The journal GigaScience just announced a partnership with protocols.io. This is the first integration by a publisher of protocols.io directly into the publication workflow. As researchers submit a manuscript to GigaScience, they are asked explicitly to detail their methods on protocols.io and to link to these records from their paper.\n\u00a0\nThis integration is a big deal for us because it answers a common concern from scientists:\n\u00a0\n \u00a0\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 Since protocols.io allows users to publish, without conducting peer review, how can it ensure the quality of the shared public protocols?\n\u00a0\nThe partnership with GigaScience illustrates a 3-part answer.\n\u00a0\n1. Protocol details are published together with a paper.\n\u00a0\nMost of the hundreds of methods shared by scientists on protocols.io correspond to a formal peer-reviewed publication. With GigaScience incorporating the sharing on protocols.io into the submission process, we now have beautiful examples of the materials & methods sections linking to protocols.io for the details:\n\u00a0\nHebert FO. et al., Reference transcriptome for the parasite Schistocephalus solidus: insights into the molecular evolution of parasitism. GigaScience. 2016. DOI:10.1186\/s13742-016-0128-3\n\u00a0\nMofiz E. et al., Genomic resources and draft reference assemblies of the human and porcine scabies mites, Sarcoptes scabiei var. hominis and var. suis. GigaScience. 2016. DOI: 10.1186\/s13742-016-0129-2\n\u00a0\n2. Moving away from \u201ccontact author for data\/code\/protocols\u201d.\n\u00a0\nReading papers in most journals, it is common to come across in the Materials and Methods sections:\n\n \u00a0\u00a0\u00a0\u00a0\u00a0We used a slightly modified version of the protocol reported in\u2026\n \u00a0\u00a0\u00a0\u00a0\u00a0Detailed protocol available upon request\n \u00a0\u00a0\u00a0\u00a0\u00a0We followed the manufacturer's instructions for the assay\n\nThe mission of protocols.io is to move away from supplementary files and the vague M&M sentences above. Our goal is to do for methods precisely what GigaScience is doing for data and software reporting in research publications.\n\u00a0\nBioinformatician Philipp Bayer wrote the day GigaScience launched in 2011:\n\u00a0\nFor every released paper [in GigaScience], all associated data will be released, too - a huge change to the usual publishing process, at least in my eyes. Standard open access journals do not enforce open data!\nI\u2019ve lost track of the times I\u2019ve read over a superb paper and wanted to tinker with their results - only to have stuff in the materials and methods part like \u201can internal pipeline was used\u201d or \u201cwe parsed the output with a custom Perl-script\u201d\u2026\n\u00a0\n3. Publishing in a journal is the first step in long the peer review cycle of a research paper.\n\u00a0\nHandled by competent reviewers with good editors, pre-publication peer review improves the submitted papers. However, improving quality is not the same as ensuring it. A typical reviewer is unlikely to verify the scripts and rerun analyses reported in a genomics paper. Similarly, it would be highly unusual for a reviewer of an experimental molecular biology paper to dash to the lab and attempt to reproduce the reported results as part of checking the paper.\n\u00a0\nThe peer review that can truly verify any given paper is the gradual process of replication and extension of the published work over time. When authors of a given paper or other researchers follow up on a publication \u2013 then and only then \u2013 do we really catch mistakes, improve, and verify the work. This is why it is so important to report not only the results, but the code, data, and the detailed methods used to produce these results. This is why the efforts of publishers like GigaScience are so important.\n\u00a0\nWe were driven to create protocols.io by the desire to establish a central place where scientists can share and discover optimizations and corrections of published methods; our hope is that through versioning and collaborative sharing post-publication, methods can evolve and remain up-to-date, long after the original publication. So, we are beyond excited to partner with GigaScience in an effort to improve the quality of protocols, before, during, and long after publication.