SWAMI: Integrating Biological Databases and Analysis Tools Within User Friendly Environment

2007 ◽  
pp. 48-58 ◽  
Author(s):  
Rami Rifaieh ◽  
Roger Unwin ◽  
Jeremy Carver ◽  
Mark A. Miller
Keyword(s):  
Biological Databases ◽  
Analysis Tools ◽  
User Friendly

scholarly journals Interactive exploration of heterogeneous biological networks with Biomine Explorer

2019 ◽  
Vol 35 (24) ◽  
pp. 5385-5388
Author(s):  
Vid Podpečan ◽  
Živa Ramšak ◽  
Kristina Gruden ◽  
Hannu Toivonen ◽  
Nada Lavrač
Keyword(s):  
Biological Networks ◽  
Web Application ◽  
Biological Knowledge ◽  
Biological Databases ◽  
Scientific Publications ◽  
Public And Private ◽  
Interactive Exploration ◽  
Probabilistic Network ◽  
Private Network ◽  
User Friendly

Abstract Summary Biomine Explorer is a web application that enables interactive exploration of large heterogeneous biological networks constructed from selected publicly available biological knowledge sources. It is built on top of Biomine, a system which integrates cross-references from several biological databases into a large heterogeneous probabilistic network. Biomine Explorer offers user-friendly interfaces for search, visualization, exploration and manipulation as well as public and private storage of discovered subnetworks with permanent links suitable for inclusion into scientific publications. A JSON-based web API for network search queries is also available for advanced users. Availability and implementation Biomine Explorer is implemented as a web application, which is publicly available at https://biomine.ijs.si. Registration is not required but registered users can benefit from additional features such as private network repositories.

Do Psychology Researchers Need Better Tools for Power Analysis of Multilevel Designs?

2021 ◽  
Author(s):  
Frederick Clavel ◽  
Jonathan Helm
Keyword(s):  
Empirical Evidence ◽  
Power Analysis ◽  
Social Economic ◽  
Cross Sectional ◽  
Analysis Tools ◽  
Youtube Videos ◽  
User Friendly

A recent grant submission proposed to develop, test, and disseminate user-friendly tools to conduct power analysis for a wide array of multilevel designs (including longitudinal, cross-sectional, two-level, and three-level designs). Among other criticisms, the review criticized the proposal’s lack of empirical evidence for researchers’ critical need of such tools. In response, the current study (N = 336 of social, economic, and behavioral scientists) aimed to empirically examine researchers’ need for user-friendly power analysis tools for multilevel designs, which generally showed that researchers (1) are relatively unfamiliar with software for power analysis of multilevel designs, (2) tend to not use software specifically designed for power analysis of multilevel designs, (3) believe that user-friendly tools (including YouTube videos and power tables) will be useful for both their own research and their field more generally; generally indicating a need for user-friendly tools to conduct power analysis for multilevel designs.

scholarly journals The EMBL-EBI search and sequence analysis tools APIs in 2019

2019 ◽  
Vol 47 (W1) ◽  
pp. W636-W641 ◽  
Author(s):  
Fábio Madeira ◽  
Young mi Park ◽  
Joon Lee ◽  
Nicola Buso ◽  
Tamer Gur ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Web Services ◽  
Search Engine ◽  
Data Retrieval ◽  
Biological Data ◽  
Free Access ◽  
Text Search ◽  
Web Interfaces ◽  
Analysis Tools ◽  
User Friendly

Abstract The EMBL-EBI provides free access to popular bioinformatics sequence analysis applications as well as to a full-featured text search engine with powerful cross-referencing and data retrieval capabilities. Access to these services is provided via user-friendly web interfaces and via established RESTful and SOAP Web Services APIs (https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/EMBL-EBI+Web+Services+APIs+-+Data+Retrieval). Both systems have been developed with the same core principles that allow them to integrate an ever-increasing volume of biological data, making them an integral part of many popular data resources provided at the EMBL-EBI. Here, we describe the latest improvements made to the frameworks which enhance the interconnectivity between public EMBL-EBI resources and ultimately enhance biological data discoverability, accessibility, interoperability and reusability.

scholarly journals A repository of web-based bioinformatics resources developed in India

2020 ◽  
Author(s):  
Abhishek Agarwal ◽  
Piyush Agrawal ◽  
Aditi Sharma ◽  
Vinod Kumar ◽  
Chirag Mugdal ◽  
...  
Keyword(s):  
Scientific Community ◽  
Biological Databases ◽  
Web Interface ◽  
Web Based ◽  
Link Type ◽  
Complete Detail ◽  
User Friendly

AbstractIndiaBioDb (https://webs.iiitd.edu.in/raghava/indiabiodb/) is a manually curated comprehensive repository of bioinformatics resources developed and maintained by Indian researchers. This repository maintains information about 543 freely accessible functional resources that include around 258 biological databases. Each entry provides a complete detail about a resource that includes the name of resources, web link, detail of publication, information about the corresponding author, name of institute, type of resource. A user-friendly searching module has been integrated, which allows users to search our repository on any field. In order to retrieve categorized information, we integrate the browsing facility in this repository. This database can be utilized for extracting the useful information regarding the present scenario of bioinformatics inclusive of all research labs funded by government and private bodies of India. In addition to web interface, we also developed mobile to facilitate the scientific community.

scholarly journals Sequencing and Annotated of Goat's Milk using Bioinformatics Tool: ClustalX

2021 ◽  
Vol 7 (1) ◽  
pp. 28-33
Author(s):  
Muhammad Najmi Mohammad Fauzi ◽  
Aisyah Aqilah Abu Bakar ◽  
Liyana Amalina Adnan ◽  
Tg Ainul Farha Tg Abdul Rahman ◽  
A’wani Aziz Nurdalila
Keyword(s):  
Dna Sequences ◽  
Deoxyribonucleic Acid ◽  
Cost Effective ◽  
Automated System ◽  
Biological Databases ◽  
Bioinformatics Tool ◽  
Goat’S Milk ◽  
Multiple Alignments ◽  
Goat's Milk ◽  
User Friendly

Bioinformatics tool is a software program made to extract meaningful information from the mass of molecular biology or biological databases and carry out sequence or structural analysis. The method of determining the order of nucleotides within a deoxyribonucleic acid (DNA) molecule is known as DNA sequencing. This analysis is meant to be run to the commercialized or factorymade goat's milk (pasteurised) from various states in Malaysia to identify the milk's authenticity, either it is pure or mixed with other foreign substances from other animals. The main objective is to compare DNA sequences of commercialized and raw goat's milk (handmilking and non-pasteurised). To achieve this, we used ClustalX to align and compare the obtained DNA from both milk samples. The sequences will be aligned using ClustalX software. ClustalX is a provider of an automated system for performing multiple alignments of sequences and profiles and evaluating the outcomes. The usage of ClustalX is helpful as it is cost-effective, user-friendly, and showing a high accuracy of the analysis.

scholarly journals MORF: An online tool for exploring microbial cell responses using multi-omics analysis

2020 ◽  
Vol 2 (7A) ◽  
Author(s):  
Vicki Springthorpe ◽  
Rosalyn Leaman ◽  
Despoina Sifouna ◽  
Joyce Bennett ◽  
Gavin Thomas
Keyword(s):  
Data Sets ◽  
Full Potential ◽  
Experimental Conditions ◽  
Statistical Knowledge ◽  
Analysis Tools ◽  
Omics Analysis ◽  
Differential Gene ◽  
Reducing Costs ◽  
Tools And Techniques ◽  
User Friendly

With continuing improvements and reducing costs of high-throughput technologies, microbiologists are increasingly collecting multi-omics datasets. However, the tools and techniques used to analyse these kinds of data are often highly specialised and require bioinformatics, statistics and often coding experience. Many studies also tend to report on a single aspect of the data whilst overlooking other potentially interesting phenomena. Consequently, many of these multi-omics data sets are not being used to their full potential. MORF was created as a solution to these problems by providing access to multi-omics datasets through an online interface which presents the data in a user-friendly and accessible way. No coding experience or specialist statistical knowledge is required, and users are free to explore the data using interactive graphics and simple analysis tools. Here we demonstrate MORF using multi-omics datasets from two experiments using bacteria in industrial fermentation processes. First, Escherichia coli engineered to produce styrene, a valuable chemical used in the manufacture of polymers, and secondly a Clostridium which produces the biofuel butanol. A key outcome was the identification of targets believed to be involved in responding to membrane stress, which we identified using MORF’s differential gene and protein analysis tools. Work is underway to further characterise and engineer these targets to improve product yields. In conclusion, MORF provides a framework for omics analysis that can be applied to any organism or set of experimental conditions, and will help researchers and collaborators to make the most of their data.

scholarly journals DaTo: an atlas of biological databases and tools

2016 ◽  
Vol 13 (4) ◽  
pp. 30-38 ◽  
Author(s):  
Qilin Li ◽  
Yincong Zhou ◽  
Yingmin Jiao ◽  
Zhao Zhang ◽  
Lin Bai ◽  
...  
Keyword(s):  
Interaction Network ◽  
Biological Databases ◽  
Web Interface ◽  
Abstract Section ◽  
Manual Curation ◽  
The Status ◽  
User Friendly ◽  
The Relationship ◽  
Geographical Locations ◽  
Insight Into

Summary This work presents DaTo, a semi-automatically generated world atlas of biological databases and tools. It extracts raw information from all PubMed articles which contain exact URLs in their abstract section, followed by a manual curation of the abstract and the URL accessibility. DaTo features a user-friendly query interface, providing extensible URL-related annotations, such as the status, the location and the country of the URL. A graphical interaction network browser has also been integrated into the DaTo web interface to facilitate exploration of the relationship between different tools and databases with respect to their ontology-based semantic similarity. Using DaTo, the geographical locations, the health statuses, as well as the journal associations were evaluated with respect to the historical development of bioinformatics tools and databases over the last 20 years. We hope it will inspire the biological community to gain a systematic insight into bioinformatics resources. DaTo is accessible via http://bis.zju.edu.cn/DaTo/.

The Added Value of Graphical Input and Display for Electron Lens Design

1990 ◽  
Vol 48 (1) ◽  
pp. 190-191
Author(s):  
B. Lencova ◽  
G. Wisselink
Keyword(s):  
Flux Density ◽  
Numerical Data ◽  
Added Value ◽  
Lens Design ◽  
Step Size ◽  
Magnetic Lens ◽  
Flux Lines ◽  
Fine Mesh ◽  
Electron Lens ◽  
User Friendly

Recent progress in computer technology enables the calculation of lens fields and focal properties on commonly available computers such as IBM ATs. If we add to this the use of graphics, we greatly increase the applicability of design programs for electron lenses. Most programs for field computation are based on the finite element method (FEM). They are written in Fortran 77, so that they are easily transferred from PCs to larger machines.The design process has recently been made significantly more user friendly by adding input programs written in Turbo Pascal, which allows a flexible implementation of computer graphics. The input programs have not only menu driven input and modification of numerical data, but also graphics editing of the data. The input programs create files which are subsequently read by the Fortran programs. From the main menu of our magnetic lens design program, further options are chosen by using function keys or numbers. Some options (lens initialization and setting, fine mesh, current densities, etc.) open other menus where computation parameters can be set or numerical data can be entered with the help of a simple line editor. The "draw lens" option enables graphical editing of the mesh - see fig. I. The geometry of the electron lens is specified in terms of coordinates and indices of a coarse quadrilateral mesh. In this mesh, the fine mesh with smoothly changing step size is calculated by an automeshing procedure. The options shown in fig. 1 allow modification of the number of coarse mesh lines, change of coordinates of mesh points or lines, and specification of lens parts. Interactive and graphical modification of the fine mesh can be called from the fine mesh menu. Finally, the lens computation can be called. Our FEM program allows up to 8000 mesh points on an AT computer. Another menu allows the display of computed results stored in output files and graphical display of axial flux density, flux density in magnetic parts, and the flux lines in magnetic lenses - see fig. 2. A series of several lens excitations with user specified or default magnetization curves can be calculated and displayed in one session.

A Review of 21 iPad Applications for Augmentative and Alternative Communication Purposes

2012 ◽  
Vol 21 (2) ◽  
pp. 60-71 ◽  
Author(s):  
Ashley Alliano ◽  
Kimberly Herriger ◽  
Anthony D. Koutsoftas ◽  
Theresa E. Bartolotta
Keyword(s):  
Augmentative And Alternative Communication ◽  
Cost Effective ◽  
Alternative Form ◽  
Alternative Communication ◽  
Text To Speech ◽  
Reference Guide ◽  
Expressive Communication ◽  
Communication Needs ◽  
User Friendly ◽  
Ipad Applications

Abstract Using the iPad tablet for Augmentative and Alternative Communication (AAC) purposes can facilitate many communicative needs, is cost-effective, and is socially acceptable. Many individuals with communication difficulties can use iPad applications (apps) to augment communication, provide an alternative form of communication, or target receptive and expressive language goals. In this paper, we will review a collection of iPad apps that can be used to address a variety of receptive and expressive communication needs. Based on recommendations from Gosnell, Costello, and Shane (2011), we describe the features of 21 apps that can serve as a reference guide for speech-language pathologists. We systematically identified 21 apps that use symbols only, symbols and text-to-speech, and text-to-speech only. We provide descriptions of the purpose of each app, along with the following feature descriptions: speech settings, representation, display, feedback features, rate enhancement, access, motor competencies, and cost. In this review, we describe these apps and how individuals with complex communication needs can use them for a variety of communication purposes and to target a variety of treatment goals. We present information in a user-friendly table format that clinicians can use as a reference guide.

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