ReaDI Program

The ReaDI Program

Resources for the Research Lifecycle

Learn More!

About

In 2014, the University launched the Research and Data Integrity (ReaDI) Program to enhance research integrity, data management, and data quality across the institution. Housed within our Office of Research Compliance and Training, the ReaDI Program engages proactively with Columbia’s research community in three ways:

  1. It maintains a wide-ranging, web-based repository of essential resources and tools to support robust science across the research lifecycle, from experimental design through data collection and management, to analysis and publication. As Monya Baker points out in her 2016 Nature article, finding these types of resources challenges many researchers, but the ReaDI Program offers a one-stop-shop for authentication methods, information on statistical consulting services, literature on reproducibility, lab management tools, and many other items. New resources are routinely added, and existing resources are continuously updated. The ReaDI resources are openly available for use by any institution.

  2. It provides outreach, training and courses on topics including safeguarding research and data integrity, and rigor and reproducibility. The ReaDI Program proactively reaches Columbia’s graduate students and postdoctoral researchers at resource fairs, orientation presentations, and department-specific seminars and Journal Clubs focused on the critical evaluation of the literature. In 2024, the program launched the first-of-its-kind web-based training on proper handling of digital scientific images, with strong uptake and evaluations.

  3. It offers individualized consultations on data management and good laboratory practices. These consultations are available to principal investigators at all levels and are customized to meet the principal investigator’s needs and to maximize efficiency and research quality.

How to Navigate

Each tab represents a distinct phase of the Research Lifecycle. In each section, you will find a wealth of resources tailored to support you at that specific stage of your research journey. Click on the short video below for a walkthrough!

The ReaDI Program
The Readi Program streamlines the research process with a comprehensive workflow designed for all researchers.
By offering tools and resources for every stage of the research lifecycle, Ready ensures you have the support you need—from launching your project to disseminating the final results.
It all starts with “Get Started,” where you focus on building a solid foundation for your research.
This includes assembling the right team, ensuring everyone has the necessary training, and creating standard operating procedures that guide daily activities.
By clearly defining roles, expectations, and SOPs at the outset, you establish a culture of rigor and reproducibility that sets the stage for success.
Investing time here helps prevent future challenges, and paves the way for a seamless research journey.
Next comes “Propose & Plan,” which emphasizes writing clear, robust research proposals and—crucially—developing data management plans.
Good data management goes beyond simple storage.
It includes organizing, documenting, and securing your data to support reproducibility and prevent issues like data loss or misinterpretation.
After carefully planning your research, it’s time to “Execute.”
In this phase, you’ll run experiments, collect and organize data, and, if needed, consult with experts on statistical analysis to maintain high-quality outcomes.
Staying on top of data management here is especially crucial—proper documentation and version control can prevent errors and make your results more reproducible.
In “Disseminate & Preserve,” the focus is on maximizing the impact of your findings while ensuring long-term accessibility.
This phase goes beyond simply choosing the right journals—it covers best practices for preparing manuscripts, formatting data for public release, and adhering to open-access or funder requirements.
Finally, the "End of the Line" phase provides tools and resources to ensure projects conclude ethically and compliantly.
For more resources and support, researchers are encouraged to contact [email protected].

1. Get Started

Beginning your Research Journey

This section lays the groundwork for initiating a successful research project by focusing on team formation and preparation. It includes guidance on hiring the right people with the necessary skills and expertise. It also covers the essential training for team members on rigor and reproducibility, ensuring that the team understands the principles of research integrity and collaboration. Finally, it provides tools for the PI to develop and communicate their own lab procedures for all team members to follow. This section is crucial for setting the stage for a successful research project by building a strong, well-prepared team.

  • Training Finder Tool | The Finder creates a personalized chart of required and recommended training courses, with links to the training and the responsible offices.  The identified courses can be added to your Rascal Training To-do List.
  • Recommended Training

Whether you call it a lab manual, an onboarding document, or standard operating procedures, a written document can streamline research processes and ensure high-quality research. The document should include your expectations for conducting research (including quality controls) and maintaining data. Other principal investigators have found these documents helpful for communicating with their group members.  Free SOP consulting and drafting services are available for Columbia PIs.

The webpage by Organizo LLC offers a suite of practical tools and templates designed to streamline organization in research labs. From managing inventories and orders to tracking applications and outlining team responsibilities, these resources aim to improve efficiency and clarity in daily operations. All documents are downloadable and customizable, making them versatile for various professional and lab settings.

Organizational Spreadsheets

  • Ordering Spreadsheet: Tracks order statuses to help lab members plan their work based on item arrivals. Can be customized for any group ordering system.
  • -80 Freezer Inventory: Simplifies freezer organization for -80°C storage and can be adapted for other temperature-controlled storage (-20°C, 4°C).
  • Antibody Inventory: Helps locate lab items like antibodies quickly with a system to define storage locations and contents.

Application Management

  • Application Tracker: A spreadsheet for managing deadlines and requirements for funding applications, shareable with institutional grant teams.

Human Resource Tools

  • Employee Expectations: A template outlining job expectations for lab aides, customizable for various research roles.
  • Lab Responsibilities: A document detailing responsibilities for different roles (e.g., Lab Aide, Research Technician, Animal Technician) to ensure smooth lab operations.

2. Propose and Plan

Preparing for all Aspects of your Research Project

In this section, the focus is on the critical planning stages of your research project. It includes resources and guidance on writing strong research proposals, designing robust research methodologies, and creating comprehensive data management plans. Additionally, it covers the importance of experimental design to ensure your study is well-structured and scientifically sound. This section helps researchers lay a solid foundation for their projects by carefully planning and proposing their research strategies.

It's never too early to start thinking about how your data will be managed throughout your research. Planning ensures that your data is collected, organized, and stored in a way that maximizes its value and utility, both for your current projects and future research. By establishing clear protocols for data handling from the outset, you can avoid common pitfalls like data loss, ethical breaches, or difficulties in data sharing and reuse. Thoughtful data management also facilitates collaboration, enhances the reproducibility of your work, and ensures compliance with institutional and funding agency requirements. Taking the time now to consider how your data will be handled can save you significant effort later and contribute to the overall integrity and impact of your research.

  • What types and formats of data will our lab collect?
  • What ethical considerations must we address when working with human or animal subjects, and what steps will we take to ensure privacy, confidentiality, and compliance?
  • What documentation and metadata standards will we use to organize and describe our data?
  • Who will need access to our data, and how can we ensure it is usable for future research or collaboration?
  • What access restrictions will we apply to protect sensitive data?
  • Where will we store our data during and after our research projects?
  • What are the projected costs associated with managing, documenting, storing, and preserving our lab's data?

3. Execute

Collecting and Analyzing Data

This section covers the execution phase of your research project. It provides effective practices for managing protocols and collecting data, ensuring data integrity is maintained throughout the process. It also includes resources on statistical analysis and interpretation to help make sense of the data collected. Furthermore, it emphasizes the importance of handling and storing research data correctly to preserve its quality and reliability. This section is critical for the accurate and ethical execution of research activities.

  • Protocols.io | A free, up-to-date, crowd-sourced protocol repository for researchers.
  • Protocol Exchange from Nature Protocols | Protocol Exchange is an open repository of community-contributed protocols sponsored by Nature Protocols.
  • Bio-protocol | Bio-protocol is an online peer-reviewed protocol journal. Its mission is to make life science research more efficient and reproducible by curating and hosting high quality, free access protocols.
  • Current Protocols (Wiley) | The Current Protocols collection includes nearly 20,000 step-by-step techniques, procedures, and practical overviews that provide researchers with reliable, efficient methods to ensure reproducible results and pave the way for critical scientific discovery.
  • Springer Nature Experiment | The largest available collection of protocols and methods from Nature Methods, Nature Protocols, Nature Research, and Springer Protocols.
  • Columbia Consulting Services for Statistical Analysis | Services below are provided to Columbia researchers, ranging from no-cost to fee-for-service.
  • Courses and Lectures
    • Biostatistics for Clinical Researchers | Part of the “Biostatistics in Action: Tips for Clinical Researcher” lecture series that is sponsored by the Irving Institute for Clinical and Translational Research - Biostatistics, Epidemiology and Research Design resource, which is supported in part by an NIH Clinical and Translational Science Award (CTSA) through its Center for Advancing Translational Sciences (Grant No, UL1TR001873). The speaker, Cody Chiuzan, PhD, is an Assistant Professor in the Department of Biostatistics at the Mailman School of Public Health.
    • Statistical Software Mini-Courses | A two-part mini-course on getting started with statistical software. The mini-course covers the basics of statistical programming in R and SAS. Topics include data manipulation, descriptive statistics, and basic analyses. Statistical Software Mini-courses are offered once per year. Open to the Columbia community at no cost.
    • Johns Hopkins University Data Science Lab | The major educational initiative of the JHUDSL is to create open-source online courses delivered through a range of platforms, including YouTube, Github, Leanpub, and Coursera.
  • Research Tools and Solutions Supported by Columbia
    • LabArchives | Paperless research notebook and lab manual solution for Columbia's researchers.
    • GraphPad Prism Discount | Graphing and statistical software for creating publication-quality graphs and analyzing scientific data with t-tests, ANOVA, linear and nonlinear regression, survival analysis.
    • SnapGene | Molecular biology software for planning, visualizing, and documenting DNA cloning and PCR; allows feature annotation and primer design.
    • ChemDraw | A program to draw structures ChemDraw is the drawing tool of choice for chemists to create publication-ready, scientifically intelligent drawings – ChemDraw Activation Code.
    • NVIVO | NVivo is a software program used for qualitative and mixed-methods research. Specifically, it is used for the analysis of unstructured text, audio, video, and image data, including (but not limited to) interviews, focus groups, surveys, social media, and journal articles – activation code .
    • CrystalMaker is the most-efficient way to visualize crystal and molecular structures. Its interactive design lets you see the wood for the trees" and build your own visual understanding of complex materials – Crystalmaker License.
    • Schrodinger PyMol License Access | Molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger – Schrodinger PyMol License Access.
  • Security and Privacy
    • Globus | Secure, efficient and reliable file transfer service for large, non-sensitive data transfers within Columbia and to external collaborators.
    • dWinSCP | Secure FTP program, recommended by CUIT for file transfers to the cunix.cc.columbia.edu server.
    • CUSpider | Windows application for scanning for Personally Identifiable Information (PII) such as Social Security numbers
    • Malwarebytes | Virus and spyware scanning program.
    • Remote Access | Remote access to network files and administrative applications on the Columbia network via VPN and Citrix.
  • Writing
    • Overleaf | Collaborative LaTeX editor for writing, editing and producing research papers and project reports (Overleaf Professional license).
    • Turnitin | Plagiarism Detection Services.

To mitigate the risk of disruption, it is recommended that all principal investigators develop research continuity plans for their laboratories and research teams.

4. Disseminate & Preserve

Sharing and Storing your Research Outcomes

This section addresses the essential processes of publishing and preserving your research outcomes, including data. It offers guidance on manuscript preparation, including checklists, ethical considerations for digital images, templates for organizing data for publication, and choosing the right repository for your data. It also covers copyright and plagiarism, providing resources to help researchers understand and avoid plagiarism while managing citations effectively. Tutorials on citation management software are included to support proper citation practices.

  • Checklist for manuscript preparation | This outlines the necessary steps and requirements that authors need to fulfill when submitting their work.
  • Data handling and figure preparation
    • Handling Digital Scientific Images: Dos &Don'ts | The course addresses the ethical considerations and challenges of digital image manipulation in scientific research. It covers the importance of using image editing responsibly to enhance clarity without compromising data integrity.
    • Community-developed checklists for publishing images and image analyses | These checklists offer authors, readers, and publishers key recommendations for image formatting and annotation, color selection, data availability, and reporting image-analysis workflows.
    • Data-to-Figure Map | This template is designed to aid in the organization of raw and manipulated data files as you prepare for publication or presentations and to fulfill requirements for open access policies.

Sometimes, plagiarism results from mismanaged or improper citation and source management.  Citation management software can help avoid such problems.

Predatory journals and publishers often operate under the auspices of open-access publishing. They charge authors fees without reviewing research for quality or providing editorial and publishing services. Below are questions and resources to help you determine if a journal is predatory.

In February 2013, the White House Office of Science and Technology Policy (OTSP) issued a memo with the purpose of increasing access to federally funded research. This memo required any Federal agency that awards at least $100 million/year in support of research to develop a plan that would increase public access to publications and data resulting from federally-funded projects. In response to this memo, a number of public and private funders have established new requirements for researchers. 

Items to Consider in Data Sharing Plan*:

  • What data will be shared?
  • Who will have access?
  • Where will shared data be located?
  • When will data be shared?
  • How will the data be located and accessed?

Additional information about the requirements for NIH and NSF are available here:

For more information please visit the Public Access Mandates and Resources page.


*Source: NIH Data Sharing Plan. Individual funders may have different requirements for data sharing plans.

Public Access Mandates and Resources

 

US Private Funders

  • Alfred P. Sloan
    • Publication Access: "Information Products" to be disseminated as outlined by "IP Plan"
    • Data Access: "Information Products" to be disseminated as outlined by "IP Plan"
    • Documentation: Grant Proposal Guidelines
  • Autism Speaks
    • Publication Access: PubMed
    • Data Access: Not specified
    • Documentation: Policy
  • Ford Foundation
  • Bill and Melinda Gates Foundation
  • Hewlett Foundation
  • Howard Hughes Medical Institute (HHMI)
    • Publication Access: PubMed
    • Data Access: Data supporting publications to be made available at no cost. Choose an appropriate discipline specific repository (if available).
    • Documentation: Policy, Publication Policy
  • MacArthur Foundation
  • Microsoft Research
    • Publication Access: Microsoft Research open-access repository
    • Data Access: Not specified
    • Documentation: Policy
  • Gordon and Betty Moore Foundation
    • Publication Access: Prospective grantees to develop a Data Sharing and/or Intellectual Property Plan
    • Data Access: Prospective grantees to develop a Data Sharing and/or Intellectual Property Plan
    • Documentation: Policy
  • World Bank
  • Note: The above list of private funders is not comprehensive. Additional private funders' open access policies can be found on the Registry of Open Access Repository Mandates and Policies

 

US Directives

Open access (OA) is the free and unrestricted availability of digital content online. It can apply to any type of content, including scholarly work, software, audio, video, and more. 

Features of open access
  • Free: OA content is available at no cost to the reader. 
  • Unrestricted: OA content has few restrictions on its use or reproduction. 
  • Digital: OA content is available in a digital format. 
  • Open licenses: OA content often uses open licenses, like Creative Commons licenses, which allow for more reuse and sharing. 
Benefits of open access
  • Increased access: OA provides greater access to information for the general public, students, teachers, and libraries. 
  • Increased visibility: OA increases the visibility of research outputs, which can lead to a greater impact. 
  • Increased transparency: OA makes scientific research more transparent and accessible. 
Open Access Policies at Columbia

For more information contact Scholarly Communication & Publishing.

    There are a number of ways to maintain and share your data in order to make it available to the scholarly community and the broader public. Check out the links and resources below to find more information about managing and sharing data, and to find a repository that is right for you and your research.

    • CU-Supported Data Repositories
      • List of options for the storage, sharing and transfer of digital research data that is available to Columbia researchers. This table is maintained by the ReaDI Program. For more detail regarding the resources listed in the table below, please download the research data storage options PDF. All systems located at Columbia University’s Morningside Heights or Manhattanville Campus that process, transmit and/or store Sensitive Data must be registered with the CU Information Security Office. All Systems located at CUMC (“CUMC Systems”) must be registered with the CUMC Information Security Office. See Data Security webpage for more information.
      • See RSAM User Guide for Registering your Device.
    • Repositories for Sharing Scientific Data (NIH)
      • Browse through this listing of NIH-supported repositories to learn more about some places to share scientific data. Select the link provided in the “Data Submission Policy” column to find data submission instructions for each repository. 
      • Learn more on how to evaluate and select appropriate data repositories.
    • Open Domain-Specific Data Sharing Repositories (BioMedical Informatics Coordinating Committee - BMIC)
    • Generalist Repositories (BioMedical Informatics Coordinating Committee - BMIC)
      • Generalist repositories accept data regardless of data type, format, content, or disciplinary focus.
      • We are currently recommending researchers to use Dryad, which is freely available to all CU researchers. You may also want to refer to the CU Data Repository Finder for other repositories that meet the NIH’s suggested requirements.

    5. End of the Line

    Ending your Research Journey

    The final section addresses the closing stages of a research project. This section ensures that your research is concluded responsibly, with all necessary procedures followed for a clean and ethical project wrap-up.

    There are a number of action items that need to be completed before a staff member leaves a research group. Below are some resources to help a PI ensure they obtain the necessary data and protocols before a group member leaves the University, as well as procedures when a PI is vacating laboratory space.

    Research Integrity

    Research Integrity Across the Research Lifecycle

    Research misconduct can occur at any stage of the research lifecycle, from proposing a study to reporting the results! Columbia University is committed to upholding the highest standards of integrity at every stage of research—from the initial proposal and design to final publication and beyond. To this end, the University has established policies and procedures that define research misconduct, outline how allegations are investigated, and detail the consequences of misconduct.

    1. Proposal Development and Design

    • Responsibilities
      • Researchers are expected to develop protocols, methodologies, and grant proposals with accuracy and honesty.
    • Potential Risks
      • Misrepresentation of data or objectives, or plagiarizing background literature in funding applications.
    • Preventing Misconduct
      • The Office of Research Compliance and Training offers guidance on proper proposal practices and can clarify questions regarding research ethics.

    2. Data Collection and Management

    • Responsibilities
      • Ensure data collection methods are transparent, reproducible, and accurately recorded.
    • Potential Risks
      • Fabrication (making up results) or falsification (altering data or results).
    • Preventing Misconduct
      • Proper recordkeeping and secure data storage are integral. The Standing Committee on the Conduct of Research, in partnership with the Office of Research Compliance and Training, helps investigators implement best practices.

    3. Analysis and Interpretation

    • Responsibilities
      • Conduct unbiased analyses and interpret results responsibly.
    • Potential Risks
      • Manipulating or selectively reporting results that skew findings.
    • Preventing Misconduct
      • Researchers should adhere to rigorous scientific standards and consult with colleagues or the Office of Research Compliance and Training if questions arise.

    4. Publication, Peer Review, and Reporting

    • Responsibilities
      • Accurately present findings in manuscripts, conference presentations, and peer reviews.
    • Potential Risks
      • Plagiarism of text or ideas and omission of critical information in publications.
    • Preventing Misconduct
      • Clear citation practices, transparent presentation of data, and ethical peer-review processes help ensure the integrity of dissemination.

    5. Post-Publication Oversight and Follow-Up

    • Responsibilities
      • Address post-publication comments, correct any errors promptly, and preserve relevant data for future reference.
    • Potential Risks
      • Failure to correct known inaccuracies or engaging in retaliatory practices against whistleblowers.
    • Preventing Misconduct
      • Institutional checks—such as the University’s Standing Committee on the Conduct of Research—support corrections and follow-up inquiries to maintain credibility and public trust in research.

    Consequences of Misconduct

    Research misconduct may lead to institutional sanctions, such as termination of grants or disciplinary action, and can result in federal penalties. By articulating a clear definition of misconduct and an established investigation process, Columbia reinforces accountability and maintains a culture of ethical, high-quality research.

    If you have concerns or questions at any point in the research lifecycle, please contact the Office of Research Compliance and Training or consult the Institutional Policy on Misconduct in Research for further guidance.

    Research Misconduct Need-to-Know

    We Want to Hear From You! The ReaDI Program is committed to bringing the most relevant and useful resources to the Columbia research community. By providing your feedback on the resources provided, you will be continuing to strengthen the ReaDI Program's robust repository. Fill out the resource feedback form.

    If you have any questions or suggestions about the ReaDI Program please email us [email protected].

    Have a suggestion? Let us know!