Software Resources


Click on the link in the Application Name column for more info from the vendor's website.
Application Name Description Availability
SEQUENCE ANALYSIS SOFTWARE
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Accelrys GCG® Wisconsin Package v11.1.3 and SeqWeb v.3.1.2 Sequence analysis suite, including 140 application programs and 11 integrated databases DBI Web Portal
BIOBASE TRANSFAC v.9.4 Web based gene transcription factor database DBI Web Portal
EMBOSS v5.0 with EMBOSS Explorer Web based suite of integrated open source sequence analysis software hosted on COH HPC LINUX clusters -DBI Web Portal
-Local installation on COH HPC LINUX clusters
Invitrogen Vector NTI suite v.10 Sequence analysis software DBI Web Portal
Invitrogen Labshare 3.0 Enable researchers to store and manage Vector NTI dataset in a secure central relational database DBI Web Portal
MacVector v.10.0.1 Sequence analysis software for Mac users Local user desktop installation by request
Oligo v.6.71 Oligonucleotides design for PCR, DNA sequencing, site-directed mutagenesis, and various hybridization applications DBI Web Portal
Sequencher v.4.8 DNA sequence assembly and analysis software -For Window and MAC OS X application
-DBI Web Portal
siRNA Site Selector and Duplex-End Energy Difference Calculator: A web-based application that calculates a theoretical difference in thermodynamic stability of the ends of a siRNA duplex, for optimal siRNA
DBI Web Portal
Solar v.4.0.7 Sequential Oligogenic Linkage Analysis software Local installation on informatics LINUX servers
Staden Package v.1.6.0 Sequence handling and analysis software Local installation on informatics LINUX servers
UCSC Genome Browser Updated UCSC Genome Browser with Human (hg18) and Mouse (mm9) database DBI Web Portal
SoftGenetics NextGENe Next Generation Sequencing software -DBI Web Portal
-BIC Workstation
MICROARRAY ANALYSIS SOFTWARE
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Agilent GeneSpring GX v7.3.1 Performs Agilent expression data analysis suite DBI Web Portal
Ingenuity Pathways Analysis v7.5 Web application to access biological function literature and pathway database DBI Web Portal
ImaGene 7.5 Microarray image analysis tool that automates the time consuming process of measuring and visualizing gene expression data from high-density array images DBI Web Portal
ImaGene 8 Microarray image analysis tool that automates the time consuming process of measuring and visualizing gene expression data from high-density array images BIC Workstations
MatLab v.R2009a A numerical computing environment and programming language for data visualization and data analysis -DBI Web Portal
-BIC Workstations
OligoArray v.2.0 Genome-scale oligonucleotide design software for microarrays DBI Web Portal
Partek Discovery Suite Data analysis and visualization with classical statistics tools to solve complext pattern analysis and recognition problems. -DBI Web Protal
-BIC Workstations
Bioconductor R v.2.5 and Rmpi Statistical computing and graphics package
Includes the Bioconductor package which is used for the analysis of DNA microarray data, and genomic data, such as SAGE, sequence, or SNP data
DBI web Portal
BIOBASE TRANSFAC v.9.4 Transcription factor database DBI Web Portal
MOLECULAR MODELING SOFTWARE
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3D bimolecular structure visualization Academic free software -4 recommended academic downloadable free software, see URL for specific information
-DBI Web Portal
AMBER v9 A bimolecular simulation program used for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to elucidate the structures and energies of molecules Local installation on informatics LINUX server
CHARMM vc32b2 A program for macromolecular simulations, including energy minimization, molecular dynamics and Monte Carlo simulations Local installation on COH HPC LINUX clusters
HADDOCK v2.0 A docking software that makes use of biochemical and/or biophysical interaction data such as chemical shift perturbation data resulting from NMR titration experiments or mutagenesis data Local installation on informatics LINUX server
HyperChem v.8.0 A sophisticated molecular modeling environment that combines 3D visualization and animation with quantum chemical calculations, molecular mechanics, and dynamics DBI Web Portal
NAMD v2.6 A parallel molecular dynamics code for large biomolecular systems. Local installation on COH HPC LINUX clusters
PyMOL A molecular visualization system useful for looking at macromolecular 3D structure and creating molecular animations -Local installation on linux server (Saturn)
-DBI Web Portal
Schrodinger modeling software suite 2007 A molecular modeling suite, including 31 application programs for visualization, homology modeling, docking, and QSAR (network accessible from multiple locations) Local installation on informatics LINUX server
TRIPOS SYBYL v7.3 Cheminformatics tool for structure based and ligand based computer assisted molecular modeling package Local installation on informatics LINUX server
Access to LINUX Molecular Modeling workstations Limited SGI O2 and LINUX workstations for access Currently available in the informatics core lab (Bldg.171 Room 1043)


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