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Transfer RNA (tRNA), a key component of the translation machinery, plays critical roles in stress conditions and various diseases. While knowledge regarding the importance of tRNA function is increasing, its biological roles are still not well understood. There is currently no comprehensive database or web server providing the expression landscape of tRNAs across a variety of human tissues and diseases. Here, we constructed a user-friendly and interactive database, DBtRend, which provides a profile of mature tRNA expression across various biological conditions by reanalyzing the small RNA or microRNA sequencing data from the Cancer Genome Atlas (TCGA) and NCBI’s Gene Expression Omnibus (GEO) in humans. Users can explore not only the expression values of mature individual tRNAs in the human genome, but also those of isodecoders and isoacceptors based on our specific pipelines. DBtRend provides the expressed patterns of tRNAs, the differentially expressed tRNAs in different biological conditions, and the information of samples or patients, tissue types, and molecular subtype of cancers. The database is expected to help researchers interested in functional discoveries of tRNAs.

Nowadays, the researchers in Cultural Heritage fields investigate more and more about advanced conservation strategies that comprehend the possibility to share and use 3D models and structured information related to them. One of the modern method adopted to achieve this goal is to use structured web-platform. These are online systems that can handle data, created to contain and support precise information. They simultaneously respond to the need for a common ground for different expert users and of a unique tool where to store several kinds of data, coming from heterogeneous sources. The article aims to show how it is possible to build a valid tool for the conservation and monitoring activities of CH, following the national and international legislation and the specific needs of the application field. In particular, it will deepen the criteria to build a 3D model that has to link a database of information, specifying the logic behind it. In the same way, it will show how to structure a database collaborating with the local institutions and experts, following the real needs of the site. The benefit is that this kind of tools gives to the multi-disciplinary works and projects a shared environment for storing and view a different type of data. They can help both the access intended to the conservation activities and both they can open to the public. The application field is the Sacri Monti circuit, which is part of the UNESCO World Heritage List since 2003.

his research aimed to develop an information system supporting research on rubber (ISSR) in Thailand. This system was designed as a web application with responsive web design. The rubber database was developed with MySQL, used Apache Server as a Web Server and programed with PHP-script. High Chart, Google Chart API and Java Technology were used to represent an online information with graphical format. The system was tested with the actual data on rubber research in Southern Thailand. The system has been available online at URL http://www.s-cm.site/issr. There are three type of users: administrator, researcher (member) and generic user. The researcher performed data entry about research with log-in to the system using username and password provided by the automatic system via online registration form. The administrator can manage the research information. The researchers can manage their research information, use searching tool and leave comments on other member’s research. The generic users can access the system without username and password to view the research and general information on rubber. Moreover, the system generates a report on rubber research with online graphical format. In conclusion, this information system enhances investigation on rubber research in Thailand and its strategy planning for rubber plantation in the future.

The goal of this exploratory study is to build a web database platform to facilitate the analysis of the relationship between health status, HRQOL, and HEO in family caregivers and cancer patients. This paper describes the whole design process of the Web database, query and data visualization platform including (1) target users’ requirement (scientific research Needs); (2) medical expenditure panel survey (MEPS) data cleaning and processing; (3) methods and technical details of developing web databases (server-side) and the front-end user interfaces. This web database platform will help researchers achieve efficient querying and visualization of big medical dataset.

As mobile devices become prevalent, there is always a need for apps. How hard is it to develop an app especially a cross-platform app? The paper shares an experience in a project involved the development of a student services web app that can be run on cross-platform mobile devices. The paper first describes the background of the project, the clients, and the proposed solution. Then, it focuses on the step-by-step development processes and provides the illustration of written codes and techniques used. The goal is for readers to gain an understanding on how to develop a mobile-friendly web app. The paper concludes with teaching implications and offers thoughts for further development. A revised version of this paper was published in the journal Journal of Information Technology Education: Innovations in Practice, Volume 14, 2015

Mining data from a web database becomes more challenging in recent years due to the exploding size of data, the rising of dynamic web, and the increasing performance of web security. Mining data from a web database differs from mining data from web sites because it is intended to collect specific data from a single web site. Collecting a very large data in a limited time tends to be detected as a cyber attack and will be banned from connecting into the web server. To avoid the problem, this paper proposes a crawling method to mine web database faster and cheaper than conventional web crawlers. The method used is to run hundreds of threads from a single web crawler in a single computer and to distribute the threads into hundreds or thousands publicly available proxy servers. This web crawler strategy highly increases the speed of mining and is more secure than using single thread of web crawler.

The AFlora (an abbreviation for "African Flora") project, "A study on the traditional use of plants in Africa, " has been operated by the Center for African Area Studies at Kyoto University since late 1980s. This project has involved many researchers interested in the ethnobotany of tropical Africa. It aims to accumulate the ethnobotanical knowledge on plant use and nomenclature collected by field researchers working in Africa to provide an effective information-retrieval system. Since 1997, the AFlora database has been available to the public as a web-based database. In 2012, the system was updated, and it now relies on the most recent web technology. It currently contains more than 6, 000 records. In this paper, I describe the structure, mode of operation, and benefits offered by this database. I also discuss issues related to the intellectual property rights with respect to ethnobotanical knowledge, which have become serious considerations in recent decades. Means of sharing scientific information are also addressed.

La enseñanza de la estructura del átomo mediante herramientas virtuales aplicadas al Aprendizaje Significativo Crítico, es un conjunto de estrategias y de actividades que se complementan mutuamente para desarrollar competencias científicas. El trabajo presentado a continuación es una propuesta didáctica que involucra el diseño y elaboración de: un texto en el que se desarrolla el tema “la estructura del átomo”, una base de datos web para que el docente prepare sus clases por competencias y un vídeo juego sobre el experimento de Míllikan llamado “el juego de la gota de Míllikan”. Estos componentes se integran en la plataforma Moodle, donde se desarrolla el Aprendizaje Significativo Crítico (ASC) para la enseñanza de la estructura del átomo, buscando que el aprendiz desarrolle competencias científicas, a la vez que sea crítico frente a los aprendizajes obtenidos, cuya característica principal es que sean significativos. Abstract: Teaching the structure of the atom using virtual tools applied to Critical Meaningful Learning, it is a set of strategies and activities that complement each other to develop scientific competences. The work presented follows is a didactic proposal that involves the design and development of: a text on the topic "the structure of the atom," a website database developed for the teacher to prepare their classes competencies and video game about Millikan experiment called "the game drop Millikan". These components are integrated into the Moodle platform where the Critical Meaningful Learning (CML) for teaching the atomic structure develops, looking for the learner develop scientific competences, while it is critical of the lessons learned, whose characteristic principal is to be significant

This paper introduces a system that realizes a simultaneous registration of scholarly papers for both a researcher database and a repository. An institutional repository is a method to realize free access to research outputs. However, the number of scholarly papers archived in institutional repositories is extremely small compared to the papers practically produced by researchers. The authors considered that an obstacle to increase the number is the efforts of researchers to register their papers to institutional repositories, and they developed a system that realizes a simultaneous registration of papers to the researcher database and the institutional repository in their university. This paper introduces the main idea of the system.

本稿は機関リポジトリへの文献登録をサポートするシステムを紹介している．機関リポジトリは学術情報への オープンアクセスを実現する重要なサービスであるが，登録されている文献数は十分とは言えない．本稿の著者らは，機関リポジトリへの文献登録作業のうち，文献の著者とリポジトリの管理者による作業を部分的に自動化するシステムを開発した．このシステムは，論文誌や学術会議等で発表された文献についての外部データベースを利用し，該当する著者へ本文の登録を促す．また，各文献の出版社等の著作権ポリシーについても，外部データベースを参照し自動的に確認を行う．本稿は，現行の機関リポジトリの問題点を挙げ，その解決方法として開発されたシステムの詳細を述べている．このシステムにより，文献著者とリポジトリ管理者の文献登録の手間を省くことができ，機関リポジトリの登録文献数の増加が期待できる．

The paper introduces a practical Web system which activates institutional repositories. Institutional repository is an important service of libraries in academic institutions. The authors of the paper developed a linking system between the institutional repository and the researcher database of their university. By the developed system papers registered in the institutional repository are linked from lists of papers in the researcher database, which improves the accessibility of the institutional repository. Additionally, the system reuses the metadata of the papers registered in the researcher database for registrations to the institutional repository, which reduces the efforts of researchers. As a result, this system is expected to encourage the registration of papers to the institutional repository. The paper describes the concepts and the details of the system. The essential idea can be applied to other academic institutions.

Antimicrobial peptides (AMPs) are increasingly being considered as novel agents against biofilms. The development of AMP-based anti-biofilm strategies strongly relies on the design of sequences optimized to target specific features of sessile bacterial/fungal communities. Although several AMP databases have been created and successfully exploited for AMP design, all of these use data collected on peptides tested against planktonic microorganisms. Here, an open-access, manually curated database of AMPs specifically assayed against microbial biofilms (BaAMPs) is presented for the first time. In collecting relevant data from the literature an effort was made to define a minimal standard set of essential information including, for each AMP, the microbial species and biofilm conditions against which it was tested, and the specific assay and peptide concentration used. The availability of these data in an organized framework will benefit anti-biofilm research and support the design of novel molecules active against biofilm. BaAMPs is accessible at http://www.baamps.it.

This paper describes a database for cell signaling enzymes. Our web database offers methods to study, interpret and compare cell-signaling enzymes. Searching and retrieving data from this database has been made easy and user friendly and it is well integrated with other related databases. We believe the end user will be benefited from this database. Availability http://www.sastra.edu/dcse/index.html

GCSDB is a web-oriented integrated database system for the Georgia Centenarian Study, a phase III, population-based, multidisciplinary study of centenarians. The Study recruited 244 centenarians and near-centenarians (age 98 and older), 80 octogenarians and 400 young controls in Northern Georgia. GCSDB incorporates more than 40 relational tables containing data about the participants including demographics, family longevity, physical health, cognition, neuropsychology, mental health, neuropathology, functional capacity, and genetics. The GCSDB web site includes detailed information about these tables and functions for genetic and other kinds of data analysis. More data and functions will be added as the study progresses. GCSDB provides a resource that could be used to identify what biological, psychological, and social factors as well as their epistatic interactions help these centenarians achieve long life. Availability http://qa.genetics.uga.edu (login information can be obtained from authors)

Deep analysis of the SRRs from Web databases (WDB) plays major important role to find exact searching for each user and improve the web pages by analysis results. The number of web pages returned from the WDB is known search result records (SRRs); it consists of the several numbers of pages. These returned web pages results becomes complex to analysis each data unit since it consists of several number of data unit .To overcome the problem of web analysis in earlier work proposes an annotation methods where the data and text unit nodes are converted in the form of table, but in these work the data and unit nodes are not semantically measured labeled .In order to conquer these problem in this paper propose an ontology based data alignment method to Semantically label each data units in the annotated table for each and every SRRs returned from WDBs. This ontology based data alignment algorithm extract data and text unit nodes features from the SRRs through PSO and then data are aligned based on the semantically labeled named results from ontology. Then perform the swarm intelligence based ABC algorithm to select best search results from annotated table result through the colony of artificial bees .The colony of the ABC consists of the three major bees such as employed, onlookers and scouts bees. Each and every bee in the ABC selects best annotated search results through the behavior of the ABC for annotated table. Then, for each selected search results annotated it again in different point of the view and combined the dissimilar annotations to anticipate an absolute annotation label intended for it. Our experiments results indicates that the proposed DA-ABC algorithm have high precision and recall result for book application when compare to existing data alignment results.

Systems for recording data on radiopharmaceuticals have changed following the Medical Care Law on concentration limits of radioisotopes in drainage, exhaust gas, and the atmosphere. A Web-based system that includes a patient information subsystem, DICOM imaging subsystem, and laboratory order subsystem has been developed for the receipt, use, stock prescription, disposal, and accounting of radiopharmaceuticals was developed using a Web-based system in order to simplify radiation safety management operations such as changes and additions to record book forms. In verifying the usefulness of the system and its recording and search times, it was found that the new Web-based system provides superior performance.

Eco-MCPS database is a web-based database system that contains data of environment-conscious materials,components, products, and services. The text data compiled in the Eco-MCPS and the access log data of Eco-MCPS were subjected to data mining. Word-frequency analysis and dependency parsing analysis were applied tothe data to obtain the frequently used terms and their situations of use. By analyzing the access log, the interestof the visitors accessed to the web-site can be understood. The results showed that eco-products' environmental performances are realized by the use of environment-friendly components or materials. The page views, which represent the visitors' interest, were related with the frequently used term in the comments of Eco-MCPS to showthe social consciousness on environment-friendly products. By further analyzing the access log, it was found thatthe word search rank followed the Zipf's Law., 2, KJ00009183659

Our age is characterized by the ease of communication and fast and free exchange of data. The use of standards and a common approach to recollect, organize and present the documentation gives a great advantage for the knowledge and dissemination of the archaeological, artistic, historical and conservation information of Cultural Heritage. Establishing a "correct" documentation policy is the main goal that guided our initiative for the documentation, preservation and valorisation of the monumental complex of the Camaldolese Abbey in Tuscany. In this project we retrieved the paper documentation in the Historical Archives of the Tuscany Region, to study the historical and conservation data of the monumental complex. Digital technologies have been used to support storing and access to this important information, including also data to monitor the current state of its preservation. The documentation has been digitized and is accessible through a web database; this resource was designed by following the Italian National standards proposed by Central Institute for Cataloguing and Documentation (ICCD). The current state of conservation of some parts of the building has been documented by taking panoramic images or panoramas (360º images) and by the acquiring 3D digital models. In particular, panoramas are used to document the state of preservation of frescoed rooms, while geometric 3D models are produced to document the degraded areas of the church, which require a constant monitoring. Moreover, an analytical virtual reconstruction of the church was modeled to depict its status before the building's collapse. The main goals of this work are to provide a good-practice example on how to document and disseminate on the web the knowledge available on an endangered monument, following national and international standards, in order to make the knowledge widely accessible. In this way, it is possible to disseminate and enhance the old results with new analysis and interpretations of documents that can be easily shared with other researches, conservation experts and the ordinary public.

Given the undeniable popularity of the Web, providing efficient and secure access to remote databases using a Web browser is crucial for the emerging cooperative information systems and applications. In this paper, we evaluate all currently available Java-based approaches that support persistent connections between Web clients and database servers. These approaches include Java applets, Java Sockets, Servlets, Remote Method Invocation, CORBA, and mobile agents technology. Our comparison is along the dimensions of performance and programmability. Our findings point out that best performance is not always achievable with high programmability and low resource requirements. Moreover, the mobile agent technology needs to improve its programmability while giving particular emphasis on its infrastructure. 10 4 401 422 Cited By :5

Telomeres and centromere are two essential features of all eukaryotic chromosomes. They provide function that is necessary for the stability of chromosomes. We developed a comprehensive database named TeCK, which covers a gamut of sequence and other related information about telomeric patterns, telomere repeat sequences, centromere sequences and centromeric patterns present in chromosomes. It also contains information about telomerase ribo-nucleoprotein complexes, centromere binding protein and centromere DNA-binding protein complexes. The database also includes a collection of all kinetochore-associated proteins including inner, outer and central kinetochore proteins. The database can be searched using a user-friendly web interface. Availability http://www.bioinfosastra.com/services/teck/index.html

The GENIA ontology is a taxonomy that was developed as a result of manual annotation of a subset of MEDLINE, the GENIA corpus. Both the ontology and corpus have been used as a benchmark to test and develop biological information extraction tools. Recent work shows, however, that there is a demand for a more comprehensive ontology that would go along with the corpus. We propose a complete OWL ontology built on top of the GENIA ontology utilizing the GENIA corpus. The proposed ontology includes elements such as the original taxonomy of categories, biological entities as individuals, relations between individuals using verbs and verb nominalizations as object properties, and links to the UMLS® Metathesaurus concepts. Availability http://www.ece.ualberta.ca/~rrak/ontology/xGENIA/

Understandings the basics of Cytochrome P450 (P450 or CYP) will help to discern drug metabolism. CYP, a super-family of heme-thiolate proteins, are found in almost all living organisms and is involved in the biotransformation of a diverse range of xenobiotics, therapeutic drugs and toxins. Here, we describe DrugMetZ DB, a database for CYP metabolizing drugs. The DB is implemented in MySQL, PHP and HTML. Availability www.bicpu.edu.in/DrugMetZDB/

The Arunachal Pradesh state in India is epidemic for malaria, caused by P.vivax and P.falciparum. Despite the implementation of several control strategies, the outbreak of malaria in the state is mainly due to lack of proper information regarding the disease. Hence, we completed a database to help implement appropriate control strategy for the public health officials in Arunachal Pradesh. Availability www.envisiict.org

Coconut crop improvement requires a number of biotechnology and bioinformatics tools. A database containing information on CG (coconut germplasm), CCI (coconut cultivar identification), CD (coconut disease), MIFSPC (microbial information systems in plantation crops) and VO (vegetable oils) is described. The database was developed using MySQL and PostgreSQL running in Linux operating system. The database interface is developed in PHP, HTML and JAVA. Availability http://www.bioinfcpcri.org

UNLABELLED Vancomycin and beta-lactams are antibiotics that inhibit gram positive bacteria by interfering with cell wall synthesis. However, continuous use of antibiotics results in the emergence of multi-drug resistant (MDR) bacterial strains. Here, we describe ARGO, a database containing gene sequences conferring resistance to these two classes of antibiotics. It is designed as a resource to enhance research on the prevalence and spread of antibiotic resistance genes. ARGO is the first attempt to compile the resistance gene sequence data with state specific information. AVAILABILITY AGRO is available for free at http://www.argodb.org/

UNLABELLED Physico-chemical properties of amino acids can be used to study protein sequence profiles, folding and function. We collated 242 properties for the 20 naturally occurring amino acids and created a dataset. The dataset is available as a database named APDbase( Amino acid Physico-chemical properties Data base). The database can be queried using either key words describing physico-chemical properties or pre-assigned database index number. The database contains corresponding references for each property value and facilitates deposition of new property values for processing and inclusion in the database. AVAILABILITY The database is available for free at http://www.rfdn.org/bioinfo/APDbase.php.

In this paper, we present a novel approach for materializing dynamic web pages by exploiting content dependencies and user access patterns. We introduce two new semantic-based data freshness metrics and show that our approach out-performs traditional balancing QoS-QoD approaches in terms of server throughput, increased data freshness and scalability. In our evaluation we use a real-world experimental system that resembles an online bookstore web database application. © 2012 Springer-Verlag. 7651 LNCS 512 525 Conference code: 93923 Cited By :1

This paper evaluates the effect of a Web system which activates institutional repositories. Institutional repository is an important service of libraries in academic institutions. The authors developed a link system between the institutional repository and the researcher database of their university. The system reduces the efforts of researchers by reusing the metadata in the researcher database for registrations of their papers to the repository. The authors observed the access log of the repository before and after the start up of the link system. The result shows that the system increased the number of access, however there was no significant change on the number of registration of papers.

The paper introduces a Web system which supports registration of scholarly papers to institutional repositories. Institutional repository is an important service for academic societies, however the number of archived papers is not enough in most of institutions. The authors of the paper developed a system that supports authors of papers (that is, researchers) and managers of repositories in registration of papers. By connecting with external databases of published research papers, the system urges researchers register their papers to repository. Additionally, the system automatically searches the copyright policy for each paper also using external databases. This paper makes clear the problem of current institutional repositories, and then describes the detailed idea of the developed system as a solution. The system is expected to decrease the efforts of researchers and managers for paper registration, and increase the number of archived papers in institutional repositories thereby.

Repositories are playing an important role in the idea of open access to scholarly information. To increase the number of repositories and the contents in each repository, the effectoveness of repositories should be clear for researchers, that is, providers of the contents. This paper proposes a system which analyzes the access log to the contents in an institutional repository and returns the result to the authors as a feedback from readers. However, the results of detailed analyses with respect to a particular researcher tend to include individual data, therefore the accesses to the results must be controlled. The proposed system solves the problem by connecting with the researcher database in the institution.

The explosive growth of World Wide Web has posed a challenging problem in extracting relevant data. Traditional web crawlers focus only on the surface web while the deep web keeps expanding behind the scene. Deep web pages are created dynamically as a result of queries posed to specific web databases. The structure of the deep web pages makes it impossible for traditional web crawlers to access deep web contents. This paper, Deep iCrawl, gives a novel and vision-based approach for extracting data from the deep web. Deep iCrawl splits the process into two phases. The first phase includes Query analysis and Query translation and the second covers vision-based extraction of data from the dynamically created deep web pages. There are several established approaches for the extraction of deep web pages but the proposed method aims at overcoming the inherent limitations of the former. This paper also aims at comparing the data items and presenting them in the required order., {"references":["XWRAP l.Liu, C.Pu and W.Han, \"XWRAP: An XML-Enable Wrapper\nConstruction System for Web Information Sources\"","A.Sahugent and F.Azavant \"Building Intelligent Web Applications\nusing Lightweighted Wrappers\"","V.Crezcenzi, G.Mecca and P.Merialdo \"RoadRunner: Towards\nAutomatic Data Extraction from Large Websites\", Proceedings of the\n27th VLDB conference, 2003","B.Liu,R.L.Grossman and Y.Zhai \"Mining Data Record in Web Pages\"\nSIGKDD .03, August 24-27, 2003, Washington, DC, USA","D.Cai , S.Yu, J.Wen and W.Ma,\"Extracting Content Structure for Web\nPages Based on Visual Representation\"","Wei Liu and X. Meng \"ViDE: A Vision-Based Approach for Deep Web\nData Extraction\" IEEE Transactions On Knowledge And Data\nEngineering, Vol. 22, No. 3, March 2010","Jayant Madhavan, David Ko, Łucja Kot, Vignesh Ganapathy, Alex\nRasmussen and Alon Halevy. \"Google-s DeepWeb Crawl\". PVLDB\n'08, August 23-28, 2008, Auckland, New Zealand"]}

Repositories are being popular as places for publication of research outputs. To make more efficient use of scholarly information on the internet, repositories are required to cooperate with other databases. One of the essential processes of the cooperation is identification of scholarly papers and their authors. The straightforward approach is string matching of the title and authors' name, however this approach cannot always solve the difficulties by basic clerical errors and same names. This paper proposes a method to compensate for the inaccuracy of the identification by connecting different databases. The main idea of the method is that different metadata of a scholarly paper is linked by the authors themselves, therefore the correspondence is guaranteed by the authors. The authors of this paper are developing a system based on the idea on the repository and the researcher database in their university.