Database Projects

Current Database Projects

The Minnesota Supercomputing Institute hosts and develops numerous databases. Below is a list of representative projects. They include public and project-specific databases that serve various fields. These include:

  1. Flat file public databases (genbank, PDB, Uniprot),
  2. NCBI BLAST sequence databases (nt, nr, swissprot etc.),
  3. Genome databases (Human, Mouse, Rat, Drosophila, Yeast, E. coli etc.)
  4. mySQL databases such as ensembl, gene ontology, ucsc genome.
  5. mySQL and Oracle databases for user-specific projects.

Many of these databases are integrated into specific software for researchers. Public databases are updated regularly. MSI staff provide hardware, software, and advanced user support for maintaining and using these databases.

MSI Developed and Hosted Database Projects

BMGC Data System

DBMS:
UNIX and files
Client:
Data Distribution system at the Biomedical Genomics Center
Phase:
Operation

Description

A Web-based system to perform QA checks at the Biomedical Genomics Center to University and to release data to the research community.

 

Sanger and 454 Sequencing Data System

URL:
http://www.genomes.umn.edu
DBMS:
UNIX and files
Client:
Sequencing Facility at the Biomedical Genomics Center
Phase:
Operation

Description

This Web-based system uses x500 authorization for distribution of Sanger DNA sequencing, Roche/454 GSFLX sequencing data, and SAGE data at the Biomedical Genomics Center.

Computational Proteomics and Mass Spectrometry System

URL:
https://tropix.msi.umn.edu
DBMS:
MySQL, UNIX and Files
Client:
The Center for Mass Spectrometry and Proteomics (CMSP)
Phase:
Operation

Description

This Web-based system is used for distribution of mass spectrometry and proteomics data at the Center for Mass Spectrometry and Proteomics at the University of Minnesota. This system is also integrated with open-source and commerical search engines for streamline of proteomics data search.

 

Laboratory Data Management System

URL:
https://ldms.msi.umn.edu/wackettldms
DBMS:
File system, Oracle
PI:
Larry Wackett, Biochemistry
Phase:
Operation

Description

The Laboratory Data Management System (LDMS) is a Web application for lab research data storage, secure data transfer, and data management. The data is transfered and stored as various flat file formats with associated metadata in an Oracle database.

The Laboratory Data Management System

URL:
https://ldsm.msi.umn.edu/dunnyldms
DBMS:
File system, Oracle
PI:
Garry Dunny, Microbiology
Phase:
Operation

Description

The Laboratory Data Management System (LDMS) is a Web application for lab research data storage, data secure transfer, and data management. The data is transfered and stored as various flat file formats associated with information in Oracle database.

Laboratory Data Management System

URL:
https://ldms.msi.umn.edu/hallldms
DBMS:
File system, Oracle
PI:
Jennifer Hall, Medicine
Phase:
Operation

Description

The Laboratory Data Management System (LDMS) is a Web application for lab research data storage, data secure transfer, and data management. The data is transfered and stored as various flat file formats. Associated metadata is stored in an Oracle database.

MSI Hosted Database Projects

 

Stanford Microarray Database Local Installation

URL:
http://www.smd2.msi.umn.edu/
DBMS:
Oracle
Phase:
Operation

Description

This database local installation of SMD. It has been used for storing microarray experiment data.

Cedar Creek Ecosystem Science Reserve with Data Document System

URL:
http://www.cedarcreek.umn.edu
http://www.lter.umn.edu
Host/Lab
SDML
DBMS:
Oracle and mySQL
Phase:
Operation

Description

This is National Science Foundation (NSF) Long Term Ecological Research Site. Databases were used for organizing and distributing decades of Ecological experiment data to Ecology research community.

National Center for Earth-Surface Dynamics

URL:
http://www.nced.umn.edu
Host/Lab
SDML
DBMS:
mySQL
Phase:
Operation

Description

The NSF Science and Technology Center. NCED is to catalyze development of an integrated predictive science of the process shaping the surface of the earth in order to transform management ecosystems, resources, and land use.

 

Commercial Web-Database-Applications Hosted and Supported at MSI

GeneData Expressionist for Microarray Data Analysis

URL:
http://dbexpr.msi.umn.edu:16000
Client:
Microarray especially Affymetrix Users at the University of Minnesota
Vendor:
GeneData Inc.

Description

GeneData Expressionist is a comprehensive microarray data analysis system. It consists of three closely integrated modules:

Refiner:
A workflow for data loading and quality assurance.
CoBi:
Oracle database for expression data and annotation information storage and management.
Analyst:
Statistic tools for data analysis.

MSI staff provides support for this this software including the genechip library, maintenance, hardware, and software, client access, and utorials. It was widely used by University of Minnesota microarray community.