Perl language

PerlMol is a module add-on to the perl language that facilitates working with molecular structures using SMILES, SMARTS, and molfiles, as well as other functionality. PerlMol is available from CPAN, the Comprehensive Perl Archive Network. In order to install PerlMol, it is recommended to use the command cpan -i PerlMol as superuser in order to install the modules into the system perl library. This will install all the necessary modules for the following functions, as well as other parts of PerlMol that may be useful. 

Make sure that your system has the following basic packages installed A compiler for the c programming language (such as gcc), the Perl scripting language, and tel / tk. Currently, all common distributions include these features in their standard setup. 

These are scripts written in some form of language (usually, but not necessarily Perl, PHP, or Python) for server communication. 

Programmers can access and update PGDB data directly by writing programs in the Java, Perl, and Common Lisp languages (13). 

Descriptive Languages Macro Languages, VBA JavaScript, VB, Python, Perl C+ t, C, Java, Python, Perl FORTRAN, Common LLSP, C Assembler... 

In addition to the requirements for data storage and integration, there are also varying requirements for interfaces to the data to support the community. Bench scientists generally require intuitive Web interfaces or click-and-install graphical user interfaces. Application developers within the bioinformatics sector require stable application programming interfaces (APIs) in their preferred language (e.g., Java, Perl, C, C++, or Python). 

There are two classes of APIs in Atlas loader and retrieval. The loader APIs are used to build the loading applications and populate instances of the relational models in the Adas databases. The retrieval APIs are required for developing custom user-retrieval applications such as the Atlas toolbox applications. The loader API for Biological Sequences has been implemented in C++ as it relies heavily on the NCBI C++ Toolkit to parse the ASN. 1 data. The Biological Sequence retrieval API, on the other hand, is provided in three languages C++, Java, and Perl. Finally, the loader and retrieval APIs for Molecular Interactions are provided in Java. 

K2 [13] is a distributed query system that has been developed at the University of Pennsylvania. K2 relies on a set of data drivers, each of which handles the low-level details of communicating with a single class of underlying data sources (e.g., Sybase relational databases, Perl/shell scripts, the BLAST family of similarity search programs, etc.). A data driver accepts queries expressed in the query language of its underlying data source. It transmits each such query to the source for evaluation and then converts the query result into K2 s internal complex value representation. Data drivers are also responsible for providing K2 with data source metadata (i.e., types and schemas), which are used to type check queries. 

Sometimes these general-purpose applications are not sufficiently specific to the needs of database users. In that case, custom applications can be written. Many programming languages have extensions that allow data to be selected from the database and read into data structures for further operations. This chapter considers ways of using ODBC (Open Database Correctivity), JDBC for Java, Perl DBI (Database Interface), pg and pgdb for Python, and PDO for PHP... 

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