Perl modules

To enhance the above analysis in a coordinated way, we have developed a gene module extraction and evaluation system called SAMURAI. The free trial version of the program coded in java/ C++/Perl is available from http //samurai.cbrc.jp/download/ SAMURAI-Progressive/ see Note 6). Here we describe briefly the usage of the system. 

Sweeney, M.J. Turck, C.W. Pallat, H. Robinson, T Motchnick, P. MassSpec.Pm—A Perl Module for Mass Spectrometric Applications, in Proceedings ofthe 50th ASMS Conference on Mass Spectrometry and Allied Topics, Orlando, Florida, June 2-6, 2002. 

L. Lindbom, J. Ribbing, and E. N. Jonsson, Perl-speaks-NONMEM (PsN)—a Perl module for NONMEM related programming. Comput Methods Programs Biomed 75 85-94 (2004). 

In any case, it is important that the Perl module file RNAz. pm resides in the same directory as the Perl programs (. pi). All the Perl programs depend on this module file. 

Some of the supplied Perl scripts use the Tk library and Perl bindings for visualization purposes, the Perl/Tk module is available from CPAN. It can be installed by typing... 

In the previously described example we see that the pair (4,70) has no inconsistent sequences, is predicted with probability 1, and occurs as a CG pair in one sequence, a GC pair in another, and a GU pair in the third. The AliDot. pi utility uses this information to display a dot plot equivalent to the postscript version. The viewer has better zoom capabilities than most postscript previewers and shows additional information, but requires the Perl Tk module to be installed. 

At many sites shell, Perl or Python scripts are used to run EMBOSS applications. BioPerl and BioPython both provide support for accessing EMBOSS programs, while the Bio Emboss module provides specific access for Perl programmers. 

A Biopipe protocol represents a series of analyses. Each unit of analysis consists of specifications for input, analysis, and output. The input layer consists of a number of adaptors for various common database formats or for remote fetching from Web sources like GenBank. The role of the input layer is to retrieve data into a common format for a subsequent analysis. The complementary output layer contains adaptors to push the analysis result out to the desired database or format. The analysis layer functions through the action of wrapper Biopipe Perl modules that make standard Bioperl runnable binaries accessible to the Biopipe system. An explicit design goal of Biopipe is to reuse the encapsulations of binary tools, importers, and exporters that Bioperl already includes, with thin wrappers that specify the inputs that the input layer must provide in a workflow context. 

This relatively new addition to the vast Perl module repository might be of interest to a proficient Perl software developer [OS3]. It supports XML definitions for the following workflow elements ... 

Once these modules are installed, the following perl script will select some rows and columns from a PostgreSQL database. 

Perl DBI module. http //search.cpan.org/ timb/DBI/DBI.pm (accessed April 18, 2008). 

Tubert-Brohman, I. PerlMol—Perl Modules for Molecular Chemistry. 2006. http //www.perlmol.org/ (accessed April 18,2008). 

After the SQL statement is executed, an array reference is returned using fetchall arraryref. The individual rows from this array are then printed. Some care needs to be taken when using fetchall arrayref when a large number of rows are returned. In that case, not all rows may be returned and the function will need to be called again until all rows are returned. The documentation for the DBI perl module discusses this more fully.1... 

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. 

The HCToolkit is a set of Perl modules that implement four equations of state, two flash algorithms and a multi-component, multiphase, temperature- and pressure-dependent viscosity prediction. The modules have been successfully run on MS Windows, Mac OSX and Redhat Linux. These modules can be called from another Perl code, or (via an ActiveX interface) from a front-end written in either Visual Basic or a VBA application such as Excel. 

In order to add an additional EOS module, the user needs to supply an object-oriented Perl module that... 

Practical Extraction Report Language Practical Extraction Report Language (Perl) is a free interpreted language mainly developed for text handling [14], A collection of Perl code is available at the Comprehensive Perl Archive Network (CPAN www.cpan.org). Bioperl provides many modules for sequences, data parsing, and databases very often used in bioinfoimatics. A perl code snippet is as follows ... 

Figure 23.28 shows two common products made with the Dycostrate process (a four-layer flex-multilayer chip-on-board (COB) for a hearing aid) and the PERL process (a six-layer FR-4 COB for a networking module). 

GeneDesign requires a few additional Perl modules to run. Some may already be installed, depending on your Perl distribution. You can run the helper script genedesign mod install. pi as a privileged user to install these Perl modules for you (see Note 2). 

This module is also available on the command line run perl GeneDesign.git/bin/Generate RSCU Table.pi --help for additional documentation. 

Check any error messages carefully. The most likely culprit is a missing Perl module. 

Check your web server s error log carefully. The most likely culprit is a missing Perl module you should also check that the GeneDesign. git/cgi-bin/gd folder has executable permissions and that the GeneDesign.git/documents/ gd/ tmp folder is world writable. 

The neutron calculations and thermal-hydraulic calculations stated in Sects. 7.5.2.1 and 7.5.2.2 are all implemented into an automatic calculation scheme written in Perl and Awk script languages. The macroscopic cross section sets and HFFs are prepared for given coolant densities and bumup states by the staged homogenization of the unit cell and the assembly transport calculation. The auxiliary mesh generation module produces the Tri-Z mesh stmcture to be used in COREBN and CITATION. 

---