As the scope and data demands of the UK Biobank biomedical database gets bigger, we’re helping UK Biobank to meet its audacious ambitions.
The latest improvement is a new cloud-based Research Analysis Platform (RAP), which will exponentially increase the scale and accessibility of the world’s most comprehensive biomedical database. Watch the short explainer video to learn more.
Since 2006, UK Biobank has been on a mission to unleash the imaginations of the global research community to go further and improve human health. This project is another example of their dedication to democratizing access to this rich, multi-dimensional data resource.
DNAnexus shares this vision. We understand that delivering on UK Biobank’s promise of improving human health requires overcoming the challenges around scale and diversity of datasets, the need for integrated multimodal analytics and comprehensive analysis tools, stringent controls on data security and regulatory compliance, and the critical need for collaboration globally and across institutional firewalls.
That’s why we partnered with UK Biobank to build a scalable, secure, and collaborative Research Analysis Platform to accelerate the speed and scale of health-related research.
Enabled by DNAnexus technology and powered by Amazon Web Services (AWS), RAP provides approved researchers with the ability to access and analyze the 11 petabytes of data in the UK Biobank database from anywhere in the world.
It also enables easier collaboration between researchers within the same team, or on the other side of the planet. Users can leverage a valuable library of tools for analyzing genomic and clinical data.
And as the UK Biobank grows, the platform is designed to grow with it, a vital requirement as the resource is expected to surpass 40 petabytes of data by 2025. To put that number into perspective, it would take over a century of continuous viewing to consume 40 petabyte’s worth of high definition 4k movies!
We are proud to partner with UK Biobank on this landmark initiative that combines our leading biomedical informatics platform and insight tools with UK Biobank’s genomics and clinical datasets. This global collaboration brings us one step closer to accomplishing our vision of democratizing data access to drive innovations in research that profoundly impact patient lives.
Hannah Gunderman, Data, Gaming, and Popular Culture Librarian, Carnegie Mellon University Libraries
Ben Busby, Director, Solution Science and Principal Scientist, DNAnexus
With the world still reckoning with the impacts of the COVID-19 pandemic, one thing that has remained constant is the need to change how people collaborate and communicate ideas, often shifting to remote and virtual formats. The COVID-19 pandemic accelerated the rate at which hackathons are hosted in a virtual format. Remote hackathons have the potential to mirror the personally and professionally transforming experiences conveyed by in-person events to those who can not travel due to financial, physical, or environmental constraints. Remote hackathons allow the intellectual wealth of scientists in these countries to be applied to the important topics and goals of the hackathon, while supporting their health and safety through virtual participation. We hope that hackathons will retain a hybrid model to maximize the scientific contributions of both in-person and remote participants.
Why are hackathons important?
Hackathons allow for concentrated, focused effort on a task or goal by bringing together scientific experts in a particular discipline, such as structural variants, or united by a common goal, such as ending neurofibromatosis. Some hackathons solve thorny problems, make life easier for practitioners of specific disciplines, or push the boundaries of what a particular scientific field can do. That said, hackathons not only produce content (usually software), but ideally also actively facilitate education and networking. Those who participate often have professionally transformative experiences that can lead to a wider scientific network, job opportunities, and increased confidence in their coding and research skills.
Hackathons largely follow the model of “disruptive innovation” by serving as a prototyping layer across scientific organizations, producing new ideas and technologies that the community can then assess for value in their larger goals and initiatives. The prototypes that emerge either push the envelope of what is possible with biomedical informatics, or make day-to-day bioinformatics easier. While the code isn’t necessarily persistent, these proof-of-concepts are intended for the community to build upon. Hackathons foster an environment with “buzz,” an economic geography concept referring to the serendipitous sharing of creative ideas that happens when people engage in face-to-face interactions. The last year has taught us that these benefits from hackathons are also afforded through hybrid or fully-remote formats, providing hope for a positive future of hybrid hackathons in scientific advancement and discovery.
How do hackathons benefit the participants?
Not only do hackathons have an undeniable benefit to the broader scientific community, but, they also can provide transformative and impactful experiences for the participants themselves. These experiences largely revolve around the areas of confidence-building, educational development, and camaraderie.
As described earlier, the “buzz” created in hackathon environments helps advance the sharing of creative and innovative ideas. Through this exchange of ideas, participants can advance their journeys in computational problem-solving and modern software development techniques. In the bioinformatics space, there are many beginner data scientists who are still learning foundational skills in computation and scientific collaboration. Hackathons, whether remote or in-person, offer a concentrated space for beginner data scientists to advance their skills in both of these areas alongside more established bioinformatics researchers. Not only does this afford educational benefits to these participants, but it can also increase their confidence as scientists who can contribute to important research endeavours.
Finally, hackathons also create the opportunity for participants to forge close personal friendships and bonds, which can lead to long-term collaborations and network-building.
Participants often find themselves in intensely challenging and time-limited environments as they race to accomplish the goals of the hackathon, and going through these transformative experiences together can lead to strong friendships and connections that span beyond the bounds of the hackathon itself. This is not limited to in-person hackathons, however: video-conferencing software such as Zoom and collaborative tools such as Slack allow participants to interact with each other and build both interpersonal and professional connections.
A Retrospective Look Into CMU-DNAnexus Virtual “Genomic Data to the Clinic” Hackathon
The CMU-DNAnexus Virtual “Genomic Data to the Clinic” Hackathon (June 1st – June 4th 2021) was focused on bringing complex genomic data into the clinic. Specifically, we focused on integrating Expressed Variants, Polygenic Risk Scores, Structural Variants and T-Cell Receptors into an Electronic Medical Record readable format using OMOP and worked on a clinically presentable interface. Remote support was offered by librarians from Carnegie Mellon University Libraries who have specialties in data management, bioinformatics, and information sciences. This support included collating important resources found by hackathon participants (such as tools, software, literature, etc.) into a single spreadsheet for easy access, reviewing the hackathon manuscript for syntax and readability, and preparing the manuscript for submission to BioHackrXiv. Communication platforms such as Zoom and Slack can offer ways to stay in touch and facilitate collaboration during a remote hackathon, but information can still get lost in translation in environments where we can’t see each other face-to-face. Librarians are trained in the information sciences and well-positioned to assist in keeping information organized and accessible during a remote or hybrid hackathon.
Participants not only effectively used online collaboration tools to create innovative workflows and deliverables supporting the goals of the hackathon, but also used tools such as Slack to develop interpersonal friendships. Much of the same dynamic energy and “buzz” felt during an in-person hackathon was also felt in this virtual space and the experience has already led to some promising future collaborations and scientific endeavors, including an accepted proposal for a presentation at the 2021 annual meeting of the American Society of Human Genetics that will share the scientific findings from this hackathon.
Upcoming hybrid hackatons
Although the pandemic is experiencing a long tail, we can still begin to envision what our post-pandemic future may look like, taking the lessons we have learned from navigating our remote environment for the past several months. One of the lessons we can bring into a post-pandemic future is that hackathons with a virtual option can help us create more equitable and diverse intellectual spaces for tackling the most pressing issues we face in bioinformatics. Moving forward, hackathons should take a hybrid model and allow for both in-person and remote participation, while allowing more team leads the sequestration they need to fully focus their energies on these efforts instead of juggling both work and the hackathon.
Further, leveraging the support of librarians in the hackathon space can lead to a more organized, cohesive, and collaborative experience for participants. This is particularly true for fully remote or hybrid hackathons, where clear communication channels are crucial for all participants. Librarians can help facilitate collaboration and coordination between remote and in-person participants, and help collate resources (such as tools, software, and literature) found during the course of the hackathon.
We are excited to see what the future of hybrid hackathons holds for our field at large, and the scientific discoveries that will result from these events. Below are some upcoming hackathons you can follow or get involved in!
Polymerase and primers. VCF and TBI. DNAnexus and AWS. Some things are just better together.
At DNAnexus, we are big believers in collaboration — among scientists, between industry and academia, and amid complementary technologies. Our platforms enable researchers to work together across geographical boundaries, and to bring together various types of multi-omics data spanning single cell expression, population genomics, microbiome, and epigenetics.
To do so, we work closely with Amazon Web Services to leverage the scalability of the AWS cloud and incorporate the latest advances in analytics and knowledge management. Life science organizations of all sizes and disciplines choose DNAnexus and AWS to help navigate the complexity and scale of their biomedical research to meet their immediate unique business needs, as well as long-term growth plans.
Join us this month as we hear from two businesses that harnessed the power of DNAnexus and AWS to greatly expand their operations.
San Diego based Human Longevity, Inc., is hoping to revolutionize precision health care with a suite of tests, services and care that help preempt disease before symptoms arise. Its Health Nucleus Clinic aggregates more than 150 gigabytes of data from whole-genome sequencing, whole-body magnetic resonance imaging, metabolomics, comprehensive blood biomarkers, and other modalities to deliver a complete, personalized picture of health.
In this webinar, Wayne Delport will discuss the development of its whole-genome sequencing product used by Health Nucleus physicians to provide personalized care based on assessment of risk. He will cover the technical and regulatory challenges posed by delivery of this product and how HLI used the DNAnexus Titan Platform on AWS for everything from data ingestion, data analysis, and data delivery, enabling the company to streamline their genomics infrastructure and focus on product improvements.
In 2014, the Regeneron Genetics Center demonstrated how cloud infrastructure can rapidly transform a drug discovery program by enabling the generation, delivery and analysis of genetic results at unprecedented speeds. Six years and two orders of magnitude later, scale is no longer measured in numbers of samples but in the diversity of the RGC’s collaborator network, the successful programs of industry partners, and the unrealized opportunities of the world’s largest genetic resource.
Find out how RGC and DNAnexus support a growing hybrid industry/academic community, including managing hundreds of collaborators with a full spectrum of use cases, ensuring participant confidentiality through unparalleled international compliance, protecting partner IP through autonomous research and billing environments, and driving the value of genetic data through cost-efficient sharing of genetic data, tools, and results.