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

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.

scholarly journals From Pacific Scoop to Asia Pacific Report: A case study in an independent campus-industry media partnership

2016 ◽  
Vol 22 (2) ◽  
pp. 64
Author(s):  
David Robie
Keyword(s):  
Asia Pacific ◽  
Pacific Region ◽  
Asia Pacific Region ◽  
Investigative Journalism ◽  
Web Based ◽  
Civic Journalism ◽  
Innovative Strategies ◽  
The Past ◽  
Current Affairs

Media convergence within the news and current affairs landscape over the past two decades has opened opportunities for competing newspapers, television stations and online publishers to form alliances to approach digital and editorial challenges with innovative strategies. The partnerships have often enabled journalists to embrace multimedia platforms with flexibility and initiative. This has fostered a trend in ‘gatewatching’ and a citizen responsive and involved grassroots media rather than legacy mainstream gatekeeping, top-down models. Such committed media attempts in search of investigative journalism accompanied by ‘public’ and ‘civic’ journalism engagement initiatives have also been emulated by some journalism schools in the Asia-Pacific region. This has paralleled the evolution of journalism as a research methodology with academic application over the past decade. Selecting two New Zealand-based complementary and pioneering Pacific digital news and analysis publications, Pacific Scoop (founded 2009) and Asia-Pacific Report (2016), produced by a journalism school programme in partnership with established independent media as a combined case study, this article will demonstrate how academia-based gatewatching media can effectively challenge mainstream gatekeeping media. Pacific Scoop was established by an Auckland university in partnership with New Zealand’s largest independent publisher, Scoop Media Limited, and launched at the Māori Expo in 2009. The article also explores the transition of Pacific Scoop into Asia-Pacific Report, launched in partnership with an innovative web-based partner, Evening Report. The study analyses the strategic and innovation efforts in the context of continuing disruptions to New Zealand’s legacy media practices related to the Asia-Pacific region.

scholarly journals How suitable is Yahoo! Groups for school librarians’ professional networking? A case study from Hong Kong

2016 ◽  
Author(s):  
Samson Choi ◽  
Zvjezdana Dukic
Keyword(s):  
Hong Kong ◽  
Qualitative Data ◽  
Case Study Research ◽  
School Librarians ◽  
Web Based ◽  
Professional Needs ◽  
Professional Networking ◽  
Group Members ◽  
User Friendly

This paper explores how members of Hong Kong based professional association of school librarians (ALESS) use Yahoo! Groups platform for their professional networking and how the platform satisfies the group’s professional needs. The case study research method is applied and both quantitative and qualitative data are collected. It is revealed that ALESS members effectively use Yahoo! Groups platform even though they do not exploit all available features. ALESS members regularly use web-based mail and occasionally Files and Polls. Although some group members think that Yahoo! Groups need to be replaced with a more user- friendly tool, most respondents agree that for the time being Yahoo! Groups platform fairly fulfils ALESS group’s needs. Further analysis of existing social networking software and ALESS group’s needs and preferences are recommended.

scholarly journals Referencing@Portsmouth: a web-based, interactive referencing tool

2010 ◽  
Author(s):  
Roisin Gwyer ◽  
Linda Jones ◽  
James Stewart Matthews ◽  
Anne Worden
Keyword(s):  
Undergraduate Students ◽  
Web Based ◽  
Selection Tool ◽  
Hierarchical Selection ◽  
Search Facility ◽  
The University ◽  
User Friendly ◽  
Web Designers

This case study describes a project at the University of Portsmouth library to create a sustainable web-based tool to help undergraduate students with the thorny issue of academic referencing of their sources for written work, using a hierarchical selection tool, backed up by an optional search facility. It is intended to encourage them to think analytically about their sources. The selection tool needed to be user-friendly and easy to manage by librarians who are not also web designers. The project went live with APA style referencing and has been expanded to cover OSCOLA (law) referencing, with Vancouver style in the pipeline.. Although intended for Portsmouth students, among whom its use is growing rapidly, others have linked to it, including the Intute website. This case study describes a project at the University of Portsmouth library to create a sustainable web-based tool to help undergraduate students with the thorny issue of academic referencing of their sources for written work, using a hierarchical selection tool, backed up by an optional search facility. It is intended to encourage them to think analytically about their sources. The selection tool needed to be user-friendly and easy to manage by librarians who are not also web designers. The project went live with APA style referencing and has been expanded to cover OSCOLA (law) referencing, with Vancouver style in the pipeline.. Although intended for Portsmouth students, among whom its use is growing rapidly, others have linked to it, including the Intute website.

scholarly journals ProCanBio: a database of manually curated biomarkers for Prostate Cancer

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.

scholarly journals Vaxjo: A Web-Based Vaccine Adjuvant Database and Its Application for Analysis of Vaccine Adjuvants and Their Uses in Vaccine Development

2012 ◽  
Vol 2012 ◽  
pp. 1-13 ◽  
Author(s):  
Samantha Sayers ◽  
Guerlain Ulysse ◽  
Zuoshuang Xiang ◽  
Yongqun He
Keyword(s):  
Data Exchange ◽  
Vaccine Development ◽  
Vaccine Adjuvant ◽  
Vaccine Adjuvants ◽  
Web Based ◽  
Host Immune Responses ◽  
Ontology Language ◽  
Analysis System ◽  
User Friendly

Vaccine adjuvants are compounds that enhance host immune responses to co-administered antigens in vaccines. Vaxjo is a web-based central database and analysis system that curates, stores, and analyzes vaccine adjuvants and their usages in vaccine development. Basic information of a vaccine adjuvant stored in Vaxjo includes adjuvant name, components, structure, appearance, storage, preparation, function, safety, and vaccines that use this adjuvant. Reliable references are curated and cited. Bioinformatics scripts are developed and used to link vaccine adjuvants to different adjuvanted vaccines stored in the general VIOLIN vaccine database. Presently, 103 vaccine adjuvants have been curated in Vaxjo. Among these adjuvants, 98 have been used in 384 vaccines stored in VIOLIN against over 81 pathogens, cancers, or allergies. All these vaccine adjuvants are categorized and analyzed based on adjuvant types, pathogens used, and vaccine types. As a use case study of vaccine adjuvants in infectious disease vaccines, the adjuvants used inBrucellavaccines are specifically analyzed. A user-friendly web query and visualization interface is developed for interactive vaccine adjuvant search. To support data exchange, the information of vaccine adjuvants is stored in the Vaccine Ontology (VO) in the Web Ontology Language (OWL) format.

scholarly journals Case study of Argus in Togo: An SMS and web-based application to support public health surveillance, results from 2016 to 2019

PLoS ONE ◽  
2020 ◽  
Vol 15 (12) ◽  
pp. e0243131
Author(s):  
José Guerra ◽  
Kokou Mawule Davi ◽  
Florentina Chipuila Rafael ◽  
Hamadi Assane ◽  
Lucile Imboua ◽  
...  
Keyword(s):  
Public Health ◽  
Public Health Surveillance ◽  
Health Surveillance ◽  
Web Based ◽  
Healthcare Facilities ◽  
Report Data ◽  
Health Surveillance Data ◽  
Time Required ◽  
User Friendly

Introduction Argus is an open source electronic solution to facilitate the reporting and management of public health surveillance data. Its components include an Android-phone application, used by healthcare facilities to report results via SMS; and a central server located at the Ministry of Health, displaying aggregated results on a web platform for intermediate and central levels. This study describes the results of the use of Argus in two regions of Togo. Methods Argus was used in 148 healthcare facilities from May 2016 to July 2018, expanding to 185 healthcare facilities from July 2018. Data from week 21 of 2016 to week 12 of 2019 was extracted from the Argus database and analysed. An assessment mission took place in August 2016 to collect users’ satisfaction, to estimate the concordance of the received data with the collected data, and to estimate the time required to report data with Argus. Results Overall completeness of data reporting was 76%, with 80% of reports from a given week being received before Tuesday 9PM. Concordance of data received from Argus and standard paper forms was 99.7%. Median time needed to send a report using Argus was 4 minutes. Overall completeness of data review at district, regional, and central levels were 89%, 68%, and 35% respectively. Implementation cost of Argus was 23 760 USD for 148 facilities. Conclusions The use of Argus in Togo enabled healthcare facilities to send weekly reports and alerts through SMS in a user-friendly, reliable and timely manner. Reengagement of surveillance officers at all levels, especially at the central level, enabled a dramatic increase in completeness and timeliness of data report and data review.

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

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Morad M. Mokhtar ◽  
Achraf El Allali ◽  
Mohamed-Elamir F. Hegazy ◽  
Mohamed A. M. Atia
Keyword(s):  
Web Based ◽  
Plant Genomes ◽  
The Past ◽  
Plant Trait ◽  
Pathway Gene ◽  
Efficient Gene ◽  
Visualization Tools ◽  
User Friendly ◽  
Specific Pathway ◽  
Radical Shift

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.

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

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

A Case Study on Web-based Learning Environment Evaluation in Higher Education: Learner Perspectives in a Private University in Malaysia.

2020 ◽  
Vol 1 (2) ◽  
pp. 18-33
Author(s):  
Zarina Che Imbi ◽  
Tse-Kian Neo ◽  
Mai Neo
Keyword(s):  
Higher Education ◽  
Learning Environment ◽  
Private University ◽  
Systematic Evaluation ◽  
Digital Learning ◽  
Mixed Method Research ◽  
Web Based ◽  
Web Based Learning ◽  
Kirkpatrick’S Model

In the era of digital learning, multimedia-based classroom has been commonly used in higher education including Malaysian higher education institutions. A case study has been performed to evaluate web-based learning using Level 1 to 3 of Kirkpatrick's model in a multi-disciplinary course at Multimedia University, Malaysia. In this study, mixed method research was employed in which triangulation was performed from multiple sources of data collection to give deeper understanding. Students perceived that learning with multimedia was enjoyable. They were also motivated in learning and engaged through the use of web module as multimedia was perceived to motivate them and make learning fun. Students showed significant improvements in their knowledge based on the pre-test and post-test results on learning evaluation. Students were perceived to transfer the learning from web-based learning into the learning outcome. The systematic evaluation can provide the feedback that educators and institution as a whole need to improve the learning environment and programme quality. This study contributes to the research field by adding another perspective in evaluations of web-based learning. It also provides empirical evidence on student perspectives, learning and behaviour in a private university. It demonstrated that the Kirkpatrick's model is useful as an evaluation tool to be used in higher education.

From hard to soft: theory and Neolithic studies in Scotland

2011 ◽  
Vol 33 (1-2) ◽  
pp. 7-19
Author(s):  
Kenneth Brophy
Keyword(s):  
The Past

The Scottish Theoretical Archaeology Group (STAG) conference organisers expressed some doubts about how far theory has changed, and impacted, archaeological establishment and academia in Scotland. In this paper, I will argue that Scotland is certainly not isolated in a theoretical sense, although in the past, Scottish archaeology could be accused of being theoretically conservative, or at least dependent on ideas and models developed elsewhere. A case-study looking at Neolithic studies will be used to illustrate that despite some recent critical historiographies of the study of the period in Scotland, archaeologists in Scotland and those working with Scottish material have been theoretically innovative and in step with wider paradigm changes. The study of the Neolithic in Scotland, it could be argued, has been shaped by theory more than the study of any other period; we are not isolated, but rather part of wider networks of discourse.

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