Computational Science and Web-Accessed Databases

Introduction

Web-accessed databases are very useful to computational science. Developing web-accessed databases for computational science involves a number of tasks. To obtain an overview of the relationships of these tasks and to increase our appreciation of the applications, we consider two examples.

The first example is for college physics classes. We want to build a website for a school's physics department in which student teams can enter data from various laboratory experiments. Moreover, by accessing the website, each student can retrieve every teams' experimental data from a particular laboratory to check some hypotheses.

To accomplish this assignment, we need to be able to do the following tasks:

1. Create web pages with forms for entering data
2. Access and create databases, which are integrated collection of files, to store the data
3. Get data from a web form to a database
4. Get data from a database to a web page

In the modules, we return to the college physics example as we cover these tasks.

The second example is for genetics researchers and biology students. We want to build a website in which researchers can record data that they discover about DNA sequences. Also, accessing such a website, biologists can locate similar sequences. Through such similarities with genetic sequences of known function, scientists hope to discover additional gene functions. Besides being able to perform the same tasks as in the college physics example, for this application we also need algorithms for comparing sequences and searching databases for similar sequences. Projects within several modules develop this genomic example.

All these tasks must be performed on some system of computers. Many schools and laboratories use computers that run the UNIX operating system, which is the collection of programs that forms the interface between the user and the hardware. Thus, we begin our study with an introduction to UNIX.

The database system we use is MySQL. We employ the language SQL to work with a common type of database, called a relational database.

After learning to access such databases with SQL, we study the creation of web pages and web forms using the language HTML. CGI programs, which can be in any number of computer languages, including C++ or Perl, provide the interface between a web page and a database. Moreover, such programs often perform additional computations, such as matching genomic sequences. Modules provide the biology background and consider algorithms for comparing genomic sequences and searching genomic databases.

Concluding modules cover how to model and develop a database, such as one for college physics laboratory data or for genomic data, and how to create a database using SQL.

Throughout these modules, we study the tasks of web-accessed databases in the context of computational science applications.

Exercises

1.  Write a paragraph describing another example employing the tasks listed in the section on "College Physics Example."

Copyright © 2014, Dr. Angela B. Shiflet
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