PyMOL Educational License Eligibility: A Comprehensive Guide
PyMOL is a powerful molecular visualization tool widely used in structural biology, bioinformatics, and related fields. Schrödinger offers Educational-use-only PyMOL builds available at no cost to teachers and high school and college students (including online courses, homeschooling, etc.) for classroom instruction, homework assignments, and to provide a means for creating high quality figures. This article aims to provide a comprehensive overview of the eligibility requirements, restrictions, and available options for obtaining and utilizing a PyMOL educational license. It will cover various aspects, including academic license restrictions, alternatives for research purposes, and where to find more information. If you intend to use PyMOL products for academic research or publication, please purchase an Academic PyMOL subscription, which includes access to technical support, screencasts, and additional resources.
Understanding PyMOL Licenses
PyMOL offers different types of licenses to cater to various user needs. These licenses typically include:
- Educational License: Specifically designed for educational purposes, this license is often free for teachers, high school and college students for classroom instruction, homework assignments, and to provide a means for creating high quality figures.
- Academic License: Intended for academic research and publication purposes. If you intend to use PyMOL products for academic research or publication, please purchase an Academic PyMOL subscription, which includes access to technical support, screencasts, and additional resources.
- Commercial License: Required for commercial use, such as in pharmaceutical companies or biotechnology firms.
- Government Use: Prices for government use. To learn more about access for your entire institution, or to verify if you already have access to a Tier 2 license, please contact us using the link below.
- Employment: To learn more about access for your entire institution, or to verify if you already have access to a Tier 2 license, please contact us using the link below. For companies with 1,000 employees or more, or to verify if you already have access to a Tier 2 license, please contact us using the link below.
Eligibility for PyMOL Educational License
Schrödinger offers Educational-use-only PyMOL builds available at no cost to teachers and high school and college students (including online courses, homeschooling, etc.) for classroom instruction, homework assignments, and to provide a means for creating high quality figures.
Restrictions on Academic Licenses
The licensee is responsible for his or her own installation and setup. CUIT provides these licenses as a service to the Columbia community. Only the most current versions will be distributed. PyMOL Academic License Restrictions: Software shall be installed solely on machines located at Licensee’s facilities in Ann Arbor, MI or remote machines affiliated with Licensee's facilities in Ann Arbor, MI or installed solely on Licensee’s cloud accounts. Consortium/Funding InfoPyMOL is an unlimited site license open to the entire Ann Arbor campus regardless of UmichITAM consortium membership. Satellite campuses are not eligible under the current license. Individuals at U-M are ultimately responsible for any infringing software on their computers or devices or for violating the terms and conditions of software licenses.
Alternatives for Academic Research and Publication
If you intend to use PyMOL products for academic research or publication, please purchase an Academic PyMOL subscription, which includes access to technical support, screencasts, and additional resources.
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Additional Software and Resources for Research and Education
Beyond PyMOL, numerous software and resources are available for researchers and students in related fields. Some notable examples include:
- ArcGIS: A geographic information system (GIS) for working with maps and geographic information.
- 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.
- Biorender: 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 September 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: 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. Most of the Apps are freely available from Cytoscape App Store.
- Endnote: 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.
- FCS Express: Analyzes raw flow cytometry data and allows production of presentations, spreadsheets and reports.
- FlowJo: 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.
- 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. Due to high demand and license cost increase from the vendor, a GraphPad license is now charged $150/year/machine (60% discount compared to public pricing). Students can receive one license for one machine per year for free upon request.
- IPA (Ingenuity Pathway Analysis): 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.
- LabArchives: 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.
- Ledidi Core: A secure web-based platform for research projects and clinical registries with functionality for study design, creation of data entry forms and eCRFs in combination with built-in-tools for statistical analysis and data visualization. The statistical analyses include descriptive statistics, parametric and non-parametric tests, regression analyses, contingency tables and survival analyses. It is suited for international collaborations, or for single or multi-center projects.
- 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.
- MATLAB: 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.
- EcoCyc: is a comprehensive, literature-curated bioinformatics database for the model bacterium Escherichia coli K-12 MG1655, detailing its complete genome, genes, proteins, metabolic pathways, transport systems, and transcriptional regulation to understand the cell's molecular workings. It serves as an electronic reference for biologists, offering tools for omics data analysis (like gene expression), comparative genomics, and metabolic modeling, accessible via a web interface.
- MetaCyc: is a comprehensive, curated database of experimentally verified metabolic pathways, enzymes, and metabolites from all domains of life, used for understanding metabolism in various organisms, supporting metabolic engineering, drug discovery, and genome analysis through its interactive diagrams, search tools, and links to external biological databases. It catalogues a diverse range of pathways, from core functions to secondary metabolism, providing rich data for researchers. MetaCyc transitioned to a subscription-only model for full access as of January 2024, meaning paid BioCyc subscriptions are needed for deeper institutional access or downloadable versions, though basic browsing remains free. WCM does no longer subscribed to BioCyc.
- Microsoft Access: 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: 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 and RStudio: 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. 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.
- REDCap: 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.
- SAS (Statistical Analysis System): A software suite developed by SAS Institute for advanced analytics, multivariate analyses, business intelligence, data management, and predictive analytics. The suite purchased through WCM includesSAS InterNet ConnectorSAS Genetics ModuleSAS Genetics Server ConnectorSAS AppDev Studio ModuleSAS Text Miner ModuleThe SAS license is valid from May 15 of each to May 14 of the following year.
- SEERStat: The SEERStat 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.
- IBM SPSS Statistics: 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. The SPSS license is valid from April 1 to March 31.
- 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.
- Stata: is a complete, integrated statistical software package.
- Blender: A free and open-source 3D creation suite.
- MiKTeX: An implementation of TeX/LaTeX and related programs for Windows, macOS and Linux.
Institutional Policies and Support
CUIT recommends that you back up all of your important work prior to any new software downloads. Note that CUIT does not provide installation or tech support for your personal computers. There are certain policies in place for all licenses procured through CUIT and others that are specific to particular products. The licensee is responsible for his or her own installation and setup. CUIT provides these licenses as a service to the Columbia community. Only the most current versions will be distributed. Davidson licenses a number of academic and productivity software packages to support teaching, learning, research, and administrative activities at the college. Depending on the license rights, this software may be available to be used or installed on classroom/lab computers; on college-owned workstations; or for use on personally-owned employee and/or student computers. This table highlights commonly used academic and productivity applications in use at Davidson and where they may be used.
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