Python script

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 Pipeline Pilot deployment includes a number of integration components that provide facilities to create a new component to capture a simple command line, or by coding up new functionality in Perl or Python scripts or in Java code, using a component API. To utilize network resources, the user can also configure telnet, ftp, or SOAP components. SOAP components can execute in a multithreaded fashion to parallelize the use of remote servers. 

Python is a general-purpose computer language with no built-in capabilities to access an RDBMS. There are modules that extend python to allow interaction with an RDBMS, for example, pygresql12 for PostgreSQL or cx oracle for Oracle. Once pygresql is installed, the following python script will fetch some rows and columns from a PostgreSQL database. 

Alternatively, a simple python script can be downloaded from the Schrodinger Script Center for generating molecular descriptors like topological. Molecular Orbital PACkage (MOPAC) and QuikProp (Script name molecular descriptors.py... 

In the last line the helper function print output (given below, but in the actual python script it needs to be defined before it is called) is called with the descriptor values and the final coverages. The variable theta is a (txc) matrix with the coverages c for each time step t. Usually, we are only interested in the last row, conveniently accessed by using —1 as index, but the time evolution is available as well for transient studies or verification that steady-state has been ... 

SciPy Statistics Scripting http //www.scipy.org Python programming... 

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

ModKit-l- is implemented in Python [824], a scripting language which per-... 

Using sdentific informatics sofiware such as Pipeline Pilot [99] or script languages such as Perl [100] and Python [101], hit lists can be filtered with respect to these lead-and druglikeness criteria. 

Python Python is a free object-oriented, easy-to-leam progranuning language and is useful in applieation development [15], It overcomes some of the drawbacks of Perl. It contains scalable, extendable scripting and can be embedded ... 

There are several nodes that have specific tasks on the data. Predefined components can be chosen from the library, configured, redesigned or even created from scratch and documented. When a new component is made by collapsing a few components together, it is called subprotocol. Many custom script components are available in Pipeline Pilot that allows to include the code directly into the pipelines and maintain a library of components based on a preferred language, such as Perl, Java, VBScript,. NET, JavaScript, Python, Matlab etc. 

Software for computing the RREF of a matrix is readily available in computer algebra packages. For completeness, here we list a script that offers the same functionality, but works in the popular open-source package Python ... 

Other languages can of course be used, such as Pascal or Basic or even Java, but the former two are rarities in digital simulation these days. There is an extensive text book on electrochemical digital simulation using Mathematica [5] by Honeychurch [6] unfortunately, the book is difficult to access. Batchelor et al. used Python and Julia [7], both script languages. MATLAB [8] has seen some use, in conjunction with COMSOL Multiphysics (formerly called FEMLAB ) [9-14]. Even Excel has been used for simulation [15, 16]. 

When Ada Meets Python Extensibility Through Scripting , Emmanuel Briot and Ben Brosgol, AdaCore, Erance and USA. 

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