PSB 2017: Methods to Ensure the Reproducibility
of Biomedical Research

Motivation

A few weeks ago, Vice President Joe Biden, in announcing his new research funding initiatives, criticized the current state of scientific research, which is “trapped in silos, preventing faster progress and greater reach to patients.” To make matters worse, the New England Journal of Medicine published a commentary calling scientists who repurpose data “research parasites” who may use data generated by others to demonstrate alternative hypotheses. We, the organizers of this session, believe this is absolutely unacceptable and that the concept of data hoarding not only runs contrary to the spirit of, but also actively damages scientific research. Scientific research is meant to seek objective truth, rather than promote a personal agenda, and we believe the only way to do so is through transparency and reproducibility.

ucsf.edu

wikimedia.org

Relevant challenges include:

• The analysis challenges of using heterogeneous measurement platforms (e.g. genomic, clinical, and exposure data)
• The tradeoff in making personalized decisions using more relevant but noisier subsets of data
• The unprecedented scale of asynchronous observational and population-level inquiry (i.e. many investigators separately mining shared/publicly-available data).

Session Topics

In this PSB 2017 session, we invite manuscripts that explore and propose solutions to the many challenges of reproducibility in the era of precision medicine. Manuscripts might describe:

• Methods for automated meta-analysis of clinical trials across diverse data sources
• New software and/or databases to help coordinate analyses across institutions
• Methods to account for uncertainty and bias from associations derived from observational studies
• New methods and extensions of visualization and pipeline tools (e.g., knitr, Jupyter, Galaxy) that promote reproducible use of heterogeneous and high-dimensional information
• Statistical methods to integrate evidence from multiple heterogeneous sources (e.g. ClinVar, PubMed).

All submissions will be required to be fully or nearly fully reproducible and freely available on a repository such as Github, Bitbucket, or Figshare.

Session Organizers

Key Dates

Submit

Papers must be submitted to the PSB paper management system

The accepted file formats are: postscript (*.ps) and Adobe Acrobat (*.pdf). Attached files should be named with the last name of the first author (e.g. altman.ps or altman.pdf). Hardcopy submissions or unprocessed TEX or LATEX files or electronic submissions not submitted through the paper management system will be rejected without review.

Each paper must be accompanied by a cover letter. The cover letter should be the first page of your paper submission. The cover letter must state the following:

• The email address of the corresponding author
• The specific PSB session that should review the paper or abstract
• The submitted paper contains original, unpublished results, and is not currently under consideration elsewhere
• All co-authors concur with the contents of the paper

Submitted papers are limited to twelve (12) pages (not including the cover letter) in our publication format. Please format your paper according to the instructions. If figures can not be easily resized and placed precisely in the text, then it should be clear that with appropriate modifications, the total manuscript length would be within the page limit.