Bioinformatics applications on-demand - standalone update-free bioinformatics application (Apr/24/2008 )

http://www.genenformics.com/download.html

BioGadgets
We are developing BioGadgets, a cluster of standalone applications which have explicit function names, like Gene2GO and SeqLoc2Snp.

Via backends of NCBI databases, BioGadgets are spontaneously concurrent with the latest annotation, which ensure its seamless and targeted data retrieval and processing.

BioGadgets Windows Cygwin Manpage Source
SeqLoc2Gene- Find Entrez Gene in any loci, i.e, regions in chromosomes, contigs, clones, or mRNA. download download manpage Original
SeqLoc2Cd - Find known coding regions in given loci, i.e, regions in chromosomes, contigs, clones or mRNA. download download manpage Original
SeqLoc2Snp - Find SNPs in given genomic loci, i.e, regions in chromosomes, contigs or clones. download download manpage Original
RefSeq2Gene- Find corresponding GeneIds and genomic loci for a set of RefSeq mRNA download download manpage Original
Snp2Gene- Find genes flanking a given SNP download download manpage Original
Gene2GO - Find GO terms for NCBI Entrez GeneId(s). Automatically synchronized with NCBI Entrez Gene Database. download download manpage Original
Gene2KEGG - Find KEGG pathways for NCBI Entrez GeneId(s). Automatically synchronized with NCBI Entrez Gene Database. download download manpage Original
id1_fetch - the fastest tool to access NCBI nucleotide and protein databases. download manpage NCBI
UTRGrabber - Output RefSeq mRNAs' 5' and/or 3' UTR in FASTA format download download manpage Original
SeqLoc2Fasta - Retrieve sequence for GenBank nucleotide/protein download download manpage Original

Great tools...i like them, but in my opinion using the KEGG API and Ensembl API is more fixable than UTRGrabber and Gene2KEGG.
i think of this work as a good start for more sophisticated software packages, now a days molecular biology labs needs GUI to make there life easier.
my be i don't have the experience that you have, my domain is computational identification of microRNA genes and targets, but i think we may have some collaboration if you are interested.