Reproducibility Resources and Guidelines by Topic

• 6 ways to access rigor checklist
   
• Six red flags for suspect work by C. Glenn Begley

Checklists and Validation Methods

• Global Biological Standards Institute (GBSI)
• Approaches to Validation (GBSI)
• Improving Reproducibility: Best Practices for Antibodies from Sigma Aldrich

Resources for Selecting Antibodies

• BenchSci - a free resource (for academic and nonprofit research institutions) that uses artificial intelligence to scan the literature to provide antibody usage data that's unbiased and experiment-specific
   
• Antibody Registry - gives researchers a way to universally identify antibodies used in their research. The Antibody Registry assigns unique and persistent identifiers to each antibody so that they can be referenced within publications. These identifiers only point to a single antibody, this allows the antibody used in your methods section to be identified by humans and search engines. 

Literature Review

• Antibody Validation" by Jennifer Bordeaux, et. al.
   
• Standardize Antibodies used in Research by Andrew Bradbury and Andreas Plückthun
   

• A Proposal for Validation of Antibodies by Mathias Uhlen et. al.

Guidelines and Resources from Professional and Non-Profit Organizations

• Federation of American Societies for Experimental Biology
  Enhancing Research Reproducibility is a collection of recommendations from FASEB that resulted from roundtable discussions. This document discusses overarching topics, mouse and other animal models, and antibodies

• Global Biological Standards Institute (GBSI)
  GBSI is a non-profit organization dedicated to enhancing the quality of biomedical research by advocating best practices and standards to accelerate the translation of research breakthroughs into life-saving therapies. (text taken from website) GBSI has assembled some key publications.

• American Physiological Society Science Policy Committee's Scientific Rigor and Reproducibility Toolbox

Science Signaling

• Criteria for Biological Reproducibility: What does "n" Mean?
• An Analysis of Critical Factors for Quantitative Immunoblotting
• Quantitative Mass Spectrometry of Posttranslational Modifications: Keys to Confidence
• Good Practices for Building Dynamical Models in Systems Biology

Statistics and Computational Analysis Specific for Biologists

• Statistics for Biologists is a collection of articles addressing important statistical issues that biologists should be aware of and provides practical advice to help them improve the rigor of their work (text adapted from Nature)
• Computing Workflow for Biologist: A Roadmap by Ashley Shade and Tracey K. Teal

Chemical Probes and Biomarkers

• The Promise and Peril of Chemical Probes - Chemical probes are powerful reagents with increasing impacts on biomedical research. However, probes of poor quality or that are used incorrectly generate misleading results. To help address these issues a community driven wiki-resource has been created to improve quality and convey current best practices. (text taken from abstract)
   
• Biomarkers, EndpointS, and Other Tools (BEST) Resource from NIH and FDA

NIH suggests "applicants proposing to use cell lines could describe the method they plan to use to verify the identity and purity of the lines, which might include short tandem repeat (STR) profiling and mycoplasma testing." Below are some resources for writing an authentication plan and procedures for authenticating cell lines.

Guidelines, Resources, and Training

• Global Biological Standards Institute (GBSI)
• International Cell Line Authentication Committee (ICLAC)
• Cell Line Authentication Training (ATCC/GBSI)

Literature Review

• Know Thy Cells: Improving Biomedical Research Reproducibility by Leonard P. Freedman
   
• Changing the Culture of Cell Culture: Applying Best Practices and Authentication to Ensure Scientific Reproducibility by Leonard P. Freeman, Mark C. Gibson and Richard M. Neve
   
• Cell Line Authentication Demystified by Vivien Marx
   
• Standards for Cell Line Authentication and Beyond Jamie L. Almeida, Kenneth D. Cole and Anne L. Plant
   
• Recommendation of Short Tandem Repeat Profiling for Authenticating Human Cell Lines, Stem Cells, and Tissues by Rita Barallon, et. al.
   
• A Resource for Cell Line Authentication, Annotation and Quality Control by Mamie Yu, et. al.

Specific for Non-Human Cell Lines

• Authentication for non-human cell lines from ICLAC
   
• Mouse Cell Line Authentication by Jamie L. Almeida, Carolyn R. Hill and Kenneth D. Cole

Mixed Methods and Qualitative Research

• Analysing Qualitative Data by Catherine Pope, Sue Ziebland, and Nicholas Mays
   
• Assessing Quality in Qualitative Research by Nicholas Mays and Catherine Pope
   
• Best Practices for Mixed Methods Research in the Health Sciences from OBSSR (NIH)
   
• Guidance on Performing Focused Ethnographies with an Emphasis on Healthcare Research By Gina M. A. Higgenbottom, et. al.
   
• Mixed Methods in Biomedical and Health Services Research by Dr. Leslie A. Curry, et. al.
   
• Qualitative and Mixed Methods Provide Unique Contributions to Outcomes Research by Dr. Leslie A. Curry, Dr. Ingrid M. Nembhard, Dr. Elizabeth H. Bradley
   
• Using Qualitative Methods in Health Related Action Research by Julienne Meyer

Retrospective Chart Review

• Compilation of suggested practices for creation of a retrospective chart review form
   
• The Retrospective Chart Review: Important Methodological Considerations by Vasser Matt and Holzmann Matthew

Preclinical and Clinical Research

• A Multidisciplinary Approach to Ensure Scientific Integrity in Clinical Research by Dr. Ko Bando, et. al.
   
• Principles and Guidelines for Reporting Preclinical Research (NIH)

Simulation-Based Research

The INSPIRE network has collaborated with global partners (including four influential journals: Simulation in Healthcare, BMJ Simulation, Clinical Simulation in Nursing, and Advances in Simulation) to develop extentions specific to simulation-based research for both the CONSORT and STROBE statements, in the documents below (text adapted from website).

• CONSORT Explanation and Elaboration
   
• STROBE Explanation and Elaboration

These guidelines are for researchers who acquire images and use image manipulation software (such as Photoshop)

• "Avoiding Twisted Pixels: Ethical Guidelines for the Appropriate use and Manipulation of Scientific Digital Images" By Douglas Cromey
   
• "Seeing is Believing? A Beginners' Guide to Practical Pitfalls in Image Acquisition" by Alison North
   
• Online Learning Tool for Research Integrity and Image Processing from ORI
   
• "What's in a Picture? The Temptation of Image Manipulation" by Mike Rossner and Kenneth M. Yamada [Specific for blots, gels, and micrographs]

Online Training Courses and Videos

• NIH-ORWH Course on Sex/Gender Differences. This online series of courses provides a foundation for sex and gender accountability in medical research and treatment. After completing the courses, researchers, clinicians, and students in the health professions will be able to integrate knowledge of sex and gender differences and similarities into their research and practice.
   
• Methods and Techniques for Integrating the Biological Variable Sex into Preclinical Research from NIH

Checklists and Decision Trees for Considering Sex as a Biological Variable and Gender

• SABV in Biomedicine Checklist from Gendered Innovations

• SABV Decision Tree

• Gender Decision Tree

Tutorials, Case Studies, and Reporting Guidelines

• Background, Methods, and Case Studies from Gendered Innovations at Stanford University
   

• Essential metrics for assessing sex & gender integration in health research proposals involving human participants by Suzanne Day, et. al.

• Sex and Gender Equity in Research: Rationale for SAGER Guidelines and Recommended Use by Shirin Heidari et. al.

Literature Review

• Studying both sexes: a guiding principle for biomedicine by Janine Austin Clayton
   
• NIH Initiative to Balance Sex of Animals in Preclinical Studies: Generative Questions to Guide Policy, Implementation, and Metrics by Louise D. McCullough, et. al. 
   
• First Steps for Integrating Sex and Gender Consideration into Basic Experimental Biomedical Research by Stacey A. Ritz, et. al.
   
• Strategies and Methods for Research on Sex Differences in Brain and Behavior by Jill B. Becker, et. al.
   
• Age and Sex in Drug Development and Testing for Adults by Cara Tannenbaum and Danielle Day
   

• Applying the new SABV (sex as a biological variable) policy to research and clinical care by Janine Austin Clayton

• How to study the impact of sex and gender in medical research: a review of resources by Alyson J. McGregor, et. al.

Guidelines from Professional Organizations, Funders and Journals

• Guide to Social Science Data Preparation and Archiving from ICPSR
   
• Social, Behavioral, and Economic Sciences Perspectives on Robust and Reliable Science from NSF

Center for Open Science (COS)

COS is part of the Open Science Framework (OSF), which has developed a series of online workshops as part of their statistical and methodological consulting services. These materials are free and can be found here, the webinars are also available on OSF's YouTube channel.

Checklists, Tables, and Tips for Statistics

• Some common statistical concepts and their uses in analysing experimental results from Know When Your Numbers are Significant by David L. Vaux

• Degrees of Freedom in Planning, Running, Analyzing, and Reporting Psychological Studies: A Checklist to Avoid p-Hacking by Wicherts et. al. (Frontiers in Psychology)

• Beyond Rigor: Appropriate Analysis by Patricia Campbell and Eric Jolly

Statistics and Computational Analysis Specific for Biologists

• Statistics for Biologists is a collection of articles addressing important statistical issues that biologists should be aware of and provides practical advice to help them improve the rigor of their work (text adapted from Nature)
   
• Computing Workflow for Biologist: A Roadmap by Ashley Shade and Tracey K. Teal

Literature Review

• Best Practices for Computational Science: Software Infrastructure and Environments for Reproducible and Extensible Research by Victoria Stodden and Shelia Miguez

Columbia Resources

• Computational Research Training Opportunities

• Rein in the four horsemen of irreproducibility by Dorothy Bishop (Nature)