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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| BIOBASE TRANSFAC v.9.4 | Web based gene transcription factor database | Citrix › Sequence Analysis › Biobase |
| BWA | Burrows-Wheeler Aligner is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. | Local installation on informatics LINUX servers |
| EMBOSS v6.2 with EMBOSS Explorer | Web based suite of integrated open source sequence analysis software hosted on COH HPC LINUX clusters | Local installation on COH HPC LINUX clusters |
| Integrative Genomics Viewer v1.4.2 | The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated datasets. It supports a wide variety of data types including sequence alignments, microarrays, and genomic annotations. | Citrix › Sequence Analysis › IGV v142 |
| Invitrogen Labshare 3.0 | Enable researchers to store and manage Vector NTI dataset in a secure central relational database | Citrix › Sequence Analysis › Labshare |
| MacVector v.11.1.1 | Sequence analysis software for Mac users | Local user desktop installation by request |
| SoftGenetics NextGENe | Next Generation Sequencing software | BIC Workstation Citrix › Sequence Analysis › NextGene |
| Oligo v.6.71 | Oligonucleotides design for PCR, DNA sequencing, site-directed mutagenesis, and various hybridization applications | Citrix › Sequence Analysis › Oligo |
| 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 |
Citrix › Sequence Analysis › R |
| Sequencher v.4.8 | DNA sequence assembly and analysis software | Citrix › Sequence Analysis › Sequencher |
| SeqLab | SeqLab is the graphical user interface for the Wisconsin Package. | Citrix › Sequence Analysis › SeqLab |
| SeqWeb v.3.1.2 | Sequence analysis suite, including 140 application programs and 11 integrated databases | Citrix › Sequence Analysis › SeqWeb 3 |
| 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 |
Link |
| Solar v.4.2.7 | Sequential Oligogenic Linkage Analysis software | Local installation on informatics LINUX servers |
| Staden Package v.2.0.0 | Sequence handling and analysis software | Local installation on informatics LINUX servers |
| UCSC Genome Browser | Updated UCSC Genome Browser with Human (hg19) and Mouse (mm9) database | Link |
| Invitrogen Vector NTI suite v.10 | Sequence analysis software | Citrix › Sequence Analysis › Vector NTI |
| MICROARRAY ANALYSIS SOFTWARE Return to Top |
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| BIOBASE TRANSFAC v.9.4 | Web based gene transcription factor database | Citrix › Microarray Analysis › Biobase |
| Gene Cluster 3.0 | Cluster 3.0 provides a Graphical User Interface to access to the clustering routines. | Citrix › Microarray Analysis › Cluster |
| Agilent GeneSpring GX v7.3.1 | Performs Agilent expression data analysis suite | Citrix › Microarray Analysis › GeneSpring 73 |
| Agilent GeneSpring GX v11 | Performs Agilent expression data analysis suite | Citrix › Microarray Analysis › GeneSpring GX |
| Integrative Genomics Viewer v1.4.2 | The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated datasets. It supports a wide variety of data types including sequence alignments, microarrays, and genomic annotations. | Citrix › Microarray Analysis › IGV v142 |
| 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 | Citrix › Microarray Analysis › ImaGene 7_5 |
| 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 |
| Ingenuity Pathways Analysis v7.5 | Web application to access biological function literature and pathway database | Citrix › Microarray Analysis › Ingenuity Pathways |
| MatLab v.R2009a | A numerical computing environment and programming language for data visualization and data analysis | BIC Workstations Citrix › Microarray Analysis › Matlab |
| OligoArray v.2.0 | Genome-scale oligonucleotide design software for microarrays | Citrix › Microarray Analysis › Oligo |
| Partek Discovery Suite | Data analysis and visualization with classical statistics tools to solve complext pattern analysis and recognition problems. | BIC Workstations Citrix › Microarray Analysis › Partek |
| 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 |
Citrix › Microarray Analysis › R |
| Roche NimbleGen SignalMap | SignalMap software is a tool that enables you to visualize NimbleGen array data. SignalMap uses GFF files as an input and provides the capability to handle large data sets for graphically-based browsing, rescaling, analysis, and export of graphical files for publication. | BIC Workstations Citrix › Microarray Analysis › Signal Map 64 |
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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 |
| AMBER v11 | 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 v. c35b3 | A program for macromolecular simulations, including energy minimization, molecular dynamics and Monte Carlo simulations | Local installation on COH HPC LINUX clusters |
| Cn3D 4.1 | Cn3D simultaneously displays structure, sequence, and alignment, and now has powerful annotation and alignment editing features. | Citrix › Molecular Modeling › Cn3D |
| Accelrys Discovery Studio | Discovery Studio is a life science modeling and simulation suite of applications focused on optimizing the drug discovery process. Discovery Studio makes it easier to examine the properties of large and small molecules, study systems, identify leads and optimize candidates. | Citrix › Molecular Modeling › Discovery Studio |
| HADDOCK v2.1 | 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.7.51 | A sophisticated molecular modeling environment that combines 3D visualization and animation with quantum chemical calculations, molecular mechanics, and dynamics | Citrix › Molecular Modeling › HyperChem 7_5 |
| MatLab v.R2009a | A numerical computing environment and programming language for data visualization and data analysis | BIC Workstations Citrix › Molecular Modeling › Matlab |
| NAMD v2.7b2 | 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) Citrix › Molecular Modeling › Pymol |
| 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 |
Citrix › Molecular Modeling › R |
| Rasmol | Molecular visualization software | Citrix › Molecular Modeling › Rasmol |
| Schrodinger modeling software suite 2010 | 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 |
| Similarity Pipeline | Ligand base Vitural Screening Pipeline | Citrix › Molecular Modeling › Similarity Pipeline |
| TRIPOS SYBYL-X 1.1 | 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) |