The Nexus platform
Traditional data analysis tools for MS and MSI are isolated desktop applications, which are easy to use for simple analyses on modest data volumes. However, in high-throughput contexts, such tools become problematic as computations slow you down and switching between tools to do your analyses eats away precious time.
The Nexus platform is designed to overcome those limitations. Nexus is a scalable cloud-based high performance computing platform that can cover the entire digital lifecycle of your molecular imaging and LC-MS data, along with all associated metadata. Owing to its scalability, it can efficiently manage petabytes of experimental data and perform complex analyses across large panels of datasets. You can retrieve data for manual analysis via dedicated API's.
This page describes the overall architecture of the Nexus platform and the advantages it brings. If you are interested in specific tools or workflows, you can navigate to the relevant pages via the "platform" menu item. If you want to learn more about our bioinformatics capabilities, we recommend checking out our scientific publications.
Overview
Nexus is a cloud-based system that acts as a one-stop shop for your data management and analysis needs. The figure below shows an architectural overview of the system. All relevant experimental data, such as MSI and LC-MS data, microscopy whole-slide images and more can be imported into the platform. Relevant metadata should also be imported along with the experimental data, for instance information about the sample, study or instrument configuration.
End users interact with the platform via a web UI, just like any other website. As such, there are virtually no requirements about your computers, including hardware or operating system. Because all number crunching is done on dedicated servers, you do not need a powerful computer for analysis, any modern device will do for most tasks, including tablets.
After importing data into Nexus, they can be analyzed within the platform using scalable data analysis workflows. An important advantage of analyzing within Nexus is that all analyses are automatically instrumented to provide full traceability, including information on who performed each analysis.
Reports can be generated within Nexus to summarize each analysis. These reports can be rendered into common enterprise formats, such as Word, Powerpoint, Excel or PDF files (or combinations thereof). Moreover, the platform itself can equally be used for reporting, since each analysis is associated with a unique, permanent link. With this link all the information about the analysis can be easily retrieved, thereby providing unmatched traceability.
Core features
The Nexus platform represents a paradigm shift in MSI data management and analysis. We outline some key differences compared to traditional tools here, as well as some notable additional features. The goal of this overview is to provide you with insights into the potential benefits of the Nexus platform for your use case. We support fully managed deployments to deliver a turnkey solution (preferred), but on-premise or hybrid strategies can also be provided.
If you are interested in a particular set of features, click the associated image to get more information. Of course, this page only covers some key elements. Do not hesitate to contact us in case you have any questions or remarks.
Data analysis workflows
Workflows provide a way to partition, structure and standardize complex data analysis pipelines, such as quantitation of MSI data. Based on a workflow definition, we can automatically determine which subtasks can be performed at a given time, and which team members it can be assigned to. This enables you to tackle complex tasks with large or remote teams, without unduly overhead. Moreover, workflows provide support for automated QC, to support reliable, high-throughput applications.
Operational scalability
Efficiently distribute and track data analysis tasks among your team, based on roles and responsibilities. Workflows have documentation and messaging support to streamline communication.
Observability
Workflows are structured data analyses processes, which means that a lot of context is available at each step. This enables data-driven QC to automatically detect potential problems. Available metadata can also be leveraged in these QC methods..
Customizable
Ideally, workflows are digital reifications of your lab protocols. The closer it matches, the better. We can tailor workflows to fit your exact use-case and analytical process for maximal efficiency.
High performance computing
The Nexus portal runs on modern high performance infrastructure, providing on-demand access to raw computation power whenever necessary. Our software is designed specifically to leverage such infrastructure, and can therefore provide a scalability that is orders of magnitude higher than traditional desktop tools could ever achieve. This scalability enables you to perform analyses that are prohibitive using other tools, but also supports parallel scheduling and execution of batch analyses, for instance in the context of studies involving many samples.
Parallel analyses
Nexus enables you to schedule many long-running data analyses. As opposed to most alternatives, these jobs can be executed in parallel within Nexus. End users can continue with other tasks in the platform and will get notified once computations are finished.
On-demand infrastructure
If you want to run massive analyses, the required infrastructure can be provisioned on-the-fly, including specialized hardware like GPUs, e.g., for deep learning workflows.
Software designed for cluster execution
Our software is built from the ground up to execute on high performance infrastructure. As such, it is inherently scalable far beyond the limitations of traditional data analysis tools.
Data management
Nexus provides scalable, tiered data storage capabilities that enable you to manage, inventorize and archive all your experimental data, along with its associated metadata. By having all assets in a single platform, you gain full traceability across the entire data analysis pipeline to enhance your reproducibility, quality control and reporting. Additionally, this future-proof approach provides a solid backbone for potential future compliance contexts.
Scalable storage
Our platform provides the capacity to store petabytes of raw data and downstream analysis artifacts. Data access follows security best practices while redundancy and backups prevent accidental loss. Data is moved transparently between multiple storage tiers.
Metadata management
In addition to experimental data, our solutions support and encourage you to input all relevant metadata. This metadata can be leveraged in your workflows, e.g., to easily configure differential expressions, to retrieve relevant datasets, e.g., all kidney samples of the past year, and enable automated in-depth QC procedures.
Traceability
Since all data and analyses are available within the Nexus platform, we can track the full lineage of your results, i.e., we can trace back all the way to the associated raw data for each result you've obtained, including which team members were involved.
User management
As a full-fledged platform solution, Nexus has a notion of users, roles and responsibilities. This enables Nexus to become a central hub to distribute complex tasks across your team. All data analysis steps are instrumented such that they can only be performed by people with the right privileges, and the information of who did what is recorded for traceability.
Roles
Roles define a set of responsibilities and associated priviliges, including which projects and workflows can be accessed, and which tasks can be performed. Each team member can have one or several roles, based on their expertise and responsibilities.
Personalized dashboards
Each team member can access personalized dashboards that display relevant information based on his or her assigned roles. Team members can access lists of actionable tasks, as well as receive notifications related to ongoing tasks.
Remote access
Our platform can be fully accessed remotely via the web, to support geographically spread teams. All you need to analyze your data is a computer with an internet connection. Enterprise users can hook our platform onto their corporate login systems to leverage the security measures they already have in place.
