Welcome to the Library's Scientific Software Hub. Here you can find information and access to all the software that is licensed to Weill Cornell Medicine faculty, staff and students, or is freely available. The library is also assisting groups of users who would like to share the licensing costs of specialized software - use the Suggest New Software form to inquire about new software costs or cost sharing. We also offer assistance in gaining access to data through many online repositories. For any questions or issues, please email scisoft@med.cornell.edu.
To view clinical databases, visit our Biomedical Research Database Resources page.
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.
"BioCyc.org is a microbial genome Web portal that combines thousands of genomes with additional information inferred by computer programs, imported from other databases and curated from the biomedical literature by biologist curators. BioCyc also provides an extensive range of query tools, visualization services and analysis software." (Karp et al., 2019)
Biorender is an online graphics tool for building high quality figures for the life sciences. Our institutional account will allow discounted access to all faculty, staff and students. All licenses expire on May 30th of each year regardless of when the license is purchased.
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.
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.
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
LabArchives is a secure, cloud-based electronic lab notebook (ELN) designed for research. This ELN system enables researchers to capture, manage, store, and share information and data. LabArchives facilitates collaboration amongst researchers within a loab, institution, and with external stakeholders.
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.
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.
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.
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.
