Our Challenge Platform is an open science, collaborative competition framework for evaluating and comparing computational algorithms. We use this platform to establish methodological benchmarks, to determine assessment metrics for developing algorithms, and to promote best-practices in bioinformatics. Using this platform, we administer challenges, serve data, interact with cloud computing servers and provide a collaborative framework for research communities to exchange ideas, data and code. Groups can use this platform to organize challenges and broadcast them to participants.The platform includes a web client where challenge organizers can register participants, broadcast a detailed challenge description, distribute data, collect submissions, post results and communicate with participants through forums and list-serves.
We have recently expanded the challenge platform infrastructure to support Challenges where participants are asked to submit algorithms in place of solutions. In these cases, the platform runs the algorithms on the data and returns results to participants. This allows organizers to perform evaluations using data that cannot be made openly available to challenge participants due to legal or ethical restrictions. Moreover, this infrastructure permits researchers outside of the challenge to access and run their pipelines for their own research purposes, thereby facilitating a clearinghouse for tools and methods.
Our Challenge Platform is used to power DREAM Challenges, which are focused exclusively on biomedicine with a strong emphasis on cancer, and has an explicit mandate for transparency, openness, and collaboration. These principles enable DREAM to focus on the overarching goal of providing a community resource for the evaluation of emerging methodologies based on practical applications. For more information – and an extended list of current and past DREAM challenges – please visit dreamchallenges.org. In addition, we have helped to launch several independent Challenges using our platform. To explore opportunities for partnering with Sage experts and using this platform to address scientific questions and foster open and collaborative science, please contact firstname.lastname@example.org.
Synapse is a collaborative research platform that allows research teams to share data, track analyses, and collaborate across organizational boundaries. At Sage Bionetworks, we use the Synapse platform to support all of our collaborative science and assessments & benchmarking projects. Synapse allows us to organize content, establish transparent and reproducible workflows, track collaborative analysis across distributed teams, and broadcast research assets.
Designed according to the Findable, Accessible, Interoperable, Reusable (FAIR) principles, Synapse supports discovery, access, and reuse of digital assets by the broader scientific community. The platform provides HIPAA-compliant security and data governance tools to ensure data is protected and accessible to scientists while respecting patients’ rights. The Synapse technology stack is REST-based, modular, and built from industry-standard components, intended to leverage public platforms and tools including cloud storage and compute, data repositories, data visualization tools, and analytical tools such as RStudio and Jupyter Notebooks. The Synapse engineering team supports integrations with external systems.
Synapse is freely available for use by external researchers. You can find it at Synapse.org. For more information, visit our Synapse documentation site.
Bridge is a technology platform for conducting biomedical research studies primarily using the ResearchKit (iOS) and ResearchStack (Android) frameworks. Bridge is composed of HIPAA-compliant web services and multi-language SDKs that facilitate the following:
- Registration and informed consent to participate in research
- Web-based tools to design and schedule study surveys and sensor-based tasks
- Acquisition and secure transfer of multiple data types (surveys, sensors, audio, video, or custom data types)
- A study management portal with daily dashboard updates
- De-identification and storage of study data in our collaborative data science environment, Synapse
Bridge has been in active use since Day 1 of the ResearchKit and ResearchStack frameworks and it facilitates many ongoing research studies including the mPower mobile Parkinson Disease study and the cross-platform Mole Mapper Melanoma Study.
Researchers interested in developing apps using this service should check out our Bridge Developer Portal for documentation, tutorials, and links to code repositories. Researchers wanting assistance with the design or execution of a mobile research study should contact us at email@example.com.