Supplemental Material

   Open Source

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Software - Open Source:

The Bioinformatics Group releases software under two separate licensing methods. This page links to open source software released under the GNU general public license (GPL).
For proprietary software, click here.

Automated Sequence Annotation Pipeline (ASAP): Bioinformatics 19(5): 675–676, 2003.
Now Available - Version II
ASAP is designed to ease routine investigation of new functional annotations on unknown sequences, such as expressed sequence tags (ESTs), through querying of web-accessible databases. A simple database is used to store query formats and parameters, as well as information for parsing data from websites.

BeoBLAST: Bioinformatics 18:765-766, 2002.
BeoBLAST is a package for performing multiple simultaneous BLAST and PSI-BLAST runs on a Beowulf cluster.

CGI-Applet Image Viewing System:
This is a linked CGI and applet system that enables users to retrieve JPEG images and adjust contrast and brightness allowing images to be viewed in browsers on multiple platforms despite different monitor responses and settings.

ClutrFree: Bioinformatics 20:2869-2871, 2004.
ClutrFree is a cluster viewer package available as a Java application. ClutrFree provides essentially the ability to compare microarray clusters issued from different experiments, i.e. the same algorithm used with different parameters or different algorithms. ClutrFree features a procedure to construct a tree from those clusters to infer which ones are more stable among different experiments. Also, ClutrFree displays genes and their memberships along with annotations and ontology. Source code, pre-compiled bytecode, documentation and test datasets are provided.

CSImage is a package for viewing and manipulating four dimensional spectroscopic data sets and linked images. The system is coded in Java and includes a number of open source classes which handle spectrum and image manipulation, zooming, linking of images and spectra, voxel shifting and interactive phasing for NMR spectral data sets. The system was created using design patterns allowing for easy addition of functionality.

Flow Cytometry Laboratory Information Management System (FlowLIMS):
The Flow Cytometry Laboratory Information Management System (FlowLIMS) is a web-accessed software system that enables users to create experimental protocols for flow cytometers. Additionally, the Flow LIMS allows users to organize protocols and results into projects, attach supplementary files, and search the LIMS archive.

Functional Genomics Data Pipeline (FGDP): Bioinformatics 20(2):282-283, 2004.
The functional genomics data pipeline (FGDP) is a Java-based, microarray data analysis system. The FGDP provides an integrated, extendable analysis environment permitting multiple, simultaneous analyses to be automatically performed and provides a web server and interface for presenting results.

ImageLIMS (beta version with minimal documentation):
The imageLIMS is a web-based Laboratory Information Management System for annotating, storing, and accessing image data.

LS-NMF: BMC Bioinformatics 2006, 7:175
LSNMF is a modified version of NMF (non-negative matrix factorization), it focus on gene expression patterns analysis on microarray datasets. The major improvement of LSNMF algorithm over NMF is that it incorporate uncertainty estimates into the update rules, so it is much more stable over the possible noise in the datasets, and it also more sensitive to the real signals. LSNMF is implemented in LAM/MPI-based parallelized C++, it was designed for running on Beowulf clusters (the desktop version is also available).

Telometric: BioTechniques 31:1614-19, 2001.
Telometric is a software package available as an NIH Image macro or as a standalone Java application. The package allows users to assess the size and distribution of telomeric fragments from digested DNA using ubiquitously available agarose gels. The hybridization from multiple matching telomeric probes is corrected for and simple statistics are calculated for each lane on a gel. A User's Guide is included in the download.

WaveRead: Journal of Biomedical Informatics In Press.
(Software will be available for downloading after publication)
WaveRead is an algorithm for automated quantitation of microarray images. The algorithm handles rotated images (up to 45°), automatic gridding, background correction, and spot irregularities. The algorithm will be available following publication.