Ensembl Mirror (being developed in collaboration with FutureSoft Corp. MI, and Oakland University MI, available at http://genomes.biosci.wayne.edu)

Ensembl is a joint project between EMBL - EBI and the Sanger Centre to develop a software system which produces and maintains automatic annotation on eukaryotic genomes. This is our mirror site which we maintain at our Center. Additional tools and capabilities will be added.

Onto Express (Licensed to Open Channel Software unlimited use of version 1 available at http://www.openchannelfoundation.org/projects/Onto-Express)

Using strings of accession or cluster identification numbers, Onto-Express searches the public databases and returns tables that correlate expression profiles with the cytogenetic gene locations, the biochemical and molecular functions, the biological processes, cellular components and cellular roles of the translated proteins.

BioMerge Discovery Tools (developed in collaboration with Dept. of Computer Science,
Sun Microsystems and Bio Discovery)

The BioMerge software system is a powerful multi-platform client/server based informatics solution for accelerating discovery. The software is a comprehensive relational database system available for storing and managing genomic and proteomic information on an enterprise-wide
basis.

SQL*GT (In development with WSU Proteomics Node)
SQL*GT is being developed to track ~11,000 yeast clones to assess protein interactions. This data will then be used to build a protein interaction map.

http://www.bch.msu.edu/labs/kuhn/web/software.html
Software Distributed by the Protein Structural Analysis and Design Lab

GP3: GenePix (pdf file) post-processing program for automated analysis of raw microarray data
M.R. Fielden, R.G. Halgren, E. Dere and T.R. Zacharewski

This is an automated and customizable program to correct, filter and normalize raw microarray data captured using GenePix, a commonly used microarray image analysis application.

Cukmody (MD program for proteins developed by R. I. Cukier,
http://www.cem.msu.edu/~cukier/)

Cukmody does Molecular Dynamics (MD) simulations on proteins, cofactors and solvent for fairly large systems. Used for mechanistic studies of enzyme catalysis, and studies of proton transfer and translocation in proteins.

SLIDE (Developed by P. C. Sanschagrin, M. I. Zavodszky, and L. A. Kuhn, available for licensing to academic and commercial researchers at http://www.bch.msu.edu/labs/kuhn/web/software.html)

SLIDE (Screening for Ligands by Induced-fit Docking, Efficiently) uses multi-stage indexing to identify drug binding sites in proteins. SLIDE can screen 100,000 compounds within 1-2 days.

EST Library Browser (Developed by M. D. Larson, R. G. Halgren, and C. Wilkerson, http://genomics.msu.edu)

The library browser allows one to conduct digital northerns to examine changes in gene expression between different tissues or following specific treatments. ESTs obtained from various cDNA libraries are grouped according to gene function. The relative expression of each EST is then graphically displayed according to library origin and functional category.

BLAST Report (Developed by R. G. Halgren, M. D. Larson, and C. Wilkerson, http://genomics.msu.edu)

Part of our EST analysis pipeline, the BLAST Report tool reduces several hundred page Blast reports to several page summaries in an Excel or HTML (Web) format that include external links to the complete blast records and to genes with the most significant similarity matches.

CIT: Cluster Identification Tool (CIT)
http://www.vai.org/vari/bioinformatics.htm
A program that assists in the analysis of microarray gene expression data by identifying differentially expressed clusters of genes based on pre-defined sample parameters. In order to facilitate compatibility, CIT was designed as a companion to the widely used gene expression analysis software CLUSTER and TREEVIEW.

SPIN: Shared Pathology Informatics Network
http://www.sharedpath.org
A project that involves hospitals from West Michigan. The System stores catalogs paraffin blocks that are older than 5 years and ordinarily would be destroyed. Currently the archive holds approximately 150,000 tissue samples/paraffin blocks. They are not linked to any personal identifiers or name and there is limited demographic information available. The demographic information is limited to age, sex, and diagnosis. Samples will be used in cellular and molecular protocols approved by VAI’s Internal Review Board (IRB). Publication: Resau JH, Kort EJ, Campbell B, Hudson R, Buckner B. A Shared Pathology Informatics Network. Abstract presented at Experimental Biology, March 31-April 1, 2001.

Tissue Acquisition System (TAS)
Users utilize a web based interface for entering descriptive information and searching for tissue samples that meet specific criteria. The interface has the ability to facilitate online requests for tissues from both internal and external research projects. We have also developed a Pocket PC (handheld) based version of the TAS software named “Frostbite” that enables users to move about freely and retrieve information regarding tissue location and descriptive data. This information is synchronized each time a user docks the device to a PC. With the use of a bar-coding attachment for the pocket PC users can also scan the specimen bar-code and instantly retrieve information regarding the tissue.

OligoArray, Dr. Jean-Marie Rouillard
(http://berry.engin.umich.edu/oligoarray/index.html)
This oligo-nucleotide design tool allows researchers to design oligo’s from their organism’s genome sequence. The oligo’s can then be manufactured and spotted on microarrays for gene expression analysis.

PRIME
(http://prime.proteome.med.umich.edu/)
PRIME, a Proteome Research Information Management Environment, is a web-based resource for tracking and managing proteomics data, developed in Phil Andrews lab with the Michigan Proteome Consortium.