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Indiana University
Biology

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Genome Informatics Lab

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Software

Software publications by Don Gilbert 2002. BioGridRunner, a preliminary bioinformatics client application for data grid computing. http://iubio.bio.indiana.edu/ grid/runner

1995 - 1998. SeqPup, biosequence editor & analysis software for for molecular
biology, available for common operating systems. Freely available, open source in C++ and Java. http://iubio.bio.indiana.edu/ soft/molbio/seqpup/

1997 - 1999. Phylodendron, software for phylogenetic tree drawing in Java. http://iubio.bio.indiana.edu/ soft/molbio/java/apps/trees/ and http://iubio.bio.indiana.edu/treeapp/

1996. loopDloop in Java, for drawing RNA secondary structure.
http://iubio.bio.indiana.edu/ soft/molbio/java/apps/loops/

1996. Bopper, a new Internet biocomputing office protocol for client-server
data analysis. This employs CORBA client-server protocols and works with the SeqPup
sequence analsysis package.
ftp://iubio.bio.indiana.edu/ util/dclap/source/bopper.tar.gz

1996. Portable FlyBase server available for Drosophila data.
http://flybase.bio.indiana.edu/ docs/Portable-server/

1996. Fruit flies in your Java: a Java mapplet for Drosophila genome map
browsing. Bionet.Software, Feb 1996. . See also
http://flybase.bio.indiana.edu/ maps/java/

1995. SRS-FastA: Similarity searches of Genbank subsets.
http://iubio.bio.indiana.edu/srsfasta/

1995. Genbank searches at IUBio archive
http://iubio.bio.indiana.edu/ Genbank-Sequences/

1995. New Sequence Retrieval Service (SRS) node at IUBio, Indiana
http://iubio.bio.indiana.edu/srs/srsc

1994. DCLAP, a C++ class application library package for bioscience applications (cross-platform)
ftp://iubio.bio.indiana.edu/ util/dclap/

1992. Booleans, partial words and other WAIS modifications in biology data searches. ftp://iubio.bio.indiana.edu/ util/wais/

1992 IUBio Archive through Internet Gopher. Feb. 1992. .
gopher://iubio.bio.indiana.edu/

1992. SeqApp, a biological sequence editor and analysis program for Macintosh computers.
ftp://iubio.bio.indiana.edu/ molbio/seqapp/

1992. GopherApp, an Internet Gopher client for Macintosh computers.
ftp://iubio.bio.indiana.edu/ util/gopher/gopherapp/

1992. loopDloop, a Macintosh application for drawing and editing RNA secondary
structure displays. August 1992.
ftp://iubio.bio.indiana.edu/ molbio/loopdloop/

1990. GenBank Search, a Hypercard stack for network searching and fetching sequences from the GenBank e-mail server. October 1990.
ftp://iubio.bio.indiana.edu/ molbio/mac/gbsearch-ncbi.hqx

1990. MulFold, a Macintosh application, port of Michael Zuker's MFOLD for estimating RNA secondary structure. October 1990.
ftp://iubio.bio.indiana.edu/ molbio/mac/mulfold.hqx

1990. TreeDraw Deck, a Hypercard implementation of Joseph Felsenstein's phylogenetic tree drawing routines. June 1990.
ftp://iubio.bio.indiana.edu /molbio/mac/treedraw-old.hqx

1989. ReadSeq, C and Pascal routines for converting among nucleic acid & protein sequence file formats, suitable for various computers.
ftp://iubio.bio.indiana.edu /molbio/readseq/

1989. GelFragSizer, a Macintosh Hypercard stack for calculating and plotting restriction fragment sizes for molecular biology.
ftp://iubio.bio.indiana.edu/ molbio/mac/gelfragsizer.hqx

1989. Enzyme Kinetix, a Macintosh Hypercard stack for calculating and plotting enzyme kinetics for biochemistry.
ftp://iubio.bio.indiana.edu/ molbio/mac/enzymekinetics.hqx

1989. Dotty Plotter, a Macintosh application for dot plot sequence comparisons.
ftp://iubio.bio.indiana.edu/ molbio/mac/dottyplot.hqx

1989. HyperGCG, an unfinished Hypercard front-end for using molecular biology software, especially GCG, on VMS Vaxes.
ftp://iubio.bio.indiana.edu/ molbio/mac/hypergcg.hqx