Software Sources

Stahl MT. Open-source software not quite endsville, Drug Discovery Today 2005 10 219-22. 

DeLano WL. The case for open-source software in drug discovery. Drug Discovery Today 2005 10 211-13. 

Dudoit, S., Gentleman, R. C., and Quackenbush, J., Open source software for the analysis of microarray data, Biotechniques, Suppl., 45, 2003. 

J. Wright and A. Wagner, The systems biology research tool Evolvable open source software. BMC Syst. Biol. 2, 55 (2008). 

List of Open Source software for image analysis and statistics and their Web sites... 

In this chapter we discuss two Open Source software we use routinely in our screening facility to analyze high content RNAi and chemical compound screens. With these software we are able to process several terabytes of data with relative ease. 

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. 

Lastly, both CellProfiler and KNIME are easily extendable Open Source software that both have a highly active and fast-growing community since the release of their first versions in 2005 and 2006, respectively, a key for further development and implementation of... 

Betamax system, and Microsoft software (though open source software is perhaps mounting a challenge) (Nye, 2006, pp50-51). 

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. 

PyMOL is useful for viewing molecules and proteins. Because it is an open source architecture, in principal, it is much more scalable for custom applications than closed source software. Although the project has relatively a limited numbers of applications at this early stage, it is envisioned to eventually become a frill molecular modeling platform. Currently it is primarily a visualization package. Three main use cases are currently envisioned first, to visualize molecule (sdfile) or protein (pdf file), second to create a publication quality figure (static content), and third to enable one to use Pymol as one does Powerpoint for generating movies. 

Cytoscape Institute of Systems Biology Open-source software platform for network data integration, analysis, and visualization (http //cytoscape.org/)... 

Real-Time Outbreak and Disease Surveillance (RODS) Project. RODS, which began in western Pennsylvania in 1999, now collects data from emergency departments, urgent care facilities, and clinical laboratories in several states (Wagner et al., 2004). In 2003, the system became available as open-source software, and it is now also in use in several foreign countries (RODS, 2006). 

Open source software (also known as freeware or shareware) is increasingly being incorporated into COTS products. Open source software is developed by informal communities who claim no ownership and refute any accountability for the code. Features and bug fixes emerge out of uncoordinated custom developments of freely available, uncontrolled copies of the source code. There is usually no formal quality umbrella for software development and support hence it is very difficult to demonstrate that such software is fit for purpose. Reverse engineering development documentation from the code and conducting comprehensive testing are likely to be extremely... 

Open Source software must be fully evaluated by the user organization to assess relevant electronic record/signatnre fnnctionality since there is no snpplier acconntable for fnnctionahty definition, product development, or maintenance. Cantion shonld be exercised since it is very difficult to truly demonstrate the trustworthiness of such software in the absence of life-cycle development and support documentation. 

Contracts to supply software are expected to list the documentation to be provided as part of the contracted deliverables. With an externally sourced software product, these generally include... 

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