MySQL Database Management System Research Articles

DESIGN MODULES FOR SENDING PRENATAL AND NEONATAL SCREENING RESULTS ONLINE ON WEBSITE DITATBAMSINH.VN

Background: This study aimed to: (1) Design the system for management, storage and send the results of the prenatal and neonatal screening online. (2) Design the search engine to find the patients. Materials and method: Programing using PHP language to store, query, process data from MySQL database management system and display the results on the website. Results: We designed four functions for administrator (import data from excel file into MySQL, editing and deleting patient informations, creating and assigning rights for users, upload the neonatal screening result files) and four functions for users (display the list of results, preview and print the results, download the neonatal screening result files, search the patients). Conclusion: The modules was designed successfully and good working now. Key words: Prenatal screening, neonatal srceening, getting results online Key words: prenatal screening, neonatal screening, getting result online

SISTEM INFORMASI GEOGRAFIS PEMETAAN SEKOLAH TINGKAT PENDIDIKAN DASAR DAN MENENGAH DI KOTA SERANG

The Spatial-based information system is one of the systems that is needed nowadays, because it serves as a foundation in supporting variety of applications in various sectors, one of which is education. Serang as the capital of Banten province indubitably becomes a model reference for other districts and cities in the development of education. Providing information regarding education, especially schools, to the people is of major importance to enhance Serang education office activity in providing service. There has not been any spatial-based information about schools in the city of Serang yet, so it is necessary to have a geographic information system of school mapping. Geographic information system of school mapping in Serang was developed using the waterfall model and built using MapServer, PHP programming language, and MySQL database management system. The system provides information on the distribution of both public and private primary education (SD/MI), secondary education (SMP/MTs), and upper secondary and vocational education (SMA/MA/SMK) in the city in the form of digital maps, containing spatial data and attribute data, and also generates information about indicators of equality on learning opportunity and gross participation rate (APK) in the city of Serang.

Analysis of expressed sequence tags (ESTs) from cocoa (Theobroma cacao L) upon infection with Phytophthora megakarya.

Phytophthora megakarya, the causative agent of cacao black pod disease in West African countries causes an extensive loss of yield. In this study we have analyzed 4 libraries of ESTs derived from Phytophthora megakarya infected cocoa leaf and pod tissues. Totally 6379 redundant sequences were retrieved from ESTtik database and EST processing was performed using seqclean tool. Clustering and assembling using CAP3 generated 3333 non-redundant (907 contigs and 2426 singletons) sequences. The primary sequence analysis of 3333 non-redundant sequences showed that the GC percentage was 42.7 and the sequence length ranged from 101 - 2576 nucleotides. Further, functional analysis (Blast, Interproscan, Gene ontology and KEGG search) were executed and 1230 orthologous genes were annotated. Totally 272 enzymes corresponding to 114 metabolic pathways were identified. Functional annotation revealed that most of the sequences are related to molecular function, stress response and biological processes. The annotated enzymes are aldehyde dehydrogenase (E.C: 1.2.1.3), catalase (E.C: 1.11.1.6), acetyl-CoA C-acetyltransferase (E.C: 2.3.1.9), threonine ammonia-lyase (E.C: 4.3.1.19), acetolactate synthase (E.C: 2.2.1.6), O-methyltransferase (E.C: 2.1.1.68) which play an important role in amino acid biosynthesis and phenyl propanoid biosynthesis. All this information was stored in MySQL database management system to be used in future for reconstruction of biotic stress response pathway in cocoa.

Web-oriented geoinformation system on alien plant species of European Russia

An open geoinformation system (GIS) Alien Plant Species of European Russia under construction is presented. The system is based on a database on species finds. The database includes information on species nomenclature, morphology, ecology, and distribution (the initial range and area of invasion) and a description of the particularities of carrying. For the publication on the Internet, the data are displayed in a free relational database management system MySql. The spatial data are presented by way of points with geographical coordinates (the finds of species) and polygons (administrative districts). Google maps are used as a cartographic basis, and the layer formed by the map server is overlaid on it. The entry of data on finds via the Internet directly and their saving in the database is provided. By means of GIS, the following tasks may be solved: automation of the information on alien species accumulation, alien species monitoring covering the whole territory of European Russia, combining of information on alien species with information on different environmental factors, and prediction of invasive species settlement based on analysis of correlations between the species features and environmental factors.

RodImAnD: a MySQL-Database for analysing functional MRI Data from rodents in drug research

RodImAnD: a MySQL-Database for analysing functional MRI Data from rodents in drug research

The input-interface of Webcam applied in 3D virtual reality systems

Our research explores a virtual reality application based on Web camera (Webcam) input-interface. The interface can replace with the mouse to control direction intention of a user by the method of frame difference. We divide a frame into nine grids from Webcam and make use of the background registration to compute the moving object. In order to make this technology apply to 3D virtual reality system, we use the Virtools Dev to build virtual scenes and the Microsoft Visual C++ to build this interface. We also use the MySQL database management system to access users’ data and the displaying data. We implement a number of Building Blocks (BB) to support Virtools Dev for using the database management system and the Webcam input-interface in this composite system. The results of research are expected to the digital content industries such that users can easy to use the input-interface to control browsing the virtual reality. Our system can supply interactive digital content, photographs, and access the questions from the database management system. In addition, the system provides the browsing mold, the question mold, and the course content describing mold with the input-interface. In order to explore the intention of users for using the system, we design the questionnaire based on the technology acceptance model (TAM). In our empirical study, we find that perceived playfulness is positive association with attitude toward using. Interface style is positive association with perceived ease of use.

Development and implementation of a web-based system to study children with malnutrition

Objectives To develop and implement a collective web-based system to monitor child growth in order to study children with malnutrition. Method The system was developed using prototyping system development methodology. The implementation was carried out using open-source technologies that include Apache Web Server, PHP scripting, and MySQL database management system. There were four datasets collected by the system: demographic data, measurement data, parent data, and food program data. The system was designed to be used by two groups of users, the clinics and the researchers. Results The Growth Monitor System was successfully developed and used for the study, “Geoinformation System (GIS) and Remote Sensing in Mapping of Children with Malnutrition.” Data collection was implemented in public clinics from two districts in the state of Kelantan, Malaysia. Conclusions The development of an integrated web-based system, Growth Monitor, for the study of children with malnutrition has been achieved. This system can be expanded to new partners who are involved in the study of children with malnutrition in other parts of Malaysia as well as other countries.

GEOMAGIA50: An archeointensity database with PHP and MySQL

The GEOMAGIA50 database stores 3798 archeomagnetic and paleomagnetic intensity determinations dated to the past 50,000 years. It also stores details of the measurement setup for each determination, which are used for ranking the data according to prescribed reliability criteria. The ranking system aims to alleviate the data reliability problem inherent in this kind of data. GEOMAGIA50 is based on two popular open source technologies. The MySQL database management system is used for storing the data, whereas the functionality and user interface are provided by server‐side PHP scripts. This technical brief gives a detailed description of GEOMAGIA50 from a technical viewpoint.

Development of a Web-based model to track patients’ self-reported symptoms related to anticancer treatment toxicities

17021 Background: Discrepancies outcropped when traditional modalities in collecting information regarding toxicities suffered by patients being exposed to anticancer treatments have been compared to direct self-reports. Owing to the availability of easily accessible informatics technologies, we hypothesized that a Web-site could be an accurate and reliable tool to directly record toxicity data. Methods: A database schema was designed, implemented with MySQL database management system and interfaced with the Web by using Java 2 Enterprise Edition on the Tomcat application container. A simplified, patient-adapted definition of type and NCI-CTCAE grade of the 15 commonest toxicities has been inserted into the database for reporting. The Web site has two areas, both accessible only with username and password, respectively devoted to patients and physicians. Through home Web access, each patient can report toxicities by choosing and grading any of them. Web site usability has been tested by 8 non-professional users with simulated scenarios. After a quick training, the users were asked to report the described toxicities. Time needed for reporting and reporting errors have been recorded. Results: The average time needed for entering a report has been 10 minutes. Users correctly reported the toxicities provided in the scenarios, but difficulties were noted in the correct identification of the week when entering reports for two or more weeks of therapy. Conclusions: In order to track patient-reported toxicities we developed a prototype Web-based model. Potential utilities of the system are being tested to demonstrate: 1) accuracy, allowing patients to easily report types and grades of the experienced toxicities; 2) flexibility, allowing patient-reporting either weekly or on demand; 3) capability to integrate and to assemble with an electronic patient record and a computerized physician order-entry. The latter capability will be provided by a patient portal with secure authentication and access being developed by the Regional Healthcare Authority. Comparative randomized analysis in 100 consecutive outpatients between clinical interviewing and Web-reported toxicity has been planned. No significant financial relationships to disclose.

SGDB: a database of synthetic genes re-designed for optimizing protein over-expression

Here we present the Synthetic Gene Database (SGDB): a relational database that houses sequences and associated experimental information on synthetic (artificially engineered) genes from all peer-reviewed studies published to date. At present, the database comprises information from more than 200 published experiments. This resource not only provides reference material to guide experimentalists in designing new genes that improve protein expression, but also offers a dataset for analysis by bioinformaticians who seek to test ideas regarding the underlying factors that influence gene expression. The SGDB was built under MySQL database management system. We also offer an XML schema for standardized data description of synthetic genes. Users can access the database at , or batch downloads all information through XML files. Moreover, users may visually compare the coding sequences of a synthetic gene and its natural counterpart with an integrated web tool at , and discuss questions, findings and related information on an associated e-forum at .

SwePep, a Database Designed for Endogenous Peptides and Mass Spectrometry

A new database, SwePep, specifically designed for endogenous peptides, has been constructed to significantly speed up the identification process from complex tissue samples utilizing mass spectrometry. In the identification process the experimental peptide masses are compared with the peptide masses stored in the database both with and without possible post-translational modifications. This intermediate identification step is fast and singles out peptides that are potential endogenous peptides and can later be confirmed with tandem mass spectrometry data. Successful applications of this methodology are presented. The SwePep database is a relational database developed using MySql and Java. The database contains 4180 annotated endogenous peptides from different tissues originating from 394 different species as well as 50 novel peptides from brain tissue identified in our laboratory. Information about the peptides, including mass, isoelectric point, sequence, and precursor protein, is also stored in the database. This new approach holds great potential for removing the bottleneck that occurs during the identification process in the field of peptidomics. The SwePep database is available to the public.

CoryneRegNet: An ontology-based data warehouse of corynebacterial transcription factors and regulatory networks

BackgroundThe application of DNA microarray technology in post-genomic analysis of bacterial genome sequences has allowed the generation of huge amounts of data related to regulatory networks. This data along with literature-derived knowledge on regulation of gene expression has opened the way for genome-wide reconstruction of transcriptional regulatory networks. These large-scale reconstructions can be converted into in silico models of bacterial cells that allow a systematic analysis of network behavior in response to changing environmental conditions.DescriptionCoryneRegNet was designed to facilitate the genome-wide reconstruction of transcriptional regulatory networks of corynebacteria relevant in biotechnology and human medicine. During the import and integration process of data derived from experimental studies or literature knowledge CoryneRegNet generates links to genome annotations, to identified transcription factors and to the corresponding cis-regulatory elements. CoryneRegNet is based on a multi-layered, hierarchical and modular concept of transcriptional regulation and was implemented by using the relational database management system MySQL and an ontology-based data structure. Reconstructed regulatory networks can be visualized by using the yFiles JAVA graph library. As an application example of CoryneRegNet, we have reconstructed the global transcriptional regulation of a cellular module involved in SOS and stress response of corynebacteria.ConclusionCoryneRegNet is an ontology-based data warehouse that allows a pertinent data management of regulatory interactions along with the genome-scale reconstruction of transcriptional regulatory networks. These models can further be combined with metabolic networks to build integrated models of cellular function including both metabolism and its transcriptional regulation.

A user-friendly, dynamic web environment for remote data browsing and analysis of multiparametric geophysical data within the MULTIMO project

In the framework of the EU-funded project “Multi-disciplinary monitoring, modelling and forecasting of volcanic hazard” (MULTIMO), multiparametric data have been recorded at the MULTIMO station in Montserrat. Moreover, several other long time series, recorded at Montserrat and at other volcanoes, have been acquired in order to test stochastic and deterministic methodologies under development. Creating a general framework to handle data efficiently is a considerable task even for homogeneous data. In the case of heterogeneous data, this becomes a major issue. A need for a consistent way of browsing such a heterogeneous dataset in a user-friendly way therefore arose. Additionally, a framework for applying the calculation of the developed dynamical parameters on the data series was also needed in order to easily keep these parameters under control, e.g. for monitoring, research or forecasting purposes. The solution which we present is completely based on Open Source software, including Linux operating system, MySql database management system, Apache web server, Zope application server, Scilab math engine, Plone content management framework, Unified Modelling Language. From the user point of view the main advantage is the possibility of browsing through datasets recorded on different volcanoes, with different instruments, with different sampling frequencies, stored in different formats, all via a consistent, user- friendly interface that transparently runs queries to the database, gets the data from the main storage units, generates the graphs and produces dynamically generated web pages to interact with the user. The involvement of third parties for continuing the development in the Open Source philosophy and/or extending the application fields is now sought.

A searchable database for proteomes of oral microorganisms

An online database of proteomes for two-dimensional electrophoresis (2DE) gel data was constructed and it is now freely accessible through a web-based interface. Proteins from three oral bacteria, Streptococcus mutans UA159, Actinobacillus actinomycetemcomitans HK1651, and Porphyromonas gingivalis W83, whose genome databases are freely available, were separated by 2DE, and protein spots were analyzed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) and identified. About 1000 spots from the gels of P. gingivalis W83 were extracted and analyzed by MALDI-TOF, and 330 proteins were identified. In addition, 160 of 240 spots of A. actinomycetemcomitans and 158 of 356 spots of S. mutans were identified. Information such as spot coordinates on the gels, protein names (predicted functions), molecular weights, isoelectroric points, and links to online databases, including Oral Pathogen Sequence Databases of the Los Alamos National Laboratory Bioscience Division (ORALGEN) and National Center for Biotechnology Information (NCBI) or The Institute Genomic Research (TIGR), were stored in tables accessible through the relational database management system MySQL on an Apache web server. To test for functionality of this database system, responses of S. mutans to environmental changes were analyzed using the database and 21 spots on the gel were identified as proteins whose expression had been increased or decreased by environmental pH change without in-gel trypsin digestion, protein extraction, or MALDI-TOF/TOF-MS (mass spectrometer) analysis. The identified proteins are agreement with those reported in previous papers on acid tolerance of S. mutans, demonstrating the usefulness of the system. This database is available at http://www.myamagu.dent.kyushu-u.ac.jp/~bioinformatics/index.html or http://www.bipos.mascat.nihon-u.ac.jp/index.html.

SiMCAL 1 algorithm for analysis of gene expression data related to the phosphatidylserine receptor

SiMCAL 1 (simple multilevel clustering and linking, version 1) is a novel clustering algorithm for time-series microarray data, presented here with an application to a specific data set. The purpose of the algorithm is to present a complete feature set not found in either Jarvis-Patrick clustering, from which it is derived, or in other popular clustering methods such as hierarchical and k-means. The data concern the activity of the phosphatidylserine receptor (PSR) which is believed to be a crucial molecular switch in the mediation of inflammatory response in apoptosis and lysis. By analyzing the behavior of PSR-related genes in mouse macrophages, we hope to elucidate the mechanisms involved in this important biological process. SiMCAL 1 is implemented in the Python programming language using the Numerical Python extensions, and the data are stored using the MySQL database management system. The data are derived from exposures of multiple Affymetrix mouse gene microarray chips to elevated levels of PSR antibody and control conditions. Code and data are available at (accessed: 17 January 2005). The algorithm meets its objectives: it is simple, in that it is computationally inexpensive; it is multilevel, in that it provides a small number of clearly defined hierarchical levels of clusters; and it offers linking between clusters at the same level in each hierarchy. Clustering and linking results indicate previously unknown co-regulation for genes expressing PGH synthase (COX2) and PGE2, appear to confirm increased production of proteins for clearance of apoptotic cells in the presence of PSR antibody, and correspond to other findings regarding the temporal relationship between PGE2 production and B cell proliferation and differentiation. These results are promising but should be taken as highly preliminary. Both the algorithm and its application to this problem show great potential for future development. We plan to improve and extend the SiMCAL family of algorithms, and to obtain new data so that the algorithm(s) may be further applied to this and other problems of interest.