Abstract
To support a diverse institutional program of genomics projects, it is often necessary to have an equally diverse and comprehensive software base. Although programs may come from many sources, it is important to make them easily accessible to the user community on a single computing platform. This chapter will outline the strategies for installing programs for a server-based molecular biology software resource, accessed by a large user base. It is assumed that the reader is familiar with basic UNIX commands and concepts, as described in the previous chapters. The approaches discussed here are implemented in the BIRCH system (see Website: http://www.home.cc.umanitoba.ca/~psgendb), but are generally applicable to any centralized multiuser software installation. The important parts of the process are described in either program documentation or UNIX documentation. The tricks and conventions that help to simplify the installation process will also be highlighted. This should give the novice an idea of what to expect before wading through the documentation.
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Suggested Readings
Introduction
Fristensky, B. (1999) Building a multiuser sequence analysis facility using freeware, in: Bioinformatics Methods and Protocols, (Misener, S. and Krawetz, S., eds.), Humana Press, Totowa, NJ, pp. 131–145.
Sobell, M. G. (1995) A Practical Guide to the UNIX System, Benjamin/Cummings Publishing Co., Redwood City, CA.
The Networked Computing Environment
Fristensky, B. (1999) Building a multiuser sequence analysis facility using freeware, in: Bioinformatics Methods and Protocols, (Misener, S. and Krawetz, S., eds.), Humana Press, Totowa, NJ, pp. 131–145.
Compilation
Pearson, W. R. (1999) Flexible sequence similarity searching with the FASTA3 program package, in: Bioinformatics Methods and Protocols, (Misener, S. and Krawetz, S., eds.) Humana Press, Totowa, NJ, pp. 185–219.
Installation
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Fristensky, B. (1986) Improving the efficiency of dot-matrix similarity searches through use of an oligomer table, Nucl. Acids Res. 14, 597–610.
Fristensky, B. (1999) Building a multiuser sequence analysis facility using freeware, in: Bioinformatics Methods and Protocols, (Misener, S. and Krawetz, S., eds.), Humana Press, Totowa, NJ, pp. 131–145.
Smith, S., Overbeek, R., Woese, C. R., Gilbert, W., and Gillevet, P. M. (1994) The Genetic Data Environment: an expandable GUI for multiple sequence analysis, Comp. Appl. Biosci. 10, 671–675. (see Website: http://megasun.bch.umontreal.ca/pub/gde/)
Staden R., Beal, K. F., and Bonfield, J. K. (1999) The Staden Package, in: Bioinformatics Methods and Protocols , (Misener, S. and Krawetz, S, eds.), Humana Press, Totowa, NJ, pp. 115–130.
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Fristensky, B. (2003). Installing Bioinformatics Software in a Server-Based Computing Environment. In: Krawetz, S.A., Womble, D.D. (eds) Introduction to Bioinformatics. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-59259-335-4_16
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DOI: https://doi.org/10.1007/978-1-59259-335-4_16
Publisher Name: Humana Press, Totowa, NJ
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Online ISBN: 978-1-59259-335-4
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