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GeneNotes - A novel information management software for biologists

Analyzing microarray data - or even a simple biological network - can get you lost - quick. Tons of genes, tons of synonyms for each, tons of known interactions, with even more being unknown, tons of database with tons of information... and your job is to make sense of this puzzle in a biologically meaningfull way. Applications are being developped to make it all easier, leaving the fun part : biology! GeneNotes is one of them; I didn't have time to try it yet, but it seems like it could help. Nothing revolutionnary judging from the tutorial videos, but still, its a step in the right direction. I encourage you to try it and share your experience in the forum (if you don't want to register) or in the comments section.

Collecting and managing information is a challenging task in a genome-wide profiling research project. Most databases and online computational tools require a direct human involvement. Information and computational results are presented in various multimedia formats (e.g., text, image, PDF, word files, etc.), many of which cannot be automatically processed by computers in biologically meaningful ways. In addition, the quality of computational results is far from perfect and requires nontrivial manual examination. The timely selection, integration and interpretation of heterogeneous biological information still heavily rely on the sensibility of biologists. Biologists often feel overwhelmed by the huge amount of and the great diversity of distributed heterogeneous biological information.

We developed a novel information management application called GeneNotes. GeneNotes is the first application that allows users to collect and manage multimedia biological information about genes/ESTs. GeneNotes provides an integrated environment for users to surf the Internet, collect notes for genes/ESTs, and retrieve notes. GeneNotes is support ed by a server that integrates gene annotations from many major databases (e.g., HGNC, MGI, etc.). GeneNotes uses the integrated gene annotations to (a) identify genes given various types of gene IDs (e.g., RefSeq ID, GenBank ID, etc.), and (b) provide quick views of genes. GeneNotes is free for academic usage. The program and the tutorials are available at:

GeneNotes provides a novel human-computer interface to assist researchers to collect and manage biological information. It also provides a platform for studying how users behave when they manipulate biological information. The results of such study can lead to innovation of more intelligent human-computer interfaces that greatly shorten the cycle of biology research.


Source:BMC Bioinformatics Abstract

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