Bioinformatics / Data mining protocols and methods

Technique / Bioinformatics / Data mining

Mass Spectrometry Data Analysis new protocol
The mass spec data analysis demonstration can be downloaded in word doc file. This example demonstrates a number of ways to classify mass spectrometry data and shows some statistical tools that can be used to look for potential disease markers. The data in thi ...

Data Mining and Text Mining for Bioinformatics European Workshop 2003 review
This page contains the papers in pdf format presented at the European Workshop on Data Mining and Text Mining for Bioinformatics, held at the European Conference on Machine Learning and the European Conference on Principles and Practice of Knowledge Discovery ...

Data Mining and Text Mining for Bioinformatics European Workshop 2004 review
Second European Workshop on Data Mining and Text Mining for Bioinformatics held in 24 September 2004, Pisa, Italy Table of content Cover, table of contents, and invited talks by Yves Moreau and Alfonso Valencia. * Hong Chai and Carlotta Domenicon ...

Dragon TF Association Miner new software
A free web data mining tool by Pan H et al., Institute for Infocomm Research, Singapore. Dragon TF Association Miner: a system for exploring transcription factor associations through text-mining. Pan H, Zuo L, Choudhary V, Zhang Z, Leow SH, Chong FT, Hua ...

FigSearch: a figure legend indexing and classification system new software
A free figure legend mining tool by Liu F et al., Institute for Cancer Research, The Norwegian Radium Hospital. FigSearch: a figure legend indexing and classification system. Liu F, Jenssen TK, Nygaard V, Sack J, Hovig E. Department of Tumor Biology, ...

Data mining in bioinformatics using Weka new software
A free java software for data mining by Frank E et al., University of Waikato, New Zealand. Weka is a collection of machine learning algorithms for data mining tasks. The algorithms can either be applied directly to a dataset or called from your own Java co ...

Genepredictions database for protein function prediction new software
The "Genepredictions" database for protein functional predictions is created by Ross King et al., University of Wales, UK. It is intended to act as an open repository for predictions for any organism. Reference: Confirmation of data mining based predicti ...

BioRAT: extracting biological information from full-length papers new software
A free software for text mining by Corney DP et al., University of college, UK. A large and growing amount of information is published every year in scientific journals. In the biomedical field, there are thousands of journals, each publishing many issues annu ...

BITOLA - Biomedical Discovery Support System software
BITOLA is an interactive literature-based biomedical discovery support system (available in either cgi-bin version or java applet version). The purpose of the system is to help the biomedical researchers make new discoveries by discovering potentially new rela ...

MILANO - Microarray Literature-based Annotation software
This program was written by Ran Rubinstein at The Hebrew University of Jerusalem, Israel. It performs automatic searches in PubMed or the GeneRIF collection for articles containing co-occurrences of search terms with a list of genes (e.g. from a microarray exp ...

iProLINK: integrated Protein Literature, INformation and Knowledge software
iProLINK is an integrated protein resource for literature mining with special focuses on bibliography mapping, annotation extraction, protein named entity recognition, and protein ontology development. Reference: iProLINK: an integrated protein resource ...

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09-May-2008 02:33 am

Related new papers and reviews

RETINOBASE: a web database, data mining and analysis platform for gene expression data on retina.

ABSTRACT: BACKGROUND: The retina is a multi-layered sensory tissue that lines the back of the eye and acts at the interface of input light and visual perception. Its main function is to capture photons and convert them into electrical impulses that travel along the optic nerve to the brain where they are turned into images. It consists of neurons, nourishing blood vessels and different cell types, of which neural cells predominate. Defects in any of these cells can lead to a variety of retinal diseases, including age-related macular degeneration, retinitis pigmentosa, Leber congenital amaurosis and glaucoma. Recent progress in genomics and microarray technology provides extensive opportunities to examine alterations in retinal gene expression profiles during development and diseases. However, there is no specific database that deals with retinal gene expression profiling. In this context we have built RETINOBASE, a dedicated microarray database for retina. Description RETINOBASE is a microarray relational database, analysis and visualization system that allows simple yet powerful queries to retrieve information about gene expression in retina. It provides access to gene expression meta-data and offers significant insights into gene networks in retina, resulting in better hypothesis framing for biological problems that can subsequently be tested in the laboratory. Public and proprietary data are automatically analyzed with 3 distinct methods, RMA, dChip and MAS5, then clustered using 2 different K-means and 1 mixture models method. Thus, RETINOBASE provides a framework to compare these methods and to optimize the retinal data analysis. RETINOBASE has three different modules, "Gene Information", "Raw Data System Analysis" and "Fold change system Analysis" that are interconnected in a relational schema, allowing efficient retrieval and cross comparison of data. Currently, RETINOBASE contains datasets from 28 different microarray experiments performed in 5 different model systems: drosophila, zebrafish, rat, mouse and human. The database is supported by a platform that is designed to easily integrate new functionalities and is also frequently updated. CONCLUSIONS: The results obtained from various biological scenarios can be visualized, compared and downloaded. The results of a case study are presented that highlight the utility of RETINOBASE. Overall, RETINOBASE provides efficient access to the global expression profiling of retinal genes from different organisms under various conditions.