About CAVATICA
About
CAVATICA was co-developed by Velsera (formerly Seven Bridges) and the Center for Data Driven Discovery in Biomedicine. CAVATICA provides toolsets to support a diverse spectrum of researchers, from low-code to packed workflows to interactive analysis. CAVATICA is FedRAMP and FISMA compliant, and meets NIH standards for data security, storage, and distribution. It is HIPAA-compliant and can be used for PHI data.
This page provides generic instructions on how to access, navigate, and leverage relevant tools in CAVATICA.
Features
The integration of CAVATICA provides users with multiple sophisticated tools to further analyze portal data, combine it with other research datasets, and make novel discoveries in the field of Exceptional Longevity.
The CAVATICA provides you:
Access to hundreds of commonly used, pre-installed bioinformatics tools through the Public Apps Gallery, including MaxQuant, Olink, and FragPipe for proteomics as well as a large selection of transcriptomic tools.
Integration with data from the ELITE Portal and other datasets. You can also bring your own files into CAVATICA.
Project spaces to collaborate with other researchers around the world without having to download datasets.
Analytical workspace with compute and storage on AWS or Google Cloud, interactive analysis with JupyterLab and R Studio, workflow execution with Common Workflow Language (CWL) and NextFlow (beta), and access to Interactive Genome Browser and Variant Browser.
CAVATICA users working with data from Sage Bionetwork’s Portals should only use AWS for compute and storage to avoid data egress charges and higher costs for analysis.
Gaining Access
Follow steps to 1) Sign in to CAVATICA and 2) Link your Synapse Account.
Getting Started
Visit the CAVATICA Onboarding YouTube channel for a series of video tutorials to help you get started on the platform, create projects, add data, collaborate, manage files, and explore the Public Apps Gallery. Visit the general Velsera YouTube channel for additional webinars and videos of interest.
Technical documentation and getting started guides can be found in the CAVATICA Knowledge Center.
Looking for some example projects? Go to the public projects page for demo projects you can access to analyze your data.
Service Support
General help is available any time while using CAVATICA by clicking the blue “?” on the bottom right of the screen or by emailing support@velsera.com.
Office Hours
Additional support is available to Exceptional Longevity Consortia members at Velsera’s office hours. Office hours are held every Tuesday at 10 AM ET and Thursday at 2 PM ET. Join the session using this Google Meet link.
Exceptional Longevity Cloud Credits
Exceptional Longevity (EL) Consortia members are eligible for cloud credits on CAVATICA that are available in scalable amounts, allowing users to explore datasets and the platform independently before writing an application to support larger analyses.
EL Consortia members are defined as researchers who are affiliated with one of the National Institute of Aging (NIA)-funded exceptional longevity translational research projects.
$300 USD Pilot Credits- All EL Consortia Members
To participate in the pilot program, please create an account on CAVATICA and then write to support@velsera.com. In your email, please include:
Your full name and institutional affiliation
Your CAVATICA account username
A statement that you are a member of the Exceptional Longevity Program.
Please allow 1-2 business days before funds will be added to your account.
$1,000 USD Limited Credits Billing Group
Users may apply for credits to support specific projects. These Limited Credits billing groups are capped at $1,000. Researchers can use these credits to build and test workflows on the platform, complete small analysis projects, or carry out benchmarking experiments in preparation for larger analysis projects.
To apply for a Limited Credits Billing Group, users should email elite-portal@sagebase.org with the Subject Line: CAVATICA Limited Credits Billing Group. Users should include a brief description of their intended use for the credits, less than one page typed.
Up to $20,000 USD Extended Credits Billing Group
Users who have received a Limited Credits billing group are eligible to apply for additional credits to complete a larger research project. These Extended Credits billing groups are capped at $20,000. A list of questions including preliminary results and benchmarking outcomes from the Limited Credits stage will be asked and reviewed during the application process.
To apply for an Extended Credits Billing Group, users should email elite-portal@sagebase.org with the Subject Line: CAVATICA Extended Credits Billing Group. Users should include a detailed description of their intended use for the credits, a description of their activities accomplished under the Limited Credits billing group, and a calculated estimate of cost based on intended workflows and datasets.
CAVATICA Data Connections
AD Knowledge Portal
The AD Knowledge Portal allows researchers to discover and download Alzheimer's Disease data, analyses, and tools from the National Institute on Aging's Alzheimer's Disease Translational Research Program.
Cancer Genomics Cloud
The Cancer Genomics Cloud (CGC) is an National Cancer Institute (NCI) dedicated platform and allows discoverability of data from the Cancer Research Data Commons. More information about datasets on the CGC can be found here: https://www.cancergenomicscloud.org/datasets
ELITE Portal
Exceptional longevity (EL) is an extreme phenotype representing the ability to achieve exceptional health span. EL may be influenced by differing domain-specific factors that affect preserved performance in physiologic systems (e.g., respiratory, cardiovascular, immune) or functional domains (e.g., mobility, cognition). Understanding the functional effects of protective human genetic variants and cellular factors associated with EL could help identify novel targets for interventions to mimic their favorable effects.
Gen3 BioDataCatalyst
Gen3 BioData Catalyst (BDC) serves as the data portal for the National Heart, Lung, and Blood Institute (NHLBI) BDC ecosystem. It includes datasets from TOPMed, the Cardiovascular Health Study (CHS), Framingham Heart Study (FHS), and others. Data is also discoverable, with a different interface, directly through the BioData Catalyst powered by Seven Bridges platform.
INCLUDE
The goal of the National Institutes of Health (NIH) INCLUDE Project is to improve the health and quality of life for people with Down syndrome (DS). INCLUDE stands for INvestigation of Co-occurring conditions across the Lifespan to Understand Down syndromE. People with Down syndrome develop certain medical conditions, like Alzheimer’s disease and autoimmune conditions, more often than the general population, yet they seem to be protected from some cancers and other common co-occurring conditions. In 2018, the NIH launched the INCLUDE Project to help understand why. INCLUDE contains a variety of data types from over 9,000 participants.
NF Portal (Synapse)
The NF Data Portal was created to help openly explore and share NF datasets, analysis tools, resources, and publications related to neurofibromatosis and schwannomatosis. Anyone can join the NF Open Science Initiative (NF-OSI) to contribute!
SRA (via SRA to DRS converter)
Unlocks the wealth of data house in the Sequence Read Archive.
Kids First
The National Institutes of Health (NIH) Common Fund-supported program aims to “accelerate research and promote discoveries for children affected with cancer and structural birth defects”. Currently the Data Resource Center (DRC) contains data from over 34,000 participants, including DNA and RNA.