Click on the link in the Application Name column for more info from the vendor's website.
| Application Name | Description | Availability |
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SEQUENCE ANALYSIS SOFTWARE Return to Top |
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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 |
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MICROARRAY ANALYSIS SOFTWARE Return to Top |
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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 |
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MOLECULAR MODELING SOFTWARE Return to Top |
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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) |