/Cas9 system utilizing a catalytically inactive Cas9 protein for transcription repression or activation, respectively. While CRISPRi and CRISPRa have tremendous potential to systematically investigate gene function in bacteria, no pan-bacterial, genome-wide tools exist for guide discovery. We have created Guide Finder: a customizable, user-friendly program that can design guides for any annotated bacterial genome.ResultsGuide Finder designs guides from NGG PAM sites for any number of genes using an annotated genome and fasta file input by the user. Guides are filtered according to user-defined design parameters and removed if they contain any off-target matches. Iteration with lowered parameter thresholds allows the program to design guides for genes that did not produce guides with the more stringent parameters, a feature unique to Guide Finder. Guide Finder has been tested on a variety of diverse bacterial genomes, on average finding guides for 95% of genes. Moreover, guides designed by the program are functionally useful—focusing on CRISPRi as a potential application—as demonstrated by essential gene knockdown in two staphylococcal species.ConclusionsThrough the large-scale generation of guides, this open-access software will improve accessibility to CRISPR/Cas studies for a variety of bacterial species.

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Investigating Diseases and Chemicals in COVID-19 Literature with Text Mining (Preprint)

10.2196/preprints.21503 ◽

2020 ◽

Author(s):

Amir Karami ◽

Brandon Bookstaver ◽

Melissa Nolan

Keyword(s):

Text Mining ◽

Literature Review ◽

Topic Modeling ◽

Large Scale ◽

Clinical Manifestations ◽

International Health ◽

Research Papers ◽

Strategic Plans ◽

Funding Agencies ◽

The Relationship

BACKGROUND The COVID-19 pandemic has impacted nearly all aspects of life and has posed significant threats to international health and the economy. Given the rapidly unfolding nature of the current pandemic, there is an urgent need to streamline literature synthesis of the growing scientific research to elucidate targeted solutions. While traditional systematic literature review studies provide valuable insights, these studies have restrictions, including analyzing a limited number of papers, having various biases, being time-consuming and labor-intensive, focusing on a few topics, incapable of trend analysis, and lack of data-driven tools. OBJECTIVE This study fills the mentioned restrictions in the literature and practice by analyzing two biomedical concepts, clinical manifestations of disease and therapeutic chemical compounds, with text mining methods in a corpus containing COVID-19 research papers and find associations between the two biomedical concepts. METHODS This research has collected papers representing COVID-19 pre-prints and peer-reviewed research published in 2020. We used frequency analysis to find highly frequent manifestations and therapeutic chemicals, representing the importance of the two biomedical concepts. This study also applied topic modeling to find the relationship between the two biomedical concepts. RESULTS We analyzed 9,298 research papers published through May 5, 2020 and found 3,645 disease-related and 2,434 chemical-related articles. The most frequent clinical manifestations of disease terminology included COVID-19, SARS, cancer, pneumonia, fever, and cough. The most frequent chemical-related terminology included Lopinavir, Ritonavir, Oxygen, Chloroquine, Remdesivir, and water. Topic modeling provided 25 categories showing relationships between our two overarching categories. These categories represent statistically significant associations between multiple aspects of each category, some connections of which were novel and not previously identified by the scientific community. CONCLUSIONS Appreciation of this context is vital due to the lack of a systematic large-scale literature review survey and the importance of fast literature review during the current COVID-19 pandemic for developing treatments. This study is beneficial to researchers for obtaining a macro-level picture of literature, to educators for knowing the scope of literature, to journals for exploring most discussed disease symptoms and pharmaceutical targets, and to policymakers and funding agencies for creating scientific strategic plans regarding COVID-19.

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Scaling Up Delivery of Biofortified Staple Food Crops Globally: Paths to Nourishing Millions

Food and Nutrition Bulletin ◽

10.1177/0379572120982501 ◽

2021 ◽

pp. 037957212098250

Author(s):

Jennifer K. Foley ◽

Kristina D. Michaux ◽

Bho Mudyahoto ◽

Laira Kyazike ◽

Binu Cherian ◽

...

Keyword(s):

Pearl Millet ◽

Large Scale ◽

Scale Up ◽

Lessons Learned ◽

Raw Material ◽

Micronutrient Deficiencies ◽

Seed Systems ◽

Public And Private ◽

Context Specific ◽

Public And Private Sector

Background: Micronutrient deficiencies affect over one quarter of the world’s population. Biofortification is an evidence-based nutrition strategy that addresses some of the most common and preventable global micronutrient gaps and can help improve the health of millions of people. Since 2013, HarvestPlus and a consortium of collaborators have made impressive progress in the enrichment of staple crops with essential micronutrients through conventional plant breeding. Objective: To review and highlight lessons learned from multiple large-scale delivery strategies used by HarvestPlus to scale up biofortification across different country and crop contexts. Results: India has strong public and private sector pearl millet breeding programs and a robust commercial seed sector. To scale-up pearl millet, HarvestPlus established partnerships with public and private seed companies, which facilitated the rapid commercialization of products and engagement of farmers in delivery activities. In Nigeria, HarvestPlus stimulated the initial acceptance and popularization of vitamin A cassava using a host of creative approaches, including “crowding in” delivery partners, innovative promotional programs, and development of intermediate raw material for industry and novel food products. In Uganda, orange sweet potato (OSP) is a traditional subsistence crop. Due to this, and the lack of formal seed systems and markets, HarvestPlus established a network of partnerships with community-based nongovernmental organizations and vine multipliers to popularize and scale-up delivery of OSP. Conclusions: Impact of biofortification ultimately depends on the development of sustainable markets for biofortified seeds and products. Results illustrate the need for context-specific, innovative solutions to promote widespread adoption.

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Microcomputer Simulations of Presidential Elections

News for Teachers of Political Science ◽

10.1017/s0197901900005110 ◽

1983 ◽

Vol 38 ◽

pp. 20-20

Author(s):

Robert S. Ross

Keyword(s):

Social Sciences ◽

Large Scale ◽

Role Playing ◽

Science Students ◽

Instructional Programs ◽

Santa Barbara ◽

Large Scale Systems ◽

The Social ◽

User Friendly ◽

Machine Interaction

Simulations have been an important adjunct to instructional programs for some time. These have ranged from games, or role playing exercises, such as SIMSOC or Internation Simulation, to student-machine interaction, such as the inter-school simulation run out of University of California, Santa Barbara in the early 70's, to the all machine activities found in some of the early SETUPS. Having social science students use the mainframe computer, however, always posed problems: it definitely was not user-friendly and most instructors had little if any training or interest in the use of large scale systems.The wide-spread use of the micro computer is not only revolutionizing areas traditionally relying upon the computer, but is going to have an impact on the social sciences as well.

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Network community structure of substorms using SuperMAG magnetometers

Nature Communications ◽

10.1038/s41467-021-22112-4 ◽

2021 ◽

Vol 12 (1) ◽

Author(s):

L. Orr ◽

S. C. Chapman ◽

J. W. Gjerloev ◽

W. Guo

Keyword(s):

Large Scale ◽

Three Dimensional ◽

Easy Access ◽

Directed Network ◽

Coherent System ◽

Dimensional System ◽

Ionospheric Currents ◽

Substorm Current Wedge ◽

Spatially Extended ◽

Current Wedge

AbstractGeomagnetic substorms are a global magnetospheric reconfiguration, during which energy is abruptly transported to the ionosphere. Central to this are the auroral electrojets, large-scale ionospheric currents that are part of a larger three-dimensional system, the substorm current wedge. Many, often conflicting, magnetospheric reconfiguration scenarios have been proposed to describe the substorm current wedge evolution and structure. SuperMAG is a worldwide collaboration providing easy access to ground based magnetometer data. Here we show application of techniques from network science to analyze data from 137 SuperMAG ground-based magnetometers. We calculate a time-varying directed network and perform community detection on the network, identifying locally dense groups of connections. Analysis of 41 substorms exhibit robust structural change from many small, uncorrelated current systems before substorm onset, to a large spatially-extended coherent system, approximately 10 minutes after onset. We interpret this as strong indication that the auroral electrojet system during substorm expansions is inherently a large-scale phenomenon and is not solely due to many meso-scale wedgelets.

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