A data gathering toolkit for biological information integration

SYSTERS is a biological information integration system containing protein sequences from many protein databases such as Swiss-Prot and TrEMBL and also protein sequences from complete genomes available at Ensembl, The Arabidopsis Information Resource, SGD and GeneDB. For some protein sequences their encoding nucleotide sequences can be found in their corresponding websites. However, for some protein sequences their encoding nucleotide sequences are missing. The goal of this thesis is to. collect all nucleotide sequences for the protein sequences in SYSTERS and store them in a common database. There are two cases. The first case is that if the nucleotide sequences can be found, we collect them and put them in our database. The second case is that if the nucleotide sequences are missing, we use back-translation and use TBLASTN to search the nucleotide sequences and store them in our database

SQL Injection analysis, Detection and Prevention

Web sites are dynamic, static, and most of the time a combination of both. Web sites need protection in their database to assure security. An SQL injection attacks interactive web applications that provide database services. These applications take user inputs and use them to create an SQL query at run time. In an SQL injection attack, an attacker might insert a malicious SQL query as input to perform an unauthorized database operation. Using SQL injection attacks, an attacker can retrieve or modify confidential and sensitive information from the database. It may jeopardize the confidentiality and security of Web sites which totally depends on databases. This report presents a “code reengineering” that implicitly protects the applications which are written in PHP from SQL injection attacks. It uses an original approach that combines static as well as dynamic analysis. [2] In this report, I mentioned an automated technique for moving out SQL injection vulnerabilities from Java code by converting plain text inputs received from users into prepared statements. [3

Using Perl for Statistics: Data Processing and Statistical Computing

In this paper we show how Perl, an expressive and extensible high-level programming language, with network and ob ject-oriented programming support, can be used in processing data for statistics and statistical computing. The paper is organized in two parts. In Part I, we introduce the Perl programming language, with particular emphasis on the features that distinguish it from conventional languages. Then, using practical examples, we demonstrate how Perl's distinguishing features make it particularly well suited to perform labor intensive and sophisticated tasks ranging from the preparation of data to the writing of statistical reports. In Part II we show how Perl can be extended to perform statistical computations using modules and by "embedding" specialized statistical applications. We provide example on how Perl can be used to do simple statistical analyses, perform complex statistical computations involving matrix algebra and numerical optimization, and make statistical computations more easily reproducible. We also investigate the numerical and statistical reliability of various Perl statistical modules. Important computing issues such as ease of use, speed of calculation, and efficient memory usage, are also considered.

Structured document comparison and scientific data mining on the world wide web

The usefulness and accessibility of programs and systems have become important issues for users and researchers alike. A program\u27s usefulness can lw measured by the frequency with which it is used. From the author\u27s or maintainer\u27s point of view, the frequency of usage can be determined by how often a request for the software is received. In the past, a user became aware of a particular tool through various means, and contacted the author or maintainer to obtain a copy of it. This presented difficulties, ranging from language barriers to machine incompatibilities to control of the use of the program. Furthermore, accessibility of the program was limited to the particular machines on which it was installed (at the remote site). By porting programs and systems to the World Wide Web, the problems of accessibility and usefulness can be mitigated. Now programs can be advertised (in a non-commercial sense) to all interested parties, problems of machine incompatibility can be reduced (with the exception of browser incompatibilities), and control of the use and modification can be maintained. This thesis discusses the porting of two tools to the World Wide Web. The tools are SDISCOVER, a data mining tool used in protein string matching, and TREEDIFF, a structured document comparison toolkit. Spinoff of this research is the development of two home pages for conference registrations and Oracle user account applications in a university environment

GRIDSITE

GridSite provides grid credential, proxy certificate and delegation support for web-based application

Exposing and harvesting metadata using the OAI metadata harvesting protocol: A tutorial

In this article I outline the ideas behind the Open Archives Initiative metadata harvesting protocol (OAIMH), and attempt to clarify some common misconceptions. I then consider how the OAIMH protocol can be used to expose and harvest metadata. Perl code examples are given as practical illustration.Comment: 13 pages, 1 figure. Example programs included (download source). HEPLW version (HTML) available online at http://library.cern.ch/HEPLW/4/papers/3

PhEDEx Data Service

The PhEDEx Data Service provides access to information from the central PhEDEx database, as well as certificate-authenticated managerial operations such as requesting the transfer or deletion of data. The Data Service is integrated with the SiteDB service for fine-grained access control, providing a safe and secure environment for operations. A plug-in architecture allows server-side modules to be developed rapidly and easily by anyone familiar with the schema, and can automatically return the data in a variety of formats for use by different client technologies. Using HTTP access via the Data Service instead of direct database connections makes it possible to build monitoring web-pages with complex drill-down operations, suitable for debugging or presentation from many aspects. This will form the basis of the new PhEDEx website in the near future, as well as providing access to PhEDEx information and certificate-authenticated services for other CMS dataflow and workflow management tools such as CRAB, WMCore, DBS and the dashboard. A PhEDEx command-line client tool provides one-stop access to all the functions of the PhEDEx Data Service interactively, for use in simple scripts that do not access the service directly. The client tool provides certificate-authenticated access to managerial functions, so all the functions of the PhEDEx Data Service are available to it. The tool can be expanded by plug-ins which can combine or extend the client-side manipulation of data from the Data Service, providing a powerful environment for manipulating data within PhEDEx

Web Texturizer: Exploring intra web document dependencies

The goal of this project is to create a customized web browser to facilitate the skimming of documents by offsetting the document with relevant information. This project added techniques of learning information retrieval to automate the web browsing experience to the web texturizer. The script runs on the web texturizer website; and it allows users to quickly navigate through the web page