Free and Open Source Software

Lakhani, K., Wolf, R. Why Hackers Do What They Do Understanding Motivation and Effort in Free/Open Source Software Projects. In Perspectives on Free and Open Source Software, MIT Press, Cambridge (2005)... 

Open ZINCPharmer (http //zincpharmer.csb.pitt.edu/) where the XYZ coordinates of Pharmacophore groups can be used to screen ZINCDatabase. ZINCPharmer is the free and open source pharmacophore search software which can identify... 

CellProfiler and CellProfiler Analyst are free Open Source software for automated image analysis, data visualization, and machine learning. Versions for Mac, Windows, and Linux are available and both software can be downloaded at http //www.cellprofiler. org. CellProfiler was developed by Anne Carpenter and Thouis Jones in the laboratory of David Sabatini at the Whitehead Institute for Biomedical Research and by Polina Golland at the CSAIL of the MIT. 

The TIGR has software systems available for free download. These include software for gene finding/annotation, alignment, sequencing/finishing, and microarray analysis. All of them are OSI (Open Source Initiative) Certified Open Source Software. 

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. 

Lakhani, K. R. and von Hippel, E. (2003], "How open source software works "free" user-to-user assistance," Research Policy, 32 (6], 923-43. 

Whether life sciences informatics software ultimately becomes a commodity, with the commercial rewards for software companies being in packaging, integration, support, and deployment (in a similar way to the Linux community), and what impact the open source movement will have. In bioinformatics and chemoinformatics, open source, free software, and shareware are increasing in quantity, and it is becoming common for smaller software companies at least to release reduced-functionality versions of their software into the public domain at no cost. 

Depending on the size of the CRO and the nature of the trial, the system may be acquired in one of the following ways (1) developed in-house by the organization s staff with off-the-shelf commercial software, (2) outsourced to outside contractors, (3) with open source/free software (OSS/FS), and (4) purchased from e-clinical proprietary vendors. 

JChem Marvin KNIME extensions are also available [22]. The modules allow researchers to handle chemical structure data using ChemAxon s software tools such as Marvin, JChem and Standardizer within the open-source KNIME workflow environment. The KNIME platform provides a modular environment to visually create data flows, analyse and build predictive models. The JChem Extensions contain some nodes that are free of charge for general use. These nodes are called Marvin Family Nodes which include a set of nodes for structure conversion, Marvin Sketch , Marvin View and Marvin Space which offer sophisticated rendering capabilities for chemical structures. 

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