THE REPLICATION CRISIS
The “replication crisis” plaguing science is a methodological one. While the use of next gen sequencing and associated analysis in the life sciences is rapidly increasing, the ability to repeat the results as published is declining. One prominent study found that only 10% of experiments in cancer biology are repeatable.
The inability to repeat results may have less to do with the quality of research than with the manner in which the details of the experiments are communicated. Most cancer biologists are not trained pipeline developers. Something as simple as leaving out a version number (a common omission even among experienced bioinformaticians) can affect results.
High throughput sequencing analyses are revolutionizing our understanding of everything from agriculture to the gut microbiome to our own heritage as a species. That so many biologists from so many diverse fields are jumping into this field and making new discoveries every day is wonderful – but the need to faithfully transmit the details of the experimental process in a repeatable way could not be higher.
The BioCompute methodological standard aims to help BioCompute is not a standardized anaylsis. It is a wrapper for all analyses, data provenance, input and output files, parameters, version numbers, and more -- the fact that a given analysis was carried out in the first place is recorded. In short, everything necessary to go from FASTQ to result.
Starting in 2014, the BioCompute project has resulted in two publications, 3 workshops, Federal funding, and trial submissions with the FDA. In total, more than 300 individuals have participated in building the standard from around the world, including NIH, FDA, several biotech and pharma companies, Harvard, The George Washington University, University of Manchester, Common Workflow Language, and many others.
BioCompute: Research is an open, community-driven approach to improving replicability in computational analyses, and we welcome input from anyone in this space. To join in the efforts or to receive updates from the Partnership, please contact us.