MySQL

MySQL Microsoft SQL Server Teradata SAS/ACCESS interface to PC file formats reads Microsoft Access and Excel files directly... 

The QCRNA database is viewable and searchable with a web browser on the internet and it is also contained as a MySQL database that is easily incorporated with parameter optimization software to allow for the rapid development of specific reaction parameters. Molecular structures can be viewed with the JMOL [47, 48] or MOLDEN [49, 50] programs as viewers for chemical MIME types. If the web browser is JAVA-enabled, then the JMOL software will automatically load as a web applet. Both programs allow the structure to be manipulated, i.e., rotated, scaled, and translated, and allow for measurement of internal coordinates, e.g., bond lengths, angles, and dihedral angles. Similarly, animations of the vibrational frequencies are available and can be viewed with either program. 

Pharmacophore profiles are defined that represent the set of all the pharmacophores found across the conformers of a series of conformers or series of molecules. Each pharmacophore added to the profile has to be unique. This profile will help in showing the spread of pharmacophores across the conformational space of a molecule or a series of molecules. No sum of the exhibited pharmacophores or normalization is done. There is no direct graphical representation of pharmacophore models. The pharmacophores can be saved to a file in CSV format that can be imported into a MySQL or Oracle database. This approach permits the use of standard SQL queries to extract common pharma-... 

At the end of 2004, the database contains 17 Gbytes. The tables presented in Section 3.3 have been implemented in a MySQL [24] database running on... 

To avoid such a problem, we make use of regular expressions. They can also be easily implemented with MySQL. Thus, if we are interested in... 

The answer is provided after 7 hours 48 minutes 21 seconds during which almost 100 % of the CPU of the machine was devoted to this single request. The major reason of such an important delay is that the tcphdr table contains more than 17,700,000 entries. On the other hand, thanks to the integrated meta data, we can submit this Mysql query ... 

MySQL Open Source Database home page http //www.mvsql.com... 

MySQL Open source (free) Light-weight free database, popularly used as the back-end for bioinformatics web-sites... 

For those who want to query PGDB data through a relational database system, the attribute-value files exported by Pathway Tools can be loaded into SRFs BioWarehouse system (14). BioWarehouse is an Oracle or MySQL-based system for integration of multiple public bioinformatics databases. PGDB data can be queried through BioWarehouse alone or in combination with other bioinformatics databases such as UniProt, Genbank, NCBI Taxonomy, ENZYME, and KEGG. 

Besides MassTRIX, several other solutions for annotation of mass spectromet-ric data exist. Two examples are the Pathos Web server (http //motif.gla.ac.uk/ Pathos/pathos.html) (41) and Paintomics (www.paintomics.org) (42). Pathos principally is based on the same functionality as MassTRIX and is written in Java and uses an underlying MySQL database. It annotates possible metabolites within an error range to experimental masses. Additionally, for this... 

The current project contains more than 20,000 terms for biological processes, cellular components, and molecular functions. The ontologies can be downloaded in different formats including extensible Markup Language (XML) and the open-source relational database scheme MySQL. 

Click the describe table schema button to view the structure of the MySQL table in which the phastConsElements data are stored in the Genome Browser database, as well as sample data records and a description of the associated Genome Browser track (see Note 14). Click the Tables link to return to the main Table Browser page. 

Biopipe [OS2] is a framework for running bioinformatics workflows and is deployable as an extension to the Bioperl project library [OS4]. It borrows heavily from the Ensembl pipeline project [OS7]. Potential users of the system should be comfortable coding Perl scripts and actually reconfiguring a Perl installation to add the necessary prerequisites. The user also needs to deal with coding raw XML to compose and configure a workflow and setting up the mySQL database that is required for the system to function. 

An introduction to SQL is provided in Chapter 3, but with an emphasis on examples relevant to chemical information rather than business information, which is often used in other books. Chapter 4 discusses some of the RDBMS that are available, namely Oracle, MySQL, and PostgreSQL. All of them use SQL to insert, delete, update, and select data. Chapter 5 shows ways in which client programs, including Web-based applications, are used to connect to the database server. Chapter 6 examines ways in which RDBMS are typically used to handle numerical and textual chemical information using relational tables. An example of using data files from the PubChem project is included. 

Much of this book discusses ways in which the RDBMS can be used and even extended to handle chemical structures correctly, quickly, and conveniently. Extensions of the capabilities of PostgreSQL are simply called extensions. Oracle uses the term data cartridge. There are chemical extensions or cartridges available for PostgreSQL, Oracle, and MySQL. 

MySQL is an open-source RDBMS. It conforms in part to the SQL 92/99 standards. The MySQL company sells and support the MySQL RDBMS. There are other companies that support MySQL and offer products that use MySQL as the underlying database. Tharun Kumar Allu describes a small molecule chemical database cartridge extension for MySQL.6... 

Some of the more advanced methods described in this book require a more specific use of the RDBMS. The choice made for this book is PostgreSQL. In cases where a particular feature of PostgreSQL is used, a note is added to alert the reader. For example, the array data type in SQL2003 is implemented in PostgreSQL very differently than in Oracle. The list matches function described in a later chapter of this book returns an array of integers that denote which atoms in a structure match a substructure query. The integration of this function into SQL would be handled quite differently in PostgreSQL, Oracle and MySQL. 

Fermilab Computing Division. 2005. Comparison of Oracle, MySQL and PostgreSQL DBMS, http //www-css.fnal.gov/dsg/external/freeware/ mysql-vs-pgsql.html (accessed April 21, 2008). 

Because of the flexibility and familiarity of Web browsers, Web-based applications have become very popular and powerful. There are many Web-based interfaces to RDBMS. For example, phpPgAdmin1 is a popular Web application for PostgreSQL. PhpMyAdmin2 is popular with users of MySQL. These applications allow one to connect to a chosen database server, browse the schemas and tables in the database, and enter SQL commands. The output from SQL commands, especially table output, is formatted nicely. Other operations, such as creating, altering, or dropping tables and schemas, are also provided. These use an HTML form interface, with text boxes, radio buttons, check boxes, and other form elements familiar to all uses of the Web. 

PgAdmin are available to be run on Linux, Windows, Mac, and other clients. Oracle users typically use Oracle s SQL Developer or Toad (Toad also works with MySQL). SQL Developer4 is a Java application that uses JDBC to mediate the communication to the database. A typical user need not be concerned with this, but a later chapter of this book discusses ways to construct new client applications using JDBC, ODBC, and other methods to communicate with the RDBMS. Toad is a Windows only application with a free version and a full-featured pay version.5... 

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