Synapse
CONTRIBUTE to the CURE
Synapse is an innovation space that brings together scientific data, tools, and disease models into a Commons that enables true collaborative research. The platform consists of a web portal, web services, and integrations with data analysis tool and is organized around novel “Analysis Communities” that any scientist can create or join.
The utility of these workspaces serves as an incentive for researchers to work collectively on complex medical problems. Synapse is designed to enable many layers of collaboration: within a single team, between research teams, between research teams and industry partners, and within pharmaceutical companies. The beta version of Synapse is available on line. The value proposition for researchers to use this Commons and to work collaboratively is that Synapse will facilitate:
Finding and using relevant data. Currently, scientists have difficulty tracking down and gaining access to data and resources generated by others, even within the same organization. Synapse provides a detailed description of available data sets and a mechanism to access data in a uniform manner using common formats, controlled vocabularies and annotation standards.
Understanding analysis workflows. Synapse is conceived with the understanding that most analytical research is experimental and ad hoc in nature. Tracking who has run what version of a method on what version of the data helps projects run more smoothly, and ultimately enables reproducible workflows that allow others to build off of prior work.
Genome-scale analysis. Analyzing large-scale datasets is currently limited to those with access to large computational resources. The Amazon Web Services core will give all participants access to high-performance computational resources as well as IT support.
Forming collaborations. The platform will help scientists track what work has already been done in an area to avoid duplicative efforts and help create and sustain collaborations. Harmonization tools developed will also improve interoperability.
Patient engagement. Ensuring that informed consent is obtained for new research purposes is currently time consuming and inefficient. The portable consent tools developed for Synapse will enable patients to give consent for new projects, to be approached for recruitment, be thanked for research uses of their data, to withdraw from research and to specify their preferences for the uses of their data. It will encourage an active patient involvement that will enhance public trust and confidence in Synapse.
The value of this computational space is that it provides an open source environment rich in curated and standardized data combined with analytical and support. While other scientific fields successfully adopted open environments for the analysis of large-scale data medical research lags badly. Genomics possesses many of the essential ingredients to implement such collaborative, open research but lacks a common source infrastructure to facilitate model development and sharing. Synapse represents a compute environment for the generation and evaluation of disease models that can drive new basic and translational research and provide the framework for new effective drug discovery. For more background and details please see Mike Kellen's Synapse Vision Statement.
Open Integrated Workspace
Synapse is different from, and complementary to, other ongoing efforts. It is distinct from the data warehouses (e.g. NCBI, EBI) in that it goes beyond the repository database model to incentivize the creation of active community-based analysis and modeling groups. Synapse will incorporate existing tools such as, GenePattern, Taverna, Galaxy, and geWorkbench. Synapse will include integrated knowledge-based systems built on the current literature or data repositories, including tranSMART, that offer a number of genomic mining tools. Importantly, our approach does not just provide the data, code, workflows, and models, but establishes an environment that allows others to readily critique the models and then refine and build new versions. Synapse will be a:
Forum for development of Robust, Reproducible and Reusable analytical methods: where it will be feasible to track the steps needed to reproduce and understand an analysis, ultimately yielding better and more reusable analysis methodology.
Disease Model Repository: Through the deployment of the best methods and access to large curated datasets, it will be possible to generate models rapidly that can be assessed and used by others.
Forum for collaboration: Groups of geographically dispersed scientists can easily work together on projects in new ways that are ethical and lawful. The open architecture makes it possible to integrate the variety of different tools and data developed by others into a coherent collaborative analysis environment.
Synapse Timeline
