scholarly journals WebGestalt 2019: gene set analysis toolkit with revamped UIs and APIs

2019 ◽  
Vol 47 (W1) ◽  
pp. W199-W205 ◽  
Author(s):  
Yuxing Liao ◽  
Jing Wang ◽  
Eric J Jaehnig ◽  
Zhiao Shi ◽  
Bing Zhang
Keyword(s):  
User Interfaces ◽  
Large Scale ◽  
Data Interpretation ◽  
R Package ◽  
Third Party ◽  
Gene Set Analysis ◽  
Functional Categories ◽  
User Friendliness ◽  
The Core ◽  
Gene Sets

Abstract WebGestalt is a popular tool for the interpretation of gene lists derived from large scale -omics studies. In the 2019 update, WebGestalt supports 12 organisms, 342 gene identifiers and 155 175 functional categories, as well as user-uploaded functional databases. To address the growing and unique need for phosphoproteomics data interpretation, we have implemented phosphosite set analysis to identify important kinases from phosphoproteomics data. We have completely redesigned result visualizations and user interfaces to improve user-friendliness and to provide multiple types of interactive and publication-ready figures. To facilitate comprehension of the enrichment results, we have implemented two methods to reduce redundancy between enriched gene sets. We introduced a web API for other applications to get data programmatically from the WebGestalt server or pass data to WebGestalt for analysis. We also wrapped the core computation into an R package called WebGestaltR for users to perform analysis locally or in third party workflows. WebGestalt can be freely accessed at http://www.webgestalt.org.

Web-based personal health records: the personal electronic health record (pEHR) multicentred trial

2007 ◽  
Vol 13 (1_suppl) ◽  
pp. 32-34 ◽  
Author(s):  
George E Karagiannis ◽  
Vasileios G Stamatopoulos ◽  
Michael Rigby ◽  
Takis Kotis ◽  
Elisa Negroni ◽  
...  
Keyword(s):  
Health Care ◽  
Electronic Health Record ◽  
Health Care Professionals ◽  
Large Scale ◽  
Study Groups ◽  
Third Party ◽  
Health Record ◽  
User Friendliness ◽  
Web Based ◽  
Electronic Health

A multicentre trial of a Web-based personal electronic health record (pEHR) service was conducted in three different European hospitals. A total of 150 patients and 22 health-care professionals were involved. The service was customised according to the needs of three groups of patients who had congenital heart disease, Parkinson's disease and type 2 diabetes. Two structured questionnaires, one for patients and one for health-care professionals, were used to collect their views on the pEHR service. The questions were about usability and user friendliness, safety and trustworthiness, reliability, functionality, satisfaction and the potential revenue model of the service in the case of future deployment. Patients perceived the service as very motivating and felt that it could help them in managing their clinical information. Health-care professionals showed a very positive attitude towards the use of the service and its potential for future large-scale deployment. They were also keen to recommend the service to their patients. Both study groups were unwilling to pay for the service and preferred it to be sponsored by a third party (e.g. the National Health Service).

scholarly journals Mitochondrial Phylogenomics of Fagales Provides Insights Into Plant Mitogenome Mosaic Evolution

2021 ◽  
Vol 12 ◽  
Author(s):  
Yanlei Feng ◽  
Xiaoguo Xiang ◽  
Delara Akhter ◽  
Ronghui Pan ◽  
Zhixi Fu ◽  
...  
Keyword(s):  
Woody Plants ◽  
Large Scale ◽  
Size Variation ◽  
Nuclear Genome ◽  
Third Party ◽  
Plastid Genomes ◽  
Gene Sets ◽  
Almost All ◽  
Similar Gene ◽  
Specific Sequences

Fagales are an order of woody plants and comprise more than 1,100 species, most of which produce economically important timbers, nuts, and fruits. Their nuclear and plastid genomes are well-sequenced and provided valuable resources to study their phylogeny, breeding, resistance, etc. However, little is known about the mitochondrial genomes (mitogenomes), which hinder a full understanding of their genome evolution. In this study, we assembled complete mitogenomes of 23 species, covering five of the seven families of Fagales. These mitogenomes had similar gene sets but varied 2.4 times in size. The mitochondrial genes were highly conserved, and their capacity in phylogeny was challenging. The mitogenomic structure was extremely dynamic, and synteny among species was poor. Further analyses of the Fagales mitogenomes revealed extremely mosaic characteristics, with horizontal transfer (HGT)-like sequences from almost all seed plant taxa and even mitoviruses. The largest mitogenome, Carpinus cordata, did not have large amounts of specific sequences but instead contained a high proportion of sequences homologous to other Fagales. Independent and unequal transfers of third-party DNA, including nuclear genome and other resources, may partially account for the HGT-like fragments and unbalanced size expansions observed in Fagales mitogenomes. Supporting this, a mitochondrial plasmid-like of nuclear origin was found in Carpinus. Overall, we deciphered the last genetic materials of Fagales, and our large-scale analyses provide new insights into plant mitogenome evolution and size variation.

scholarly journals MAVTgsa: An R Package for Gene Set (Enrichment) Analysis

2014 ◽  
Vol 2014 ◽  
pp. 1-11 ◽  
Author(s):  
Chih-Yi Chien ◽  
Ching-Wei Chang ◽  
Chen-An Tsai ◽  
James J. Chen
Keyword(s):  
Enrichment Analysis ◽  
R Package ◽  
Ordinary Least Squares ◽  
Gene Set Enrichment Analysis ◽  
Gene Set Analysis ◽  
Gene Set Enrichment ◽  
Experimental Conditions ◽  
Gene Set ◽  
Gene Sets ◽  
Significant Difference

Gene set analysis methods aim to determine whether an a priori defined set of genes shows statistically significant difference in expression on either categorical or continuous outcomes. Although many methods for gene set analysis have been proposed, a systematic analysis tool for identification of different types of gene set significance modules has not been developed previously. This work presents an R package, called MAVTgsa, which includes three different methods for integrated gene set enrichment analysis. (1) The one-sided OLS (ordinary least squares) test detects coordinated changes of genes in gene set in one direction, either up- or downregulation. (2) The two-sided MANOVA (multivariate analysis variance) detects changes both up- and downregulation for studying two or more experimental conditions. (3) A random forests-based procedure is to identify gene sets that can accurately predict samples from different experimental conditions or are associated with the continuous phenotypes. MAVTgsa computes thePvalues and FDR (false discovery rate)q-value for all gene sets in the study. Furthermore, MAVTgsa provides several visualization outputs to support and interpret the enrichment results. This package is available online.

Risk Assessment of Core Banking System Replacement based on ISACA Framework

2014 ◽  
Vol 1 (1) ◽  
pp. 35-45
Author(s):  
Fenty Simanjuntak ◽  
Bobby Suryajaya
Keyword(s):  
Risk Assessment ◽  
Banking System ◽  
Residual Risk ◽  
Project Teams ◽  
Third Party ◽  
Project Delivery ◽  
Business Growth ◽  
Regulatory Requirements ◽  
The Core ◽  
Medium Risk

Many banks are looking for a better core banking system to support their business growth with a more efficient and flexible core banking system to improve their sales and services in the competitive market and to fulfill regulatory requirements. The decision of replacing the legacy core banking system is difficult due to the high IT investment cost required for banks because they are also trying to cut costs. But maintaining the legacy system is costly in terms of upgrade. Changing the core banking system is also a difficult process and increases risks. To have a successful Core Banking System implementation, risk assessment is required to be performed prior to starting any activities. The assessment can help project teams to identify the risks and then to mitigate the risks as part of the plan. In this research the Core Banking System replacement risks were assessed based on ISACA Framework for IT Risk. Fourteen risk scenarios related to Core Banking System Replacement were identified. The high and medium rated inherent risks can become medium and low residual risk after assessment by putting the relevant control in place. The result proves that by adding mitigation plan it will help to mitigate the Residual Risk to become low risk. There are still three residual risk which categorized as medium risk and should be further mitigated they are Software Implementation, Project Delivery and Selection/Performance of Third Party Suppliers. It is also found that COBIT 5 has considered some specific process capabilities that can be used to improve the processes to mitigate the medium risks.

scholarly journals NoRCE: non-coding RNA sets cis enrichment tool

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Gulden Olgun ◽  
Afshan Nabi ◽  
Oznur Tastan
Keyword(s):  
Expression Patterns ◽  
Target Prediction ◽  
Enrichment Analysis ◽  
Fruit Fly ◽  
Relevant Information ◽  
R Package ◽  
Data Repository ◽  
Biologically Relevant ◽  
Gene Sets ◽  
Data Files

Abstract Background While some non-coding RNAs (ncRNAs) are assigned critical regulatory roles, most remain functionally uncharacterized. This presents a challenge whenever an interesting set of ncRNAs needs to be analyzed in a functional context. Transcripts located close-by on the genome are often regulated together. This genomic proximity on the sequence can hint at a functional association. Results We present a tool, NoRCE, that performs cis enrichment analysis for a given set of ncRNAs. Enrichment is carried out using the functional annotations of the coding genes located proximal to the input ncRNAs. Other biologically relevant information such as topologically associating domain (TAD) boundaries, co-expression patterns, and miRNA target prediction information can be incorporated to conduct a richer enrichment analysis. To this end, NoRCE includes several relevant datasets as part of its data repository, including cell-line specific TAD boundaries, functional gene sets, and expression data for coding & ncRNAs specific to cancer. Additionally, the users can utilize custom data files in their investigation. Enrichment results can be retrieved in a tabular format or visualized in several different ways. NoRCE is currently available for the following species: human, mouse, rat, zebrafish, fruit fly, worm, and yeast. Conclusions NoRCE is a platform-independent, user-friendly, comprehensive R package that can be used to gain insight into the functional importance of a list of ncRNAs of any type. The tool offers flexibility to conduct the users’ preferred set of analyses by designing their own pipeline of analysis. NoRCE is available in Bioconductor and https://github.com/guldenolgun/NoRCE.

scholarly journals Research on Blockchain-Based E-Bidding System

2021 ◽  
Vol 11 (9) ◽  
pp. 4011
Author(s):  
Dan Wang ◽  
Jindong Zhao ◽  
Chunxiao Mu
Keyword(s):  
Data Transmission ◽  
Privacy Protection ◽  
Graph Isomorphism ◽  
Third Party ◽  
Business Logic ◽  
Core Concept ◽  
The Core ◽  
Blockchain Technology ◽  
Smart Contract ◽  
Bidding Process

In the field of modern bidding, electronic bidding leads a new trend of development, convenience and efficiency and other significant advantages effectively promote the reform and innovation of China’s bidding field. Nowadays, most systems require a strong and trusted third party to guarantee the integrity and security of the system. However, with the development of blockchain technology and the rise of privacy protection, researchers has begun to emphasize the core concept of decentralization. This paper introduces a decentralized electronic bidding system based on blockchain and smart contract. The system uses blockchain to replace the traditional database and uses chaincode to process business logic. In data interaction, encryption techniques such as zero-knowledge proof based on graph isomorphism are used to improve privacy protection, which improves the anonymity of participants, the privacy of data transmission, and the traceability and verifiable of data. Compared with other electronic bidding systems, this system is more secure and efficient, and has the nature of anonymous operation, which fully protects the privacy information in the bidding process.

scholarly journals Sprayable User Interfaces: Prototyping Large-Scale Interactive Surfaces with Sensors and Displays

2020 ◽  
Author(s):  
Michael Wessely ◽  
Ticha Sethapakdi ◽  
Carlos Castillo ◽  
Jackson C. Snowden ◽  
Ollie Hanton ◽  
...  
Keyword(s):  
User Interfaces ◽  
Large Scale ◽  
Interactive Surfaces

Contour clustering: A field-data-driven approach for documenting and analysing prototypical f0 contours

2021 ◽  
pp. 1-30
Author(s):  
Constantijn Kaland
Keyword(s):  
Cluster Analysis ◽  
User Interfaces ◽  
Data Driven ◽  
Language Documentation ◽  
Cluster Number ◽  
Automatic Data ◽  
Speaker Variability ◽  
The Core ◽  
Data Driven Approach ◽  
Confirmatory Analysis

ABSTRACT This paper reports an automatic data-driven analysis for describing prototypical intonation patterns, particularly suitable for initial stages of prosodic research and language description. The approach has several advantages over traditional ways to investigate intonation, such as the applicability to spontaneous speech, language- and domain-independency, and the potential of revealing meaningful functions of intonation. These features make the approach particularly useful for language documentation, where the description of prosody is often lacking. The core of this approach is a cluster analysis on a time-series of f0 measurements and consists of two scripts (Praat and R, available from https://constantijnkaland.github.io/contourclustering/). Graphical user interfaces can be used to perform the analyses on collected data ranging from spontaneous to highly controlled speech. There is limited need for manual annotation prior to analysis and speaker variability can be accounted for. After cluster analysis, Praat textgrids can be generated with the cluster number annotated for each individual contour. Although further confirmatory analysis is still required, the outcomes provide useful and unbiased directions for any investigation of prototypical f0 contours based on their acoustic form.

scholarly journals Implantable computer-controlled adaptive multielectrode positioning system

2018 ◽  
Vol 119 (4) ◽  
pp. 1471-1484 ◽  
Author(s):  
E. Ferrea ◽  
L. Suriya-Arunroj ◽  
D. Hoehl ◽  
U. Thomas ◽  
A. Gail
Keyword(s):  
Cerebral Cortex ◽  
Large Scale ◽  
Nonhuman Primates ◽  
Tissue Response ◽  
High Signal ◽  
Signal Quality ◽  
Positioning System ◽  
Multielectrode Arrays ◽  
User Friendliness ◽  
Computer Controlled

Acute neuronal recordings performed with metal microelectrodes in nonhuman primates allow investigating the neural substrate of complex cognitive behaviors. Yet the daily reinsertion and positioning of the electrodes prevents recording from many neurons simultaneously, limiting the suitability of these types of recordings for brain-computer interface applications or for large-scale population statistical methods on a trial-by-trial basis. In contrast, chronically implanted multielectrode arrays offer the opportunity to record from many neurons simultaneously, but immovable electrodes prevent optimization of the signal during and after implantation and cause the tissue response to progressively impair the transduced signal quality, thereby limiting the number of different neurons that can be recorded over the lifetime of the implant. Semichronically implanted matrices of electrodes, instead, allow individually movable electrodes in depth and achieve higher channel count compared with acute methods, hence partially overcoming these limitations. Existing semichronic systems with higher channel count lack computerized control of electrode movements, leading to limited user-friendliness and uncertainty in depth positioning. Here we demonstrate a chronically implantable adaptive multielectrode positioning system with detachable drive for computerized depth adjustment of individual electrodes over several millimeters. This semichronic 16-channel system is designed to optimize the simultaneous yield of units in an extended period following implantation since the electrodes can be independently depth adjusted with minimal effort and their signal quality continuously assessed. Importantly, the electrode array is designed to remain within a chronic recording chamber for a prolonged time or can be used for acute recordings with high signal-to-noise ratio in the cerebral cortex of nonhuman primates. NEW & NOTEWORTHY We present a 16-channel motorized, semichronic multielectrode array with individually depth-adjustable electrodes to record in the cerebral cortex of nonhuman primates. Compared with fixed-geometry arrays, this system allows repeated reestablishing of single neuron isolation. Compared with manually adjustable arrays it benefits from computer-controlled positioning. Compared with motorized semichronic systems it allows higher channel counts due to a robotic single actuator approach. Overall the system is designed to optimize the simultaneous yield of units over the course of implantation.

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