GeoMx Spatial Transcriptomics
Best-in-class GeoMx SolutionFrom DCC files to pathway enrichment and beyond
Single Cell Gene Expression
From FASTQ to cell clusters and beyond
Gene Expression: RNA-seq
Complete guide to RNA-seq data analysis
NanoString: Gene & miRNA Expression
Visualize and collaborate on NanoString nCounter datasets
Gene Regulation & Anti-Sense: Small RNA-seq
Small RNA-seq data analysis designed for the biologist
Histone Mark & Transcription Factor: ChIP-seq
Comprehensive ChIP-seq data analysis
Chromatin Accessibility: ATAC-Seq
Genome-wide chromatin accessibility analysis
Sharing & Collaboration
Accelerate teamwork anywhere in the world
Knowledge Graph and Search
Data organized for semantic queries
COVID-19 Diagnostic Monitoring System
SARS-CoV-2 Viral Mutation Tracking
COVID Research Community
Global research analyzing COVID-19 genomic datasets
Immuno Oncology
Making discoveries on IO research
Breast Cancer
Identifying differentially expressed miRNAs in breast cancer
HIV
Transcriptional and genomic profiling study of HIV+ DLBCL
Diabetes
Discover and accelerate T1D
Multi-Omics Dataset
Explore multi-omics datasets in epigenetics research
Single Cell Data
Explore datasets with our Cell Ranger graph-based clustering
nanoString Gene Expression
Analyze your nCounter data in minutes
nanoString Mouse Glial Profiling Panel
Explore neuroinflammatory astrocyte subtypes in the mouse brain
RNA-Seq Data
Get started with bulk RNA-Seq data
Subscription and Pricing Comparison
Learn about Enterprise, Professional, and Academic subscriptions
Enterprise Offering
Expand the depth and reach of your scientific data teams
Single Cell Gene Expression
Gene Expression: RNA-seq
A complete guide to RNA-seq data analysis
NanoString: Gene, miRNA & Protein Expression
A complete guide to NanoString nCounter data analysis and collaboration
Gene Regulation & Anti-Sense: Small RNA-seq
Small RNA-seq data analysis designed for the biologist
Histone Mark & Transcription Factor: ChIP-seq
Comprehensive ChIP-seq data analysis
Chromatin Accessibility: ATAC-Seq
Sharing & Collaboration
Accelerate teamwork by connecting experts and datasets anywhere in the world
Knowledge Graph and Search
Every scientist should benefit from Knowledge Graphs and have access to its advanced Search and insights
Knowledge Graphs integrate data by describing entities and their relationships. These allow logical inference for retrieving implicit knowledge rather than only allowing queries requesting explicit knowledge. Knowledge Graphs are crucial for advanced search, machine learning, and for uncovering patterns & correlations.
Empowers every user to search & collaborate across their personal Knowledge Graph, automatically integrating every result, sample, comparison, and much more
Search for any gene, pathway, disease, or drug to find matching showcases, projects, experiment, collaboration space and more
Unify knowledge and empower greater insight across organizations with Enterprise Knowledge Graphs
ROSALIND Enterprise Knowledge Graph provides secure, private, and highly scalable Knowledge Graph functionality for teams & Enterprise customers. This unlocks the full potential of Search and enables organizations to achieve the greatest value from their research investments by empowering every authorized scientist to search, explore and collaborate on every available dataset
Every dataset and record is automatically added and available, including public data and private signatures
SSO integration with Active Directory permissions provides discrete authorization for sensitive data collections, such as clinical trials
Achieving ROI on research projects requires FAIR data access
Search globally, access instantly
Search for any gene, pathway, disease, drug or term. Search for anything that describes your Projects, Experiments, Comparisons, Filters, Meta-Analyses, Collaboration Spaces and more.
Don't worry about spelling adalimumab, ROSALIND uses fuzzy logic to find the best search results.
Graph powers every search and interpretation with hybrid search providing valuable insights for each query
Focus on your results even when your favorite pathway doesn't show up
Within any experiment, search over 300,000 terms and pathways to find the ones that most closely match your research focus and observe the gene expression directly in your experiment.
Find any pathway or term from the integrated knowledge bases
Each search result includes Graph insights on the comparisons, samples and attributes of each experiment
Everything you need to know when you're looking for it
Hybrid search broadly queries the knowledge management system to provide context and insights as query results including significance, genes up and downregulated, descriptions, locations and storage hierarchy, as well as related and similar results.
Inspect pathway source knowledge bases and each of the genes contained in each
Search results in the context of your experiment
Explore search results within your experiments to see focused insights on gene expression and pathway significance from any knowledge base
Aggregate pathways of interest in one concise view with custom plots
Click on the pathway magnifier to inspect pathway details across Search results
Dive deeper into Search results with detailed pathway exploration
Inspect pathways and terms from Search to see genes in term, up and downregulated genes as well as p-values
Click on table headers to adjust sorting
Toggle plot types to see interactive heatmaps and bar plots
Click download to access aggregated knowledge base records
The ROSALIND Knowledge Graph unifies knowledge and accelerates every aspect of ROSALIND, enabling advanced intelligence and powerful Search. Every analysis evaluates over 100 million relationships across 300,000 gene signatures and terms from the 50+ ROSALIND Knowledge Bases.
ROSALIND organizes data into a knowledge graph that enables semantic search and AI applications. Each new analysis is integrated into the knowledge graph thus connecting it to past analyses and enabling deeper comparisons. Knowledge graphs can be limited to individual users or expanded to cover all users within an organization via Enterprise SSO and permissions-based access. ROSALIND makes the knowledge graph accessible to users via a simple search box and can enable expanded access to machine learning tools via API.
A knowledge graph integrates collections of data and information by describing entities and their relationships. Knowledge Graphs allow logical inference for retrieving implicit knowledge rather than only allowing queries requesting explicit knowledge. Knowledge Graphs are crucial for advanced search and machine learning, and are being used for uncovering patterns and new relationships in ROSALIND.
Long Do
Sr. Manager, Informatics at Samumed LLC
Every user has access to search and collaborate across their own personal Knowledge Graph, which automatically integrates every sample, comparison, filter, gene list, meta-analysis, and experiment that the user has access to. Enterprise users can be granted permissions for search functionality that cuts across the entire organization.
Users can search for any gene, pathway, disease, drug, or term as well as any descriptive text that may describe any Project, Experiment, Comparison, Filter, Meta-Analysis, Collaboration Space, or Gene List. ROSALIND Search returns the results globally and contextually, linking directly to datasets or showing the statistical significance and gene-level details within any experiment.
Examples:
To search, select the magnifying glass from the ROSALIND header menu and enter a query in the search box.
Team and Enterprise Subscriptions unlock the Institutional Knowledge Graph, empowering authorized scientists to search, explore and collaborate with the Unified Intelligence of all insights across the organization. To learn more, please contact sales@rosalind.bio.
ROSALIND secures all information and every Space by encrypting all data transmissions and data storage. Using an access-control system architecture ensures that access is only granted to authenticated users with permissions to a shared dataset. Only Space owners have the ability to delete Spaces they create and may also remove any experiment, meta-analysis, or participant at any time. Each participant has the ability to remove their own experiments and meta-analyses or to leave a Space. All changes within a Space are reported on the activity feed.
IT departments may define detailed policies to administer and restrict sharing such that teamwork is enabled without compromising corporate security policies. Learn more about Enterprise Subscriptions by contacting sales.
ROSALIND is designed for the Scientist, so you can focus on the biology and science without having to invest months and months trying to learn bioinformatics, programming or biostatistics
Capable of performing advanced analyses including contamination detection, covariate correction, batch correction and multi-omic analyses
Utilizing a clean, intuitive and immersive user interface, Scientists new to the platform ramp quickly with little training to focus on discovery
Explore experiment results in high-quality, publiction-ready, interactive diagrams and plots
ROSALIND is designed for the Scientist, so you can focus on the biology and science without having to invest months and months trying to learn bioinformatics, programming or biostatistics
Start new experiments by importing FASTQ files from sequencing, or counts (raw or normalized)
Built-in pipelines are tuned to utilize industry standard, widely published bioinformatics tools. For more information, review the ROSALIND specifications and method section
Every communication and data transfer on ROSALIND is encrypted and secured. Multiple layers of data protection ensure availability
Is a subscription required to join a Space?
A subscription is not required to accept an invite and join a Space. However, all users must have a ROSALIND account to join a Space.
Can I share an experiment in more than one Space?
Yes, an experiment may be shared in any number of spaces to enable collaboration across multiple groups. Consistency, and security are preserved for the experiment within every space that it is included.
How do I register for a ROSALIND account?
ROSALIND accounts can be setup by clicking New User on the https://rosalind.onramp.bio login page, or by completing a Trial Request. To learn more about Subscriptions, visit the Product Comparison.
Can I remove my experiment or meta-analysis from a Space?
Any participant can remove an experiment or meta-analysis that they have shared within a Space at anytime. Doing so immediately removes access to the shared resource.
How do I create a new Space and begin sharing an experiment?
Any user with a ROSALIND account can create a collaboration Space. Users may only add experiments and meta-analyses that they own, including public data experiments they have imported.
Can I leave a Space and remove myself from the collaboration?
Any participant can leave a Space at anytime. Doing so removes their access and will require a new invite to join the collaborative Space again. Only the owner of a Space or an Enterprise Administrator may remove participants.
What can I do if I’m invited to a collaboration Space?
After joining a Space, every user can view and explore the shared experiments and meta-analyses, including all of the applicable pathway intepretation. ROSALIND Scientists, Directors and Explorers can add new filters to change cut-offs, or add new comparions and meta-analyses.
Can the API be used to add experiments to a Space?
Yes, API integration enables production informatics teams to centrally process and distribute results within Spaces to each program or project team requesting an analysis. This is a best practice among pharma R&D teams. API integration also includes Single-Sign-On (SSO) support. Contact sales to learn more sales@onramp.bio