Weill Cornell Medicine Samuel J. Wood Library

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Bioinformatics Software

This page provides access to all bioinformatics software. Click on a subject area to view available software. Click on the software name to view details, register for update alerts, download, or obtain a license.


Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. Cytoscape core distribution provides a basic set of features for data integration, analysis, and visualization. Additional features are available as Apps (formerly called Plugins). Apps are available for network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases. They may be developed by anyone using the Cytoscape open API based on Java™ technology and App community development is encouraged. Most of the Apps are freely available from Cytoscape App Store.

Information links

System requirements

Java

Library Access

This software is installed on the library computer lab PCs.

Costs and fees

This software is open source and can be freely downloaded using the link below.

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Agilent's GeneSpring provides powerful, accessible statistical tools for intuitive data analysis and visualization. Designed specifically for the needs of biologists, GeneSpring offers an interactive environment that promotes investigation and enables understanding of Transcriptomics, Genomics, Metabolomics, Proteomics and NGS data within a biological context. GeneSpring allows you to quickly and reliably identify targets of interest that are both statistically and biologically meaningful.

Information links

System requirements

Windows,Mac, or Linux

Costs and fees

This software is available at no cost to WCM faculty, staff and students.

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IPA is a web-based software application for the analysis, integration, and interpretation of data derived from 'omics experiments, such as RNAseq, small RNAseq, microarrays including miRNA and SNP, metabolomics, proteomics, and small scale experiments that generate gene and chemi- cal lists. Powerful analysis and search tools uncover the significance of data and identify new targets or candidate biomarkers within the context of biological systems.

Information links

System requirements

Windows or Mac

Costs and fees

This software is available at no cost to WCM faculty, staff and students.

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KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.
Access to the FTP database is freely available, by accessing ftp.bioinformatics.jp from the WCM network.

Information links

System requirements

Costs and fees

This software is available at no cost to WCM faculty, staff and students.

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DNASTAR's Lasergene Molecular Biology Suite is our comprehensive package of molecular biology software, meeting all of your sequence analysis needs. Supported workflows include performing multiple and pairwise sequence alignments, identifying genes, assembling contigs of Sanger sequences, creating virtual clones, designing primers, and more.

Information links

System requirements

Windows,Mac, or Linux

Costs and fees

This software is available at no cost to WCM faculty, staff and students.

Request software service from the library

Find related software by function

RStudio is an integrated development environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.

Information links

System requirements

Windows,Mac, or Linux

Costs and fees

This software is open source and can be freely downloaded using the link below.

Request software service from the library

Find related software by function


CLC Genomics Workbench allows users to analyze and visualize nexg generation sequencing (NGS) data. CLC Genomics Workbench supports the complete resequencing pipeline for detecting and comparing genetic variants.

Information links

System requirements

Costs and fees

This software is not currently licensed by ITS. If you would like to share the licensing costs of this product with other interested users, please register your name using the link below.

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Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution. Available through the bioconductor package in R

Information links

System requirements

R or Anaconda

Costs and fees

This software is open source and can be freely downloaded using the link below.

Request software service from the library

Find related software by function

DNASTAR's Lasergene Molecular Biology Suite is our comprehensive package of molecular biology software, meeting all of your sequence analysis needs. Supported workflows include performing multiple and pairwise sequence alignments, identifying genes, assembling contigs of Sanger sequences, creating virtual clones, designing primers, and more.

Information links

System requirements

Windows,Mac, or Linux

Costs and fees

This software is available at no cost to WCM faculty, staff and students.

Request software service from the library

Find related software by function

RStudio is an integrated development environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.

Information links

System requirements

Windows,Mac, or Linux

Costs and fees

This software is open source and can be freely downloaded using the link below.

Request software service from the library

Find related software by function


Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. Cytoscape core distribution provides a basic set of features for data integration, analysis, and visualization. Additional features are available as Apps (formerly called Plugins). Apps are available for network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases. They may be developed by anyone using the Cytoscape open API based on Java™ technology and App community development is encouraged. Most of the Apps are freely available from Cytoscape App Store.

Information links

System requirements

Java

Library Access

This software is installed on the library computer lab PCs.

Costs and fees

This software is open source and can be freely downloaded using the link below.

Request software service from the library

Find related software by function

MacVector provides numerous functions for DNA and protein analysis, including sequence editing, primer design, internet database searching, protein analysis, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, and agarose gel simulation.

Information links

System requirements

Mac only

Costs and fees

The licensing cost for this product is administered by the library. To view costs, or acquire a license, please use the link below.

Request software service from the library

Find related software by function

RStudio is an integrated development environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.

Information links

System requirements

Windows,Mac, or Linux

Costs and fees

This software is open source and can be freely downloaded using the link below.

Request software service from the library

Find related software by function


Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. It has two releases each year, 1296 software packages, and an active user community.

Information links

System requirements

R

Costs and fees

This software is open source and can be freely downloaded using the link below.

Request software service from the library

Find related software by function

Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization. Cytoscape core distribution provides a basic set of features for data integration, analysis, and visualization. Additional features are available as Apps (formerly called Plugins). Apps are available for network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases. They may be developed by anyone using the Cytoscape open API based on Java™ technology and App community development is encouraged. Most of the Apps are freely available from Cytoscape App Store.

Information links

System requirements

Java

Library Access

This software is installed on the library computer lab PCs.

Costs and fees

This software is open source and can be freely downloaded using the link below.

Request software service from the library

Find related software by function

R is a free software environment for statistical computing and graphics. It compiles and runs on a wide variety of UNIX platforms, Windows and MacOS.

Information links

System requirements

Windows,Mac, or Linux

Library Access

This software is installed on the library computer lab PCs.

Costs and fees

This software is open source and can be freely downloaded using the link below.

Request software service from the library

Find related software by function

RStudio is an integrated development environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.

Information links

System requirements

Windows,Mac, or Linux

Costs and fees

This software is open source and can be freely downloaded using the link below.

Request software service from the library

Find related software by function


MacVector provides numerous functions for DNA and protein analysis, including sequence editing, primer design, internet database searching, protein analysis, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, and agarose gel simulation.

Information links

System requirements

Mac only

Costs and fees

The licensing cost for this product is administered by the library. To view costs, or acquire a license, please use the link below.

Request software service from the library

Find related software by function

RStudio is an integrated development environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.

Information links

System requirements

Windows,Mac, or Linux

Costs and fees

This software is open source and can be freely downloaded using the link below.

Request software service from the library

Find related software by function


MacVector provides numerous functions for DNA and protein analysis, including sequence editing, primer design, internet database searching, protein analysis, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, and agarose gel simulation.

Information links

System requirements

Mac only

Costs and fees

The licensing cost for this product is administered by the library. To view costs, or acquire a license, please use the link below.

Request software service from the library

Find related software by function

RStudio is an integrated development environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.

Information links

System requirements

Windows,Mac, or Linux

Costs and fees

This software is open source and can be freely downloaded using the link below.

Request software service from the library

Find related software by function


RStudio is an integrated development environment (IDE) for R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.

Information links

System requirements

Windows,Mac, or Linux

Costs and fees

This software is open source and can be freely downloaded using the link below.

Request software service from the library

Find related software by function


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