PlantPathMarks (PPMdb): an interactive hub for pathways-based markers in plant genomes

AbstractOver the past decade, the problem of finding an efficient gene-targeting marker set or signature for plant trait characterization has remained challenging. Many databases focusing on pathway mining have been released with one major deficiency, as they lack to develop marker sets that target only genes controlling a specific pathway or certain biological process. Herein, we present the PlantPathMarks database (PPMdb) as a comprehensive, web-based, user-friendly, and interactive hub for pathway-based markers in plant genomes. Based on our newly developed pathway gene set mining approach, two novel pathway-based marker systems called pathway gene-targeted markers (PGTMs) and pathway microsatellite-targeted markers (PMTMs) were developed as a novel class of annotation-based markers. In the PPMdb database, 2,690,742 pathway-based markers reflecting 9,894 marker panels were developed across 82 plant genomes. The markers include 691,555 PGTMs and 1,999,187 PMTMs. Across these genomes, 165,378 enzyme-coding genes were mapped against 126 KEGG reference pathway maps. PPMdb is furnished with three interactive visualization tools (Map Browse, JBrowse and Species Comparison) to visualize, map, and compare the developed markers over their KEGG reference pathway maps. All the stored marker panels can be freely downloaded. PPMdb promises to create a radical shift in the paradigm of the area of molecular marker research. The use of PPMdb as a mega-tool represents an impediment for non-bioinformatician plant scientists and breeders. PPMdb is freely available at http://ppmdb.easyomics.org.

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Bioinformatic Teaching Resources – For Educators, by Educators – Using KBase, a Free, User-Friendly, Open Source Platform

Frontiers in Education ◽

10.3389/feduc.2021.711535 ◽

2021 ◽

Vol 6 ◽

Author(s):

Ellen G. Dow ◽

Elisha M. Wood-Charlson ◽

Steven J. Biller ◽

Timothy Paustian ◽

Aaron Schirmer ◽

...

Keyword(s):

Energy Systems ◽

Department Of Energy ◽

Student Survey ◽

Teaching Resources ◽

Web Based ◽

The Past ◽

Instructional Units ◽

Bioinformatics Education ◽

User Friendly

Over the past year, biology educators and staff at the U.S. Department of Energy Systems Biology Knowledgebase (KBase) initiated a collaborative effort to develop a curriculum for bioinformatics education. KBase is a free web-based platform where anyone can conduct sophisticated and reproducible bioinformatic analyses via a graphical user interface. Here, we demonstrate the utility of KBase as a platform for bioinformatics education, and present a set of modular, adaptable, and customizable instructional units for teaching concepts in Genomics, Metagenomics, Pangenomics, and Phylogenetics. Each module contains teaching resources, publicly available data, analysis tools, and Markdown capability, enabling instructors to modify the lesson as appropriate for their specific course. We present initial student survey data on the effectiveness of using KBase for teaching bioinformatic concepts, provide an example case study, and detail the utility of the platform from an instructor’s perspective. Even as in-person teaching returns, KBase will continue to work with instructors, supporting the development of new active learning curriculum modules. For anyone utilizing the platform, the growing KBase Educators Organization provides an educators network, accompanied by community-sourced guidelines, instructional templates, and peer support, for instructors wishing to use KBase within a classroom at any educational level–whether virtual or in-person.

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ProCanBio: a database of manually curated biomarkers for Prostate Cancer

10.1101/2021.06.06.447247 ◽

2021 ◽

Author(s):

Dikscha Sapra ◽

Harpreet Kaur ◽

Anjali Dhall ◽

Gajendra P.S. Raghava

Keyword(s):

Prostate Cancer ◽

Cancer Biomarkers ◽

Research Community ◽

Web Browsers ◽

Detailed Data ◽

Research Groups ◽

Web Based ◽

The Past ◽

Diagnosis And Prognosis ◽

User Friendly

Background: Prostate Cancer is the second lethal malignancy in men worldwide. In the past, numerous research groups investigated the omics profiles of patients and scrutinized biomarkers for the diagnosis and prognosis of prostate cancer. However, information related to the biomarkers is widely scattered across numerous resources in complex textual format, which poses hindrance to understand the tumorigenesis of this malignancy and scrutinization of robust signature. To the best of authors knowledge, there is no resource that can consolidate the information contained in all the published literature. Results: Here, we present ProCanBio, a manually curated database that maintains detailed data on 2053 entries of potential prostate cancer biomarkers obtained from 412 publications in user friendly tabular format. Among them, 766 protein-based, 488 RNA-based, 157 genomic mutations, 261 miRNA-based, and 122 are metabolites-based biomarkers. To explore the information in the resource, a web-based interactive platform was developed with searching, and browsing facilities. ProCanBio is freely available and is compatible with most web browsers and devices. Eventually, we anticipated this resource will be highly useful for the research community involved in the area of prostate malignancy.

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Connecting omics signatures of diseases, drugs, and mechanisms of actions with iLINCS

10.1101/826271 ◽

2019 ◽

Cited By ~ 12

Author(s):

Marcin Pilarczyk ◽

Michal Kouril ◽

Behrouz Shamsaei ◽

Juozas Vasiliauskas ◽

Wen Niu ◽

...

Keyword(s):

Conceptual Understanding ◽

Drug Repositioning ◽

Omics Data ◽

Data Types ◽

Web Based ◽

Integrative Analyses ◽

Action Analysis ◽

Analysis Strategy ◽

Visualization Tools ◽

User Friendly

AbstractThere are only a few platforms that integrate multiple omics data types, bioinformatics tools, and interfaces for integrative analyses and visualization that do not require programming skills. Among these, iLINCS is unique in scope and versatility of the data provided and the analytics facilitated. iLINCS (http://ilincs.org) is an integrative web-based platform for analysis of omics data and signatures of cellular perturbations. The platform facilitates analysis of user-submitted omics signatures of diseases and cellular perturbations in the context of a large compendium of pre-computed signatures (>200,000), as well as mining and re-analysis of the large collection of omics datasets (>12,000), pre-computed signatures, and their connections. Analytics workflows driven by user-friendly interfaces enable users with only conceptual understanding of the analysis strategy to execute sophisticated analyses of omics signatures, such as systems biology analyses and interpretation of signatures, mechanism of action analysis, and signature-driven drug repositioning. In summary, iLINCS workflows integrate vast omics data resources and a range of analytics and interactive visualization tools into a comprehensive platform for analysis of omics signatures.

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TRIAGE: A web-based iterative analysis platform integrating pathway and network approaches optimizes hit selection from high-throughput assays

10.1101/2020.07.15.204917 ◽

2020 ◽

Author(s):

Samuel Katz ◽

Jian Song ◽

Kyle P. Webb ◽

Nicolas W. Lounsbury ◽

Clare E. Bryant ◽

...

Keyword(s):

High Throughput ◽

Ad Hoc ◽

Web Based ◽

Trade Offs ◽

Genome Wide ◽

Efficient Gene ◽

Iterative Analysis ◽

Network Approaches ◽

User Friendly ◽

Analysis Platform

ABSTRACTComprehensive and efficient gene hit selection from high throughput assays remains a critical bottleneck in realizing the potential of genome-scale studies in biology. Widely used methods such as setting of cutoffs, prioritizing pathway enrichments, or incorporating predicted network interactions offer divergent solutions yet are associated with critical analytical trade-offs, and are often combined in an ad hoc manner. The specific limitations of these individual approaches, the lack of a systematic way by which to integrate their rankings, and the inaccessibility of complex computational approaches to many researchers, has contributed to unexpected variability and limited overlap in the reported results from comparable genome-wide studies. Using a set of three highly studied genome-wide datasets for HIV host factors that have been broadly cited for their limited number of shared candidates, we characterize the specific complementary contributions of commonly used analysis approaches and find an optimal framework by which to integrate these methods. We describe Throughput Ranking by Iterative Analysis of Genomic Enrichment (TRIAGE), an integrated, iterative approach which uses pathway and network statistical methods and publicly available databases to optimize gene prioritization. TRIAGE is accessible as a secure, rapid, user-friendly web-based application (https://triage.niaid.nih.gov).Graphical Abstract

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The Role of Web Based Accounting Online System 2.0 as the Company's Income and Expense Management

Aptisi Transactions on Management (ATM) ◽

10.33050/atm.v1i1.655 ◽

2017 ◽

Vol 1 (1) ◽

pp. 44-49

Author(s):

Nur Azizah ◽

Dedeh Supriyanti ◽

Siti Fairuz Aminah Mustapha ◽

Holly Yang

Keyword(s):

Financial Management ◽

Accounting System ◽

Bank Account ◽

Web Based ◽

Online System ◽

Version 2.0 ◽

User Friendly ◽

The Impact ◽

A Company

In a company, the process of income and expense of money must have a profit-generating goal base. The success of financial management within the company, can be monitored from the ability of the financial management in managing the finances and utilize all the opportunities that exist with as much as possible with the aim to control the company's cash (cash flow) and the impact of generating profits in accordance with expectations. With a web-based online accounting system version 2.0, companies can be given the ease to manage money in and out of the company's cash. It has a user friendly system with navigation that makes it easy for the financial management to use it. Starting from the creation of a company's cash account used as a cash account and corporate bank account on the system, deletion or filing of cash accounts, up to the transfer invoice creation feature, receive and send money. Thus, this system is very effective and efficient in the management of income and corporate cash disbursements. Keywords:Accounting Online System, Financial Management, Cash and Bank

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eMap: A Web Application for Identifying and Visualizing Electron or Hole Hopping Pathways in Proteins

10.26434/chemrxiv.7889993 ◽

2019 ◽

Author(s):

Ruslan N. Tazhigulov ◽

James R. Gayvert ◽

Melissa Wei ◽

Ksenia B. Bravaya

Keyword(s):

Web Application ◽

Shortest Paths ◽

Coarse Grained ◽

Decay Parameter ◽

Electron Hole ◽

Web Based ◽

Aromatic Amino Acid Residue ◽

Pathways Model ◽

Visualization Tools ◽

Effective Decay

<p>eMap is a web-based platform for identifying and visualizing electron or hole transfer pathways in proteins based on their crystal structures. The underlying model can be viewed as a coarse-grained version of the Pathways model, where each tunneling step between hopping sites represented by electron transfer active (ETA) moieties is described with one eﬀective decay parameter that describes protein-mediated tunneling. ETA moieties include aromatic amino acid residue side chains and aromatic fragments of cofactors that are automatically detected, and, in addition, electron/hole residing sites that can be speciﬁed by the users. The software searches for the shortest paths connecting the user-speciﬁed electron/hole source to either all surface-exposed ETA residues or to the user-speciﬁed target. The identiﬁed pathways are ranked based on their length. The pathways are visualized in 2D as a graph, in which each node represents an ETA site, and in 3D using available protein visualization tools. Here, we present the capability and user interface of eMap 1.0, which is available at https://emap.bu.edu.</p>

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Web-Based Peer and Self-Assessment System Design and Development for Elementary School Students

Journal of Education in Black Sea Region ◽

10.31578/jebs.v3i1.121 ◽

2018 ◽

Vol 3 (1) ◽

Author(s):

Mehmet EMIN KORTAK

Keyword(s):

Elementary School ◽

Elementary School Students ◽

Primary Schools ◽

Peer Assessment ◽

Assessment System ◽

Assessment Process ◽

School Students ◽

Self Assessment ◽

Web Based ◽

User Friendly

This research aimed at designing and improving the web-based integrated peer and self- assessment. WesPASS (web-based peer-assessment system), developed in this research, allows students to assess their own or their peers’ performance and project assignments and to report about the result of these assessments so that they correct their assignments. This study employed design-based research. The participants included 102 fourth grade primary school students and their 4 teachers from 2 state and 2 private primary schools in Ankara, Kecioren (Turkey) who employed the system and were engaged in a questionnaire survey to assess its quality. The findings were analyzed through quantitative data analysis. The findings revealed that the system can be used by elementary school students for peer and self-assessment system. The participants stated that WesPASS is simple and user-friendly, and it accelerates the assessment process by employing information technology and allows to share opinions

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Knowledge and perceptions of cardiopulmonary resuscitation amongst New Zealand podiatrists: a web-based survey

Journal of Foot and Ankle Research ◽

10.1186/s13047-021-00481-9 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Angela Brenton-Rule ◽

Daniel Harvey ◽

Kevin Moran ◽

Daniel O’Brien ◽

Jonathon Webber

Keyword(s):

New Zealand ◽

Cardiopulmonary Resuscitation ◽

Life Support ◽

Survival Rates ◽

Sudden Cardiac Arrest ◽

Cross Sectional Study ◽

Trial Registration ◽

Cross Sectional ◽

Web Based ◽

The Past

Abstract Background Podiatrists in New Zealand have a duty of care to assist patients in an emergency, and current cardiopulmonary resuscitation (CPR) certification is a requirement for registration. However, it is unknown how competent and confident podiatrists are in administering CPR and how they would respond in an emergency. Having a health professional who has a competent knowledge of CPR and skills in basic life support, can improve survival rates from sudden cardiac arrest. Therefore, the aim of this study was to survey New Zealand podiatrists to determine their CPR knowledge and qualifications; beliefs about the application of CPR; and perceptions of their competency in CPR. Methods This cross-sectional study used a web-based survey. Participants were New Zealand registered podiatrists with a current annual practising certificate. The 31-item survey included questions to elicit demographic information, CPR practice and attitudes, and CPR knowledge. Responses were collected between March and August 2020. Results 171 podiatrists responded to the survey. 16 % of the podiatrists (n = 28) had performed CPR in an emergency, with a 50 % success rate. Participants were predominantly female (n = 127, 74 %) and working in private practice (n = 140,82 %). Nearly half of respondents were younger than 40 years (n = 75,44 %) and had less than 10 years of clinical experience (n = 73, 43 %). Nearly all (n = 169,97 %) participants had received formal CPR training in the past two years, with 60 % (n = 105) receiving training in the past 12 months. Most respondents (n = 167,98 %) self-estimated their CPR ability as being effective, very effective, or extremely effective. Participants’ knowledge of CPR was variable, with the percentage of correct answers for CPR protocol statements ranging between 20 and 90 %. Conclusions This study provides the first insight into New Zealand podiatrists’ CPR knowledge and perceptions. Podiatrists were found to have high levels of CPR confidence but demonstrated gaps in CPR knowledge. Currently, New Zealand registered podiatrists require biennial CPR re-certification. However, resuscitation authorities in New Zealand and overseas recommend an annual update of CPR skills. Based on this study’s findings, and in line with Australia and the United Kingdom, the authors recommend a change from biennial to annual CPR re-certification for podiatrists in New Zealand. Trial registration The study was registered with the Australian New Zealand Clinical Trials Registry (ACTRN12620001144909).

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The Metano Modeling Toolbox MMTB: An Intuitive, Web-Based Toolbox Introduced by Two Use Cases

Metabolites ◽

10.3390/metabo11020113 ◽

2021 ◽

Vol 11 (2) ◽

pp. 113

Author(s):

Julia Koblitz ◽

Sabine Will ◽

S. Riemer ◽

Thomas Ulas ◽

Meina Neumann-Schaal ◽

...

Keyword(s):

Metabolic Networks ◽

Point Of View ◽

Use Cases ◽

Mathematical Methods ◽

State Behavior ◽

Web Based ◽

Research Fields ◽

Balance Analysis ◽

Metabolic Models ◽

User Friendly

Genome-scale metabolic models are of high interest in a number of different research fields. Flux balance analysis (FBA) and other mathematical methods allow the prediction of the steady-state behavior of metabolic networks under different environmental conditions. However, many existing applications for flux optimizations do not provide a metabolite-centric view on fluxes. Metano is a standalone, open-source toolbox for the analysis and refinement of metabolic models. While flux distributions in metabolic networks are predominantly analyzed from a reaction-centric point of view, the Metano methods of split-ratio analysis and metabolite flux minimization also allow a metabolite-centric view on flux distributions. In addition, we present MMTB (Metano Modeling Toolbox), a web-based toolbox for metabolic modeling including a user-friendly interface to Metano methods. MMTB assists during bottom-up construction of metabolic models by integrating reaction and enzymatic annotation data from different databases. Furthermore, MMTB is especially designed for non-experienced users by providing an intuitive interface to the most commonly used modeling methods and offering novel visualizations. Additionally, MMTB allows users to upload their models, which can in turn be explored and analyzed by the community. We introduce MMTB by two use cases, involving a published model of Corynebacterium glutamicum and a newly created model of Phaeobacter inhibens.

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An Interactive Web Application for the Statistical Analysis of Continuous Glucose Monitoring Data in Epidemiological Studies

Journal of Diabetes Science and Technology ◽

10.1177/1932296820985570 ◽

2021 ◽

pp. 193229682098557

Author(s):

Alysha M. De Livera ◽

Jonathan E. Shaw ◽

Neale Cohen ◽

Anne Reutens ◽

Agus Salim

Keyword(s):

Continuous Glucose Monitoring ◽

Web Application ◽

Diabetes Management ◽

Glucose Monitoring ◽

Epidemiological Studies ◽

Interactive Software ◽

Web Based ◽

Software Applications ◽

Visualization Of Data ◽

User Friendly

Motivation: Continuous glucose monitoring (CGM) systems are an essential part of novel technology in diabetes management and care. CGM studies have become increasingly popular among researchers, healthcare professionals, and people with diabetes due to the large amount of useful information that can be collected using CGM systems. The analysis of the data from these studies for research purposes, however, remains a challenge due to the characteristics and large volume of the data. Results: Currently, there are no publicly available interactive software applications that can perform statistical analyses and visualization of data from CGM studies. With the rapidly increasing popularity of CGM studies, such an application is becoming necessary for anyone who works with these large CGM datasets, in particular for those with little background in programming or statistics. CGMStatsAnalyser is a publicly available, user-friendly, web-based application, which can be used to interactively visualize, summarize, and statistically analyze voluminous and complex CGM datasets together with the subject characteristics with ease.

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