Open-Source Tools

The main applications of this subject are in the fields of medical science for developing novel and effective drugs and in material science to develop new and superior materials [4]. The other alhed fields that benefit from the pursuit of chemoinformatics ate agrochemicals and biotechnology [5]. These operations differ from the classical storage of data in a computer because the data associated with the chemical information system are mostly structural that requite special algorithms and methods to handle unlike textual data. 

With the availability and access to modem high-performance computing infra-stmcture, it is now possible to add value to the diverse field of chemoinformatics in terms of speed and efficiency. Open-source tools are now playing a pivotal role in revolutionizing the way chemoinformatics data can be handled in a high-through-put manner, and e q)eriments requiring intensive computational power can be performed in an in-silico environment. 

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CellProfiler and KNIME Open Source Tools for High Content Screening... 

If any of the above testing fails, the developer is notified right away so that the bugs get fixed in the next build. Some open source tools can help to automate the testing. CruiseControl is a tool that automatically builds, deploys, and runs regression testing every time a code is checked into source control and notifies the person who checked in the code should problems be found. 

Binding an XML File to CRS objects is a much simpler task because open source tools are available that can help us to do the work. Castor XML Mapping and Apache Xerces are the two examples. Using the Data Binder API and implementing an XMLBinder that uses any open source XML parser should do the work. 

Data pipelining via enterprise server applications such as Pipeline Pilot (Accelrys/Scitegic), Inforsense, or the Talend (http //www.talend.com/) and KNIME (http //www.knime.org/) open source tools represent a powerful approach to integrate applications and develop custom functionality. As a specific application, Pipeline Pilot 7.0 includes a plate analytics collection for the development of complex plate-based data analysis and visualization protocols. 

Simulation techniques have been used in scientific studies for decades, but only the advent of open source tools, increases in desktop computational power and broad access to commodity super-computers have made these techniques readily available to individual investigators. So, what is "spectral simulation" For the purpose of this chapter we will define it as "The estimation of the results of an... 

The use of free, open source tools is suggested for pharmacometricians who may not have licenses for commercial software. Flowever, the expenses associated with the licenses may not be significant for many organizations. A pharmacometrican can utilize the similarities between the proprietary and open source tools by developing the skills using the free tools and, if needed, transition to the proprietary versions later on. 

The use of open source tools is one way to investigate how you might use a workflow system without having to make any cash investment. They can provide a workable system for an individual researcher or a small group, if you are able to supply the software development and IT skill set (with the necessary time) to configure and extend the system and to handle low-level administration. 

There are now a number of commercial and open source tools for the development, maintenance, merging, and visualization of ontologies. A comprehensive survey of ontology tools was conducted in July 2004 by XML.com.11 We do not attempt to reproduce that survey here, but it is worth mentioning some tools and organizations that are notable within the ontology field. 

Open-Source Tools, Techniques, and Data in Chemoinformatics... 

Table 1.1 Open-source tools, languages, and resources available for performing chemoinformatics experiments...

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