e-Nelayan the Fishery Marketplace App

Smartphones have become an essential device that not only acts as a communication media, but it is also able to assist its user to do multiple tasks. A fisherman is an example of a community member that uses a smartphone. If a smartphone is fully utilised, it can be a huge help for the fishermen to sell their catch and fishery products. However, there is no proper medium, such as an mobile application, for this group of people to sell their catch. Hence, the e-Nelayan Marketplace App is introduced. This app enables the fishermen mainly in Kota Samarahan to sell their catch and other fishery products more effectively. The functionalities of this app include the ability to advertise the catch and let customers and fishmongers know the type of fish being sold. In addition, an interactive graphical user interface was designed to display the output of each functional module. In order to evaluate the user acceptance towards the app, several tests were conducted, such as the performance, portability, compatibility, and usability testing. With the development of this project, it is hoped that the application will benefit not only fishermen but also customers and fishmongers.

Development of 3D models for faculty of education database system via monitor’s graphical user interface interactive for perception and utilization

This study is a research and development study that used systematic approaches as an operational concept. The objectives of the study included: (1) To study the usage demands of an on-screen interactive Graphical User Interface (GUI) for the Faculty of Education database. (2) To create 3D models and study their efficiency in the usage of an on-screen interactive GUI for the Faculty of Education database. (3) To evaluate the perception and utilization of 3D models in the usage of an on-screen interactive GUI for the Faculty of Education database. The population in this study included; (1) 100 staff and students in the Faculty of Education – who were selected using Purposive Sampling to study usage demands of an on-screen interactive GUI for the Faculty of Education database. (2) 5 experts and 40 staff and students of the Faculty of Education – who were selected using Purposive Sampling to study the efficiency of 3D models in the usage of an on-screen interactive GUI for the Faculty of Education database. (3) 300 staff and students of Ramkhamhaeng University who used 3D models with the on-screen interactive GUI of the Faculty of Education database within the 1-month test period of the study. The research instruments used in this study were: (1) a questionnaire about usage demands of an on-screen interactive GUI for the Faculty of Education database, (2) an expert opinion evaluation form, and (3) an assessment form for perception and utilization of 3D models in the usage of an on-screen interactive GUI for the Faculty of Education database – all of which were found with .930 reliability and item discrimination values between .71 - .85.

The antiSMASH database version 3: increased taxonomic coverage and new query features for modular enzymes

Microorganisms produce natural products that are frequently used in the development of antibacterial, antiviral, and anticancer drugs, pesticides, herbicides, or fungicides. In recent years, genome mining has evolved into a prominent method to access this potential. antiSMASH is one of the most popular tools for this task. Here, we present version 3 of the antiSMASH database, providing a means to access and query precomputed antiSMASH-5.2-detected biosynthetic gene clusters from representative, publicly available, high-quality microbial genomes via an interactive graphical user interface. In version 3, the database contains 147 517 high quality BGC regions from 388 archaeal, 25 236 bacterial and 177 fungal genomes and is available at https://antismash-db.secondarymetabolites.org/.

Pre-clustering data sets using cluster4x improves the signal-to-noise ratio of high-throughput crystallography drug-screening analysis

Drug and fragment screening at X-ray crystallography beamlines has been a huge success. However, it is inevitable that more high-profile biological drug targets will be identified for which high-quality, highly homogenous crystal systems cannot be found. With increasing heterogeneity in crystal systems, the application of current multi-data-set methods becomes ever less sensitive to bound ligands. In order to ease the bottleneck of finding a well behaved crystal system, pre-clustering of data sets can be carried out using cluster4x after data collection to separate data sets into smaller partitions in order to restore the sensitivity of multi-data-set methods. Here, the software cluster4x is introduced for this purpose and validated against published data sets using PanDDA, showing an improved total signal from existing ligands and identifying new hits in both highly heterogenous and less heterogenous multi-data sets. cluster4x provides the researcher with an interactive graphical user interface with which to explore multi-data set experiments.

SEPIA - SuscEptibility mapping PIpeline tool for phAse images

Quantitative susceptibility mapping (QSM) is a physics-driven computational technique that has a high sensitivity in quantifying iron deposition based on MRI phase images. Furthermore, it has a unique ability to distinguish paramagnetic and diamagnetic contributions such as haemorrhage and calcification based on image contrast. These properties have contributed to a growing interest to use QSM not only in research but also in clinical applications. However, it is challenging to obtain high quality susceptibility map because of its ill-posed nature, especially for researchers who have less experience with QSM and the optimisation of its pipeline. In this paper, we present an open-source processing pipeline tool called SuscEptibility mapping PIpeline tool for phAse images (SEPIA) dedicated to the post-processing of MRI phase images and QSM. SEPIA connects various QSM toolboxes freely available in the field to offer greater flexibility in QSM processing. It also provides an interactive graphical user interface to construct and execute a QSM processing pipeline, simplifying the workflow in QSM research. The extendable design of SEPIA also allows developers to deploy their methods in the framework, providing a platform for developers and researchers to share and utilise the state-of-the-art methods in QSM.

MLDSP-GUI: An alignment-free standalone tool with an interactive graphical user interface for DNA sequence comparison and analysis

SummaryMLDSP-GUI (Machine Learning with Digital Signal Processing) is an open-source, alignment-free, ultrafast, computationally lightweight, standalone software tool with an interactive Graphical User Interface (GUI) for comparison and analysis of DNA sequences. MLDSP-GUI is a general-purpose tool that can be used for a variety of applications such as taxonomic classification, disease classification, virus subtype classification, evolutionary analyses, among others.AvailabilityMLDSP-GUI is open-source, cross-platform compatible, and is available under the terms of the Creative Commons Attribution 4.0 International license (http://creativecommons.org/licenses/by/4.0/). The executable and dataset files are available at https://sourceforge.net/projects/mldsp-gui/[email protected] informationSupplementary data are available online.

A “Human-in-the-Loop” Approach for Semi-automated Image Restoration in Electron Microscopy

ABSTRACTThe recent advent of 3D in Electron Microscopy (EM) has allowed for detection of detailed sub-cellular nanometer resolution structures. While being a scientific breakthrough, this has also caused an explosion in dataset size, necessitating the development of automated workflows. Automated workflows typically benefit reproducibility and throughput compared to manual analysis. The risk of automation is that it ignores the expertise of the microscopy user that comes with manual analysis. To mitigate this risk, this paper presents a hybrid paradigm. We propose a ‘human-in-the-loop’ (HITL) approach that combines expert microscopy knowledge with the power of large-scale parallel computing to improve EM image quality through advanced image restoration algorithms. An interactive graphical user interface, publicly available as an ImageJ plugin, was developed to allow biologists to use our framework in an intuitive and user-friendly fashion. We show that this plugin improves visualization of EM ultrastructure and subsequent (semi-)automated segmentation and image analysis.

locBLAST v2.0 - an improved PHP library for embedding standalone NCBI BLAST+ program to an interactive graphical user interface

BackgroundNCBI BLAST is a most popularly used sequence analysis platform in a broad range of applications. The final release of standalone WWW BLAST server (wwwBLAST v2.2.26) of NCBI was officially released on May 10, 2004, and discontinued its support. Due to the popularity and high demand, the BLAST algorithms were refined with rich features and released as online BLAST, standalone BLAST+, BLAST RESTful service, and cloud BLAST server. locBLAST v2.0 is a lightweight PHP library, designed in preference to WWW BLAST server. It masks command-line BLAST+ programs to a rich graphical user interface (GUI).MethodsThe locBLAST v2.0 library was designed using PHP, CSS, pure JavaScript, and standalone NCBI BLAST+ executables.ResultslocBLAST v2.0 provides an interactive web interface to input query sequences through the web form and provides a graphical report of the sequence alignment result. The graphical overview, tabular summary, and formatted sequence alignment of locBLAST v2.0 result mimic to the native format of online NCBI BLAST result. It allows users to perform both local and online database search.AvailabilityFreely available at https://github.com/AshokHub/locBLAST