Weill Cornell Medicine Samuel J. Wood Library

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All Scientific Software

This page provides access to all scientific software available on the library software hub. Software is listed alphabetically by name. Click on the software name to view details, register for update alerts, download, or obtain a license.

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.

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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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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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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.

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The FlowJo workspace is a powerful statistical environment that is used for immunophenotyping, cell cycle, proliferation, kinetics studies, quantitative population comparison, or plate screening assays.

Annual license cost is determined by the number of active users each quarter. Thus we can only provide an estimate of the cost based on current usage.

Information links

System requirements

Windows or Mac

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.

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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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GraphPad Prism combines scientific graphing, comprehensive curve fitting (nonlinear regression), understandable statistics, and data organization. While it won't replace a heavy-duty statistics program, Prism lets you easily perform basic statistical tests commonly used by laboratory and clinical researchers. Prism offers t tests, nonparametric comparisons, one-, two- and three-way ANOVA, analysis of contingency tables, and survival analysis. Analysis choices are presented in clear language that avoids unnecessary statistical jargon.

Information links

Notice

11/22/2017
Due to high demand, we are currently experiencing delays in provisioning the full license.
Please visit https://www.graphpad.com/demos to install the 30 day trial version while you wait for the full license to be made available.
We apologise for the delay, and thank you for your understanding and patience.

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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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

Information links

System requirements

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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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.

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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.

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The MATLAB platform is optimized for solving engineering and scientific problems. The matrix-based MATLAB language is the world’s most natural way to express computational mathematics. Built-in graphics make it easy to visualize and gain insights from data. A vast library of prebuilt toolboxes lets you get started right away with algorithms essential to your domain. The desktop environment invites experimentation, exploration, and discovery. These MATLAB tools and capabilities are all rigorously tested and designed to work together.

Cornell’s MATLAB license is only valid for personnel located in North America. Students, staff, and faculty at the Weill Cornell College of Medicine in Qatar are not currently eligible for this license. We are working on extending our license to that campus. We apologize for any inconvenience.

Information links

System requirements

Windows,Mac, or Linux

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.

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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.

Information links

System requirements

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.

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nan

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

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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.

Information links

System requirements

Costs and fees

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

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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.

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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.

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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.

Information links

System requirements

Chrome,Firefox,Internet Explorer or Safari

Costs and fees

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

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SAP Lumira (formerly called SAP Visual Intelligence) is a self-service, data visualization application for business users.

Information links

System requirements

Library Access

This software is installed on the library computer lab PCs.

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.

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SAS (Statistical Analysis System) is a software suite developed by SAS Institute for advanced analytics, multivariate analyses, business intelligence, data management, and predictive analytics. The suite purchased through WCM includes

  • SAS InterNet Connector
  • SAS Genetics Module
  • SAS Genetics Server Connector
  • SAS AppDev Studio Module
  • SAS Text Miner Module
SAS licenses purchased through WCM will expire May 14th, 2018. License fees are not pro-rated for purchases made mid-year.

Information links

System requirements

Windows or Linux (not available for Mac)
Chrome,Firefox, or Internet Explorer
Flash

Library Access

This software is installed on the library computer lab PCs.

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.

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nan

Information links

System requirements

Windows or Mac

Library Access

This software is installed on the library computer lab PCs.

Costs and fees

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

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sciNote is an open source electronic lab notebook which helps you organize your scientific data and safely stores it in one place.

Information links

System requirements

Java

Costs and fees

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

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The SEER*Stat statistical software provides a convenient, intuitive mechanism for the analysis of SEER and other cancer-related databases. It is a powerful PC tool to view individual cancer records and to produce statistics for studying the impact of cancer on a population. SEER*Stat software is distributed with the SEER Research Data and you must have access to the data before using the software.

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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IBM SPSS Statistics is an integrated family of products that helps to address the entire analytical process, from planning and data collection to analysis, reporting and deployment. With more than a dozen fully integrated modules to choose from, you can find the specialized capabilities you need to increase revenue, outperform competitors and make better decisions. SPSS Statistics Base provides a range of statistical procedures suitable for many problems, including crosstabs, linear regression, Monte Carlo simulation, geospatial analytics, and the ability to extend built-in capabilities with Python, R, or Java code.

SPSS is offered as an annual license running from April 1 through March 31.

Information links

System requirements

Windows,Mac, or Linux

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.

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Stat/Transfer is designed to simplify the transfer of statistical data between different programs. Stat/Transfer will automatically read statistical data in the internal format of one of the supported programs and will then transfer as much of the information as is present and appropriate to the internal format of another. Stat/Transfer preserves all of the precision in your data, while automatically minimizing the size of your output data set. Stat/Transfer also allows control over the storage format of your output variables. In addition to converting the formats of variables, Stat/Transfer also processes variable names, missing values, and value and variable labels automatically.

Information links

System requirements

Windows,Mac, or Linux

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.

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Stata is a complete, integrated statistical software package.

Information links

System requirements

Windows,Mac, or Linux

Library Access

This software is installed on the library computer lab PCs.

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.

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TreeAge Pro provides visual modeling tools, allowing you to build and analyze decision trees to study any kind of problem. Healthcare decision trees are normally much more complicated and often include a Markov model for each treatment option. More complex healthcare trees may have many Markov models included in each strategy. Healthcare models can also incorporate heterogeneity and event tracking.

Information links

System requirements

Windows, Mac, or Linux
Java 1.6 or higher

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.

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