BioWorkbench: A High-Performance Framework for Managing and Analyzing Bioinformatics Experiments

Advances in sequencing techniques have led to exponential growth in biological data, demanding the development of large-scale bioinformatics experiments. Because these experiments are computation- and data-intensive, they require high-performance computing (HPC) techniques and can benefit from specialized technologies such as Scientific Workflow Management Systems (SWfMS) and databases. In this work, we present BioWorkbench, a framework for managing and analyzing bioinformatics experiments. This framework automatically collects provenance data, including both performance data from workflow execution and data from the scientific domain of the workflow application. Provenance data can be analyzed through a web application that abstracts a set of queries to the provenance database, simplifying access to provenance information. We evaluate BioWorkbench using three case studies: SwiftPhylo, a phylogenetic tree assembly workflow; SwiftGECKO, a comparative genomics workflow; and RASflow, a RASopathy analysis workflow. We analyze each workflow from both computational and scientific domain perspectives, by using queries to a provenance and annotation database. Some of these queries are available as a pre-built feature of the BioWorkbench web application. Through the provenance data, we show that the framework is scalable and achieves high-performance, reducing up to 98% of the case studies execution time. We also show how the application of machine learning techniques can enrich the analysis process

ANALISA PENERAPAN SERVER DEPLOYMENT MENGGUNAKAN KUBERNETES UNTUK MENGHINDARI SINGLE OF FAILURE

Sistem komputasi terdistribusi menjadi salah satu kebutuhan dalam implementasi aplikasi berbasis server seperti database server dan web server agar tercapainya tingkat performansi tinggi. Masalah yang sering terjadi adalah kegagalan pada server sehingga perfrorma dari sebuah server terganggu, sehingga dibutuhkan suatu teknik deploy dapat digunakan untuk menyediakan sistem terdistribusi dengan performansi tinggi. Virtualisasi berbasis container menjadi pilihan untuk menjalankan sistem terdistribusi karena arsitektur yang ringan, kinerja yang cepat, dan efisiensi sumber daya. Salah satu virtualisasi berbasis container adalah memperkenalkan alat pengembangan sistem terdistribusi yang disebut Kubernetes, yang memungkinkan memanajemen deploy server untuk menyediakan sistem dengan availability yang tinggi. Metodologi pengembangan system yang digunakan adalah Network Development Life Cycle (NDLC). Dari 6 tahapan yang ada, hanya digunakan 3 tahapan yaitu Analysis, Design, dan Simulation Prototyping. Uji coba atau scenario pengujian yang dilakukan adalah Ftp Deploy dan Web Server Nginx sehingga dapat menjaga ketersediaan dan sistem mampu melakukan failover saat terjadi kegagalan pada serverDistributed computing systems are one of the requirements in implementing server-based applications such as database servers and web servers in order to achieve high levels of performance. The problem that often occurs is failure on the server so that the performance of a server is disrupted, so it takes a deployment technique that can be used to provide a distributed system with high performance. Container-based virtualization is the choice for running distributed systems because of its lightweight architecture, fast performance and resource efficiency. One of the container-based virtualisations is the introduction of a distributed systems development tool called Kubernetes, which allows managing server deployments to provide high availability systems. The system development methodology used is the Network Development Life Cycle (NDLC). Of the 6 stages, only 3 stages are used, namely Analysis, Design, and Simulation Prototyping. The test or test scenario carried out is Ftp Deploy and Nginx Web Server so that it can maintain availability and the system is able to failover when a server failure occur

An Examination of Multi-Tier Designs for Legacy Data Access

This work examines the application of Java and the Common Object Request Broker Architecture (CORBA) to support access to remote databases via the Internet. The research applies these software technologies to assist an Air Force distance learning provider in improving the capabilities of its World Wide Web-based correspondence system. An analysis of the distance learning provider\u27s operation revealed a strong dependency on a non-collocated legacy relational database. This dependency limits the distance learning provider\u27s future web-based capabilities. A recommendation to improve operation by data replication is proposed, and the implementation details are provided for two alternative test systems that support data replication between heterogeneous relational database management systems. The first test system incorporates a two-tier architecture design using Java, and the second system employs a three-tier architecture design using Java and CORBA. Data on replication times for the two-tier and three-tier designs are presented, revealing a greater performance consistency from the three-tier design over the two-tier design for varying client platforms and communications channels. Discussion of a small-scale proof-of-concept system based on the three-tier design is provided, along with a presentation of the potential for the technologies applied in this system to benefit Air Force web-based distance learning

Design of IoT-based System for Smart Temporary Waste Shelter

Internet of Things (IoT) is a concept where all products can interact with each other to help human activities by utilizing the internet. The IoT system can help solve problems such as the schedule-based retrieval system at a temporary shelter in Indonesia. This paper creates a web-based geographic information system along with the IoT-based waste temporary shelter prototype. The prototype also integrated with an Arduino Microcontroller so that it can sort the waste automatically into three types of waste, then record data in the form of height and weight, and send the results of the data to the database so that the geographic information system can display the results of the data. Node-RED serves as an Application Programming Interface (API) that sends data from the server to the database belonging to a web-based geographic information system. The results of the performance analysis are that the prototype has sorted waste well, and the system also produced good QoS by ETSI standards when looking at the network traffic from the MQTT server to the database, and from the end-user to the web. As for the QoE results for tools and systems have produced good results according to the ITU-T standard

Database server workload characterization in an e-commerce environment

A typical E-commerce system that is deployed on the Internet has multiple layers that include Web users, Web servers, application servers, and a database server. As the system use and user request frequency increase, Web/application servers can be scaled up by replication. A load balancing proxy can be used to route user requests to individual machines that perform the same functionality. To address the increasing workload while avoiding replicating the database server, various dynamic caching policies have been proposed to reduce the database workload in E-commerce systems. However, the nature of the changes seen by the database server as a result of dynamic caching remains unknown. A good understanding of this change is fundamental for tuning a database server to get better performance. In this study, the TPC-W (a transactional Web E-commerce benchmark) workloads on a database server are characterized under two different dynamic caching mechanisms, which are generalized and implemented as query-result cache and table cache. The characterization focuses on response time, CPU computation, buffer pool references, disk I/O references, and workload classification. This thesis combines a variety of analysis techniques: simulation, real time measurement and data mining. The experimental results in this thesis reveal some interesting effects that the dynamic caching has on the database server workload characteristics. The main observations include: (a) dynamic cache can considerably reduce the CPU usage of the database server and the number of database page references when it is heavily loaded; (b) dynamic cache can also reduce the database reference locality, but to a smaller degree than that reported in file servers. The data classification results in this thesis show that with dynamic cache, the database server sees TPC-W profiles more like on-line transaction processing workloads

Development of a Novel Media-independent Communication Theology for Accessing Local & Web-based Data: Case Study with Robotic Subsystems

Realizing media independence in today’s communication system remains an open problem by and large. Information retrieval, mostly through the Internet, is becoming the most demanding feature in technological progress and this web-based data access should ideally be in user-selective form. While blind-folded access of data through the World Wide Web is quite streamlined, the counter-half of the facet, namely, seamless access of information database pertaining to a specific end-device, e.g. robotic systems, is still in a formative stage. This paradigm of access as well as systematic query-based retrieval of data, related to the physical enddevice is very crucial in designing the Internet-based network control of the same in real-time. Moreover, this control of the end-device is directly linked up to the characteristics of three coupled metrics, namely, ‘multiple databases’, ‘multiple servers’ and ‘multiple inputs’ (to each server). This triad, viz. database-input-server (DIS) plays a significant role in overall performance of the system, the background details of which is still very sketchy in global research community. This work addresses the technical issues associated with this theology, with specific reference to formalism of a customized DIS considering real-time delay analysis. The present paper delineates the developmental paradigms of novel multi-input multioutput communication semantics for retrieving web-based information from physical devices, namely, two representative robotic sub-systems in a coherent and homogeneous mode. The developed protocol can be entrusted for use in real-time in a complete user-friendly manner

How did we assess the outcomes of tradable green certificates? A review

When policy support schemes are in reevaluation process, academic literature play pivotal role. This paper presents a literature review of studies that have assessed the performance of Tradable green certificates (TGC) schemes in stimulating investments in Electricity from Renewable Energy Sources (RES-E). To do so, we conduct an extensive and systemic literature review on the Web of Science database. This paper?s outcomes in addition to the descriptive statistics that provide an overview of the publications, intend to gain insights in two important aspects. First, we categorize the typical research approaches (i.e. analysis criteria) to the assessment of TGC systems performance in different, mainly European countries and summarize their outcomes. Second, we illustrate which of research approaches have had the highest impact on the literature of its nature, based on the average number of citations. This paper provides several intriguing direction for future studies

Spreadsheets for Analyzing and Optimizing Space Missions

XCALIBR (XML Capability Analysis LIBRary) is a set of Extensible Markup Language (XML) database and spreadsheet- based analysis software tools designed to assist in technology-return-on-investment analysis and optimization of technology portfolios pertaining to outer-space missions. XCALIBR is also being examined for use in planning, tracking, and documentation of projects. An XCALIBR database contains information on mission requirements and technological capabilities, which are related by use of an XML taxonomy. XCALIBR incorporates a standardized interface for exporting data and analysis templates to an Excel spreadsheet. Unique features of XCALIBR include the following: It is inherently hierarchical by virtue of its XML basis. The XML taxonomy codifies a comprehensive data structure and data dictionary that includes performance metrics for spacecraft, sensors, and spacecraft systems other than sensors. The taxonomy contains >700 nodes representing all levels, from system through subsystem to individual parts. All entries are searchable and machine readable. There is an intuitive Web-based user interface. The software automatically matches technologies to mission requirements. The software automatically generates, and makes the required entries in, an Excel return-on-investment analysis software tool. The results of an analysis are presented in both tabular and graphical displays