Sharing Reproducible Analyses with Binder at Scale
Creators: name: Gibson, Sarah
Publisher: name: Zenodo
Year: 2020

description: 15 minute talk given by Sarah Gibson during the Tools, Practices and Systems session at CognitionX 2020 (https://cogx.co) <strong>Abstract</strong> The reproducibility crisis in scientific research is well known (https://www.nature.com/collections/prbfkwmwvz). The combination of 'publish or perish' incentives, secrecy around data and the drive for novelty at all costs can result in fragile advances and lots of wasted time and money. Even in data science, when a paper is published there is generally no way for an outsider to verify its results, because the data from which the findings were derived are not available for scrutiny. Such science cannot be built upon very easily: siloed science is slow science. As reproducibility gains traction in the data science and research communities, the need to package code, data and computational environments is growing. There are many tools that address different aspects of this type of packaging, such as Jupyter Notebooks (https://jupyter-notebook.readthedocs.io/en/stable/notebook.html) for literate programming, Docker (https://docs.docker.com/engine/docker-overview/) for containerising and porting computational environments, and so on. But they represent barriers to reproducibility as each one requires time and effort to learn. Scientists work with multiple tools, pipelines and collaborators to produce insights. Project Binder (https://jupyter.org/binder) integrates Notebooks and Docker for generating reproducible computational analyses and combines them with a web-based interface and cloud orchestration engines. This means that analysts do not have to worry about all the moving parts so long as they have followed basic software best practices: their code is version controlled and they've captured the dependencies the analysis needs to run. Binder, as a platform, provides easy access to the research for stakeholders by hosting the compute in the cloud and providing a unique URL to make it easily shareable, without imposing additional overheads on the analyst. mybinder.org (https://mybinder.org) is both a public service and a proof of concept of Binder's technologies. This site serves over 140,000 sessions per week and combines resources from four entities in the US and Europe, including The Alan Turing Institute. We support many programming languages and analysts from a range of research domains, and even facilitate a number of remote workshops and tutorials. For example, the Natural Language Processing course powered by mybinder.org (https://course.spacy.io) has over 5000 users, and the Institute of Computer Science at the University of St. Gallen uses our infrastructure for their university-wide Machine Learning course for explainable AI (https://ics.unisg.ch). During the Covid-19 pandemic, mybinder.org has seen a significant increase in usage correlating with the beginning of lockdown and many researchers began working and collaborating remotely. It is quickly becoming the "go to" tool for sharing results and facilitating remote teaching in this new landscape of research culture Dr Sarah Gibson is a member of the mybinder.org operating team and is personally responsible for maintaining the Binder infrastructure deployed at the Turing. During this talk, she will introduce Binder (the service), BinderHub (the technological infrastructure) and mybinder.org (a public instance of a Binder service, free for anyone to use) and demonstrate how it can be utilised to share reproducible computational environments and analyses. <strong>Descriptors</strong> Big picture Detailed Prospective <strong>Domain Application</strong> Engineering Society &amp; Culture <strong>Methodological Application</strong> Empowering citizens to access, understand and exploit the world's data Effectively and efficiently convey information to varying audiences <strong>Relevance</strong> Project Binder represents one pathway that technology can be utilised to lower the barrier to producing and sharing reproducible scientific insights with all stakeholders across domains and organisational structure, such as management teams. Binder is also an open source tool in and of itself and can therefore be deployed and modified within an organisation to suit their specific needs and be more opinionated regarding who has access than the free implementation at mybinder.org. CogX 2019 convened 20,000 visitors from government, third sector organisations, and businesses of all sizes. They represented expertise in technology, finance, advertising, media, and energy and aerospace engineering. Many of these audience members use open source tools and systems to leverage insights from data. It is because of these demographics that a talk on Project Binder would be of interest and relevant to the CogX audience. This talk will be relevant to attendees interested in the next generation of infrastructure and cloud computing and educational tech revolution tracks. I will explain how cloud computing resources can be accessed with no overheads imposed on the users. I will also give examples on how mybinder.org is being utilised for remote workshops and teaching in such a way that the students don't have to worry about setting up their environments correctly. The talk will be accessible for all audiences, there will be no assumed knowledge or technological expertise required.