GeneNotes – A novel information management software for biologists

We developed an 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 supported 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: http://bayes.fas.harvard.edu/genenotes/ webcite.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.In a genome-wide profiling project, researchers usually select many sets of genes (or ESTs) for further investigation based on the computational analyses of the experimental data. For example, a set of genes is selected because they are clustered together based on their mRNA levels. To generate or support biologically meaningful hypotheses, researchers need to selectively and systematically collect information about the genes/ESTs from various sources. For example, huge amount of gene annotations have been accumulated over decades in distributed databases. In addition, there are plenty of online computational tools (e.g., BLAST [1], TMHMM [2], MEME [3], etc.) that can be customized to generate invaluable information complementary to the local computational analyses of researchers. Most databases and online computational tools require a direct human involvement. Somet