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)
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
Endnote is a bibliographic management tool for storing and accessing shared references, documents and files. Endnote allows the autmated insertion of citations in MS Word in over 6000 styles. Endnote can retrieve the full text of all articles in your library from freely available sources and the Samuel J. Wood library's subscriptions.
i2b2 enables researchers to discover cohorts of patients using data from EHR systems. Through a point-and-click interface, researchers can build queries drawing from demographics, diagnoses, procedures, medications, and results recorded in Epic, the EHR system of Weill Cornell Physician Organization outpatient clinics (access to data from Eclipsys/Allscripts Sunrise Clinical Manager, the EHR system of NewYork-Presbyterian inpatient units, is planned). i2b2 supports different types of queries of clinical data, including whether clinical concepts occurred at any point in a patient’s medical history, during a particular visit, or in a sequence of events. Using de-identified data, investigators can determine potential cohorts of interest for later obtaining identified or limited data sets with Institutional Review Board (IRB) approval
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.
Microsoft Access is a database management system (DBMS) from Microsoft that combines the relational Microsoft Jet Database Engine with a graphical user interface and software-development tools. MS Access is freely available for WCM ITS-tagged PCs through the Software Center application.
Qualtrics is web based software that allows the user to create surveys and generate reports without having any previous programming knowledge. Qualtrics enables you to do surveys, feedback and polls using a variety of distribution means. Results can be viewed in reports and can be downloaded. Qualtrics allows you to share surveys and results as well as collaborating with other users.
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.
REDCap is a PHP-based system, developed by Vanderbilt University and currently managed and updated through a national consortium, that supports the rapid setup of secure, Web-based study-specific database systems and associated forms. It provides full field validation capabilities (customized to each study), import/export (including export to common statistical packages such as SAS, SPSS and Excel), and file upload/management functions. It includes a complete suite of features to support HIPAA compliance, including a full audit trail, user-based privileges, and integration with the institutional LDAP server. REDCap is available free of charge to any clinical/translational research study being conducted at Weill Cornell or any of its CTSA partner institutions. Many studies can be supported with REDCap alone. For those studies that require a higher level of complexity and/or customization than is readily supported by REDCap, programmers experienced in clinical research data management are available through the Core Informatics Group. Depending upon the nature of the study and the extent of its needs for customized programming, a charge-back arrangement may be required.
