scholarly journals MADMAX – Management and analysis database for multiple ~omics experiments

2011 ◽  
Vol 8 (2) ◽  
pp. 59-74 ◽  
Author(s):  
Ke Lin ◽  
Harrie Kools ◽  
Philip J. de Groot ◽  
Anand K. Gavai ◽  
Ram K. Basnet ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Pilot Study ◽  
Easy Access ◽  
Omics Data ◽  
Web Based ◽  
Sequencing Technologies ◽  
Integrated Platform ◽  
Access To Data ◽  
Generation Sequencing ◽  
The Web

Summary The rapid increase of ~omics datasets generated by microarray, mass spectrometry and next generation sequencing technologies requires an integrated platform that can combine results from different ~omics datasets to provide novel insights in the understanding of biological systems. MADMAX is designed to provide a solution for storage and analysis of complex ~omics datasets. In addition, analysis results (such as lists of genes) can be merged to reveal candidate genes supported by all datasets. The system constitutes an ISA-Tab compliant LIMS part, which is linked to the different analysis pipelines. A pilot study of different type of ~omics data in Brassica rapa demonstrates the possible use of MADMAX. The web-based user interface provides easy access to data and analysis tools on top of the database.

Language history questionnaire (LHQ 2.0): A new dynamic web-based research tool

2013 ◽  
Vol 17 (3) ◽  
pp. 673-680 ◽  
Author(s):  
PING LI ◽  
FAN ZHANG ◽  
ERLFANG TSAI ◽  
BRENDAN PULS
Keyword(s):  
Language Learners ◽  
Second Language Learners ◽  
Web Design ◽  
Web Based ◽  
Language History ◽  
Dynamic Web ◽  
Access To Data ◽  
Multiple Languages ◽  
Privacy Issues ◽  
The Web

The language history questionnaire (LHQ) is an important tool for assessing the linguistic background of bilinguals or second language learners and for generating self-reported proficiency in multiple languages. Previously we developed a generic LHQ based on the most commonly asked questions in published studies (Li, Sepanski & Zhao, 2006). Here we report a new web-based interface (LHQ 2.0) that has more flexibility in functionality, more accuracy in data recording, and more privacy for users and data. LHQ 2.0 achieves flexibility, accuracy, and privacy by using dynamic web-design features for enhanced data collection. It allows investigators to dynamically construct individualized LHQs on the fly and allows participants to complete the LHQ online in multiple languages. Investigators can download and delete the LHQ results and update their user and experiment information on the web. Privacy issues are handled through the online assignment of a unique ID number for each study and password-protected access to data.

scholarly journals ASAP 2020 update: an open, scalable and interactive web-based portal for (single-cell) omics analyses

2020 ◽  
Vol 48 (W1) ◽  
pp. W403-W414
Author(s):  
Fabrice P A David ◽  
Maria Litovchenko ◽  
Bart Deplancke ◽  
Vincent Gardeux
Keyword(s):  
Big Data ◽  
Single Cell ◽  
Single Cell Analysis ◽  
Omics Data ◽  
Cell Analysis ◽  
Rna Seq ◽  
Analysis Pipeline ◽  
Web Based ◽  
Data Analyses ◽  
The Web

Abstract Single-cell omics enables researchers to dissect biological systems at a resolution that was unthinkable just 10 years ago. However, this analytical revolution also triggered new demands in ‘big data’ management, forcing researchers to stay up to speed with increasingly complex analytical processes and rapidly evolving methods. To render these processes and approaches more accessible, we developed the web-based, collaborative portal ASAP (Automated Single-cell Analysis Portal). Our primary goal is thereby to democratize single-cell omics data analyses (scRNA-seq and more recently scATAC-seq). By taking advantage of a Docker system to enhance reproducibility, and novel bioinformatics approaches that were recently developed for improving scalability, ASAP meets challenging requirements set by recent cell atlasing efforts such as the Human (HCA) and Fly (FCA) Cell Atlas Projects. Specifically, ASAP can now handle datasets containing millions of cells, integrating intuitive tools that allow researchers to collaborate on the same project synchronously. ASAP tools are versioned, and researchers can create unique access IDs for storing complete analyses that can be reproduced or completed by others. Finally, ASAP does not require any installation and provides a full and modular single-cell RNA-seq analysis pipeline. ASAP is freely available at https://asap.epfl.ch.

scholarly journals SysPIMP: the web-based systematical platform for identifying human disease-related mutated sequences from mass spectrometry

2009 ◽  
Vol 37 (Database) ◽  
pp. D913-D920 ◽  
Author(s):  
H. Xi ◽  
J. Park ◽  
G. Ding ◽  
Y.-H. Lee ◽  
Y. Li
Keyword(s):  
Mass Spectrometry ◽  
Human Disease ◽  
Web Based ◽  
The Web

Use of Web-Based Portfolios as Tools for Reflection in Preservice Teacher Education

2011 ◽  
Vol 62 (5) ◽  
pp. 477-492 ◽  
Author(s):  
Diler Oner ◽  
Emine Adadan
Keyword(s):  
Preservice Teachers ◽  
Reflective Thinking ◽  
Preservice Teacher Education ◽  
Mixed Methods Study ◽  
Easy Access ◽  
Web Based ◽  
High Level ◽  
Reflective Skills ◽  
The Web

This mixed-methods study examined the use of web-based portfolios for developing preservice teachers’ reflective skills. Building on the work of previous research, the authors proposed a set of reflection-based tasks to enrich preservice teachers’ internship experiences. Their purpose was to identify (a) whether preservice teachers demonstrated evidence of reflective thinking throughout a semester and, if so, the types of reflective thinking indicators; (b) whether there was an increase in the number of high-level reflective indicators over time; and (c) the role of the web-based portfolio construction, as perceived by the participants, in developing reflective skills. The findings suggested that preservice teachers demonstrated high- and low-level reflective skills throughout a semester. There was a statistically significant improvement in the number of high-level reflective indicators in the second reflection task compared with the first. In addition, the web-based platform was perceived by participants as a medium that enabled easy access and the development of better portfolio artifacts.

Definitions of Entrepreneurship

2003 ◽  
Vol 4 (2) ◽  
pp. 140-141 ◽  
Keyword(s):  
Small Business ◽  
Similar Process ◽  
Easy Access ◽  
Personal Interest ◽  
Web Based ◽  
Critical Commentary ◽  
The Web ◽  
Similar Text

‘Internet Review’ provides critical commentary on entrepreneurship, small business and innovation information on the Web. This article explores definitions of entrepreneurship as used by ‘practitioners’ across the Web. This is not a novel suggestion; many others (including the author) have conducted similar text or Web-based exercises. Indeed, the reviewer found a classroom topic sheet for schoolchildren that suggested a similar process (see www.ednet10.net/omomitems.nsf354da12738c3e9c0862568050000fa1986256792007ae6b5862568e9006df0e0?OpenDocument ). Yet, the review still seems worthwhile; there appear to be no agreed definitions (Kirby, 2003); the Web provides easy access to a wealth of example definitions for analysis, and the reviewer was interested in the types of definitions that would emerge: such personal interest often bodes well for an interesting review.

scholarly journals Gathering Evidence of Learning in Library Curriculum Center Spaces with Web GIS

2020 ◽  
Vol 15 (3) ◽  
pp. 21-35
Author(s):  
Rick Stoddart ◽  
Bruce Godfrey
Keyword(s):  
Information System ◽  
Pilot Study ◽  
Learning Outcomes ◽  
Learning Activities ◽  
Web Gis ◽  
Observation Data ◽  
Learning Spaces ◽  
Web Based ◽  
Different Types ◽  
The Web

Abstract Objective –This article reports on a pilot research project that gathered usage statistics in specifically designated library learning spaces using a Web-based Geographic Information System (GIS). These learning spaces were then mapped to expected learning activities that would occur in these areas based on its intention or design. In this way, the library could begin to associate the usage of a space with different types of learning. The researchers then mapped these learning activities to campus learning outcomes to create learning impact statements. Methods – The researchers used observation data gathered with a Web GIS tool to examine space usage within the library’s curriculum center. Results – The pilot study found that student usage of the curriculum center was mainly associated with two campus learning outcomes: (1) Communicate and (2) Learning and Integrate. The evidence also indicated possible design improvements that may make the curriculum centers spaces more functional for students. Conclusions – The Web GIS tool proved to be a useful tool to gather evidence of student space usage within the library environment. The mapping of individual spaces to learning activities further enhanced the usefulness in interpreting how students are using library spaces. Leveraging the space usage data within learning outcomes statements created another means for the library to communicate its learning impact with campus stakeholders.

scholarly journals Enabling the democratization of the genomics revolution with a fully integrated web-based bioinformatics platform

2016 ◽  
Author(s):  
Po-E Li ◽  
Chien-Chi Lo ◽  
Joseph J. Anderson ◽  
Karen W. Davenport ◽  
Kimberly A. Bishop-Lilly ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Initial Attempt ◽  
Web Based ◽  
Fully Integrated ◽  
Sequencing Technologies ◽  
Number Of Factors ◽  
Wide Range ◽  
Flood Current ◽  
Wide Assortment ◽  
Generation Sequencing

Continued advancements in sequencing technologies have fueled the development of new sequencing applications and promise to flood current databases with raw data. A number of factors prevent the seamless and easy use of these data, including the breadth of project goals, the wide array of tools that individually perform fractions of any given analysis, the large number of associated software/hardware dependencies, and the detailed expertise required to perform these analyses. To address these issues, we have developed an intuitive web-based environment with a wide assortment of integrated and cutting-edge bioinformatics tools. These preconfigured workflows provide even novice next-generation sequencing users with the ability to perform many complex analyses with only a few mouse clicks, and, within the context of the same environment, to visualize and further interrogate their results. This bioinformatics platform is an initial attempt at Empowering the Development of Genomics Expertise (EDGE) in a wide range of applications.

Protecting Datasources Over the Web

2003 ◽  
pp. 299-330
Author(s):  
Silvana Castano ◽  
Eena Ferrari
Keyword(s):  
Access Control ◽  
Relevant Information ◽  
Security Policies ◽  
Web Based ◽  
Information Release ◽  
Private And Public ◽  
Definition Of ◽  
Access To Data ◽  
Acquisition Processes ◽  
The Web

Since the Web is becoming the main means of disseminating information in private and public organizations, both at internal and external levels, several applications at Internet and intranet level need mechanisms supporting a selective access to data available over the Web. Through XML, the document exchange and acquisition processes, which can be very frequent in Web-based systems, are simplified and standardized. The development of suitable security policies for both access control and information release and distribution are relevant research topics in the security field, and XML compatibility is an important requirement for Web datasource protection. This chapter covers the issues related to the definition of security policies, models and mechanisms for access control and dissemination of Web data, and is organized in two parts. In the first part, we introduce the general issues and requirements related to the definition of different types of security policies for access control and for information release in Web datasources. Then, we present security policies and mechanisms specifically devoted to the protection of XML data. In the second part, we describe the use of XML for the specification of security relevant information, focusing on security policies, subject credentials, and content protection.

MoBiFlow

2013 ◽  
pp. 300-313
Author(s):  
Markus Held ◽  
Wolfgang Küchlin ◽  
Wolfgang Blochinger
Keyword(s):  
General Purpose ◽  
Easy Access ◽  
Web Based ◽  
Workflow Systems ◽  
Problem Solving Environments ◽  
Industry Standard ◽  
Computer Scientists ◽  
Programming Skills ◽  
Application Specific ◽  
The Web

Web-based problem solving environments provide sharing, execution and monitoring of scientific workflows. Where they depend on general purpose workflow development systems, the workflow notations are likely far too powerful and complex, especially in the area of biology, where programming skills are rare. On the other hand, application specific workflow systems may use special purpose languages and execution engines, suffering from a lack of standards, portability, documentation, stability of investment etc. In both cases, the need to support yet another application on the desk-top places a burden on the system administration of a research lab. In previous research the authors have developed the web based workflow systems Calvin and Hobbes, which enable biologists and computer scientists to approach these problems in collaboration. Both systems use a server-centric Web 2.0 based approach. Calvin is tailored to molecular biology applications, with a simple graphical workflow-language and easy access to existing BioMoby web services. Calvin workflows are compiled to industry standard BPEL workflows, which can be edited and refined in collaboration between researchers and computer scientists using the Hobbes tool. Together, Calvin and Hobbes form our workflow platform MoBiFlow, whose principles, design, and use cases are described in this paper.

Development of a Web-Based Nationwide Korean Pediatric Dental Sedation Registry

2017 ◽  
Vol 41 (6) ◽  
pp. 478-481 ◽  
Author(s):  
Sung Chul Choi ◽  
Yeonmi Yang ◽  
Seunghoon Yoo ◽  
Jiyeon Kim ◽  
Taesung Jeong ◽  
...  
Keyword(s):  
Literature Review ◽  
Pediatric Dentistry ◽  
Small Samples ◽  
Easy Access ◽  
Extensive Literature ◽  
Efficacy And Safety ◽  
Clinical Practices ◽  
University Hospitals ◽  
Web Based ◽  
The Web

Objective: Finding a balance between sedation efficacy and safety remains an ongoing challenge. In children, the risk of sedation-related complications is relatively high. It is of utmost importance to determine the factors related to improved overall sedation outcomes. However, most previous reports have been based on small samples at single institutions. The Korean Academy of Pediatric Dentistry (KAPD) developed a Korean Pediatric Dental Sedation Registry using a web-based platform. Study design: Specialists in pediatric dental sedation selected the itemized list included within the registry through an extensive literature review. The web-based registry was built into the KAPD homepage to facilitate easy access to the sedation data. All teaching and university hospitals agreed to participate in the Korean Pediatric Dental Sedation Registry. Conclusion: This is the first attempt to collect sedation data on a nationwide scale in the field of pediatric dentistry. The sedation database established with the registry may facilitate standardizing and improving pediatric dental sedation clinical practices.

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