OpenCravat.bsky.social

GitHub - KarchinLab/oc-mcp Contribute to KarchinLab/oc-mcp development by creating an account on GitHub.

github.com/KarchinLab/o...

Post 4/4
Hosted MCP endpoint: mcp.opencravat.org/sse (not a web page).
Claude: connect MCP server → URL above → No Auth → enable tools.
ChatGPT: Settings → Apps → Developer Mode → Create App → URL above → No Auth.
Also open source + runnable locally.

Post 3/4
Tools: coords, rsIDs, CAids, HGVS (g/c/p), protein missense → genomic HGVS via SynVar, + discover annotators/output fields. Uses GRCh38/hg38 + public OpenCRAVAT annotation service.

Post 2/4
More than “lookup”: give it a variant (rsID/HGVS/coords) and it returns clinical assertions (ClinVar/ClinGen, CIViC), population freqs (gnomAD + cohorts), effect predictors, + specialized resources (e.g., BRCA1 functional assay scores). Research/decision support ≠ clinical confirmation.

Post 1/4
🚀 Announcing the OpenCRAVAT MCP Server — variant annotation for AI tools via the Model Context Protocol (MCP). Lets LMs/clients call tools so they can fetch authoritative annotations on demand (not from model memory).

Looking for new ways to enrich your variant data? 🔍

We’ve made it simple to browse the OpenCRAVAT ecosystem. From ClinVar and gnomAD to calibrated variant effect predictions and visualization widgets, see what the store has to offer!

🍌 ocstore.opencravat.org

#Genomics #VariantAnnotation #BioSky

OpenCRAVAT Roadmap • KarchinLab This is the roadmap for the OpenCRAVAT Project.

Discover the latest updates and project status of OpenCRAVAT by exploring the roadmap available on GitHub. Stay informed about the progress and developments by visiting this link: [OpenCRAVAT Roadmap](github.com/orgs/Karchin...). #annotator #opencravat #bioinformatics #opensource #genomics 🧬 🧪 🖥️

; (3) run non-sensitive analyses locally and scale compute in cloud for bulk jobs; (4) automate QC and reporting templates; (5) train non-programmer staff using the GUI. #annotator #opencravat #bioinformatics #opensource #genomics

Stuck with a three-month VCF backlog? Try these five rapid changes to cut turnaround time in half. (1) prioritize with calibrated predictors; (2) use OpenCRAVAT modular annotators to remove tool fragmentation#annotator #opencravat #bioinformatics #opensource #genomics🧬 🖥️ 🧪

We are planning to launch a new collection of Jupyter notebooks and would love to know if you're interested. If so, please share topics or features you'd like included. Your feedback will help us tailor these notebooks to your needs and preferences.#annotator #opencravat #opensource 🧬 🧪 🖥️

Introducing our latest offering: the Calibrated Classification Package for clinical interpretation of variant effect predictor scores. This innovative package aids users in applying ACMG/AMP variant interpretation guidelines.#annotator #opencravat #bioinformatics #opensource #genomics 🧬 🧪 🖥️

Bringing Genetic Diversity to the Forefront: Moez Dawood on the AllofUs 250k Annotator for OpenCRAVAT Moez Dawood, an MD/PhD student at Baylor College of Medicine, has recently developed the AllofUs 250k annotator for OpenCRAVAT, a genomic annotation platform designed to handle both single variant…

@moezdawood.bsky.social created the AllofUs 250k annotator for OpenCRAVAT to improve genomic research by integrating diverse data, including ancestry-specific allele frequencies. You can read more about Moez's experience developing the annotator here: www.opencravat.org/bringing-gen...
#opensource

OpenCRAVAT Community Contributor Interest Form Help shape the future of genomic variant annotation! We’re looking for members of the genomics, bioinformatics, and clinical variant interpretation community to help improve OpenCRAVAT. As a…

Help shape the future of genomic variant annotation! We’re looking for community contributors to support OpenCRAVAT — from testing new features to improving documentation and outreach.
📝 Sign up here: forms.gle/v5t2ErBxYzqn...
#Genomics #Bioinformatics #OpenScience #Annotation

Would you be interested in organizing or speaking at meetups, writing blog posts, or promoting the project?
Are you part of any communities or organizations where you could share our project?
#annotator #opencravat #bioinformatics #opensource #genomics

Would you be open to helping improve documentation or writing user guides?
Do you have skills in UI/UX design, and would you be interested in helping us improve the user interface?
#annotator #opencravat #bioinformatics #opensource #genomics

Would you be willing to review pull requests or help triage GitHub issues?
Can you help test new features or provide feedback on pre-release versions?
Would you be interested in setting up automated test cases or improving test coverage?
#annotator #opencravat #bioinformatics #opensource #genomics

We are seeking community members interested in taking part in OpenCRAVAT's future.
Let us know if you might contribute in any of these areas:
Would you be interested in contributing code, bug fixes, or performance improvements?
Are there features or issues you’d like to help implement or debug?🧬🖥️

Welcome! You are invited to join a webinar: Exploring Personal Genomes with OpenCRAVAT. After registering, you will receive a confirmation email about joining the webinar. One-hour webinar teaching how to utilize OpenCRAVAT as an annotation tool for personal genomic data.

🧪 🧬 Want to explore your own genome?

Join our free webinar on how to use OpenCRAVAT to annotate & interpret your personal variants.

📅 July 10 | 🕐 1 PM EDT
🎙️ With Jasmine Baker, PhD & Rachel Karchin, PhD
🔗 tinyurl.com/3ur6vv35
#Genomics #Bioinformatics #OpenSource #OpenCRAVAT🖥️

🧬 Curious about your genome?
Join our free webinar on OpenCRAVAT to explore and annotate your own data!

📅 July 10 – 1 PM EDT
🎙️ Baker & Karchin (JHU)
🔗 tinyurl.com/3ur6vv35
#Genomics #Bioinformatics #OpenScience
#annotator #opencravat #bioinformatics #opensource #webinar #genomes 🖥🧪

Ever wonder what secrets your personal genome might hold? 🧬
Join us live on July 10 to explore how OpenCRAVAT helps annotate your data & turn it into meaningful insight.
Perfect for researchers & curious minds alike.
🔬 Registration link coming soon!🖥

Discover the power of OpenCRAVAT's cutting-edge annotation features that ensure seamless collaboration among users. Its intuitive design makes it easy for everyone to navigate, while enhancing productivity across the board.#annotator #opencravat #bioinformatics #opensource #genomics 🖥️ 🧬

Discover the power of the All of Us annotator with Open Cravat! This tool uses allele frequency data from the All of Us Research Program to explore genetic variations in diverse populations, enhancing precision medicine. Let's innovate healthcare together! #PrecisionMedicine #Genomics #AllOfUs🖥️ 🧬

Introducing the Regeneron Million Exome Annotator curated by Regeneron Genetics Center. Developed with major biobanks and health systems, it provides valuable genetic insights for research. We encourage its use in your research toolkit. #annotator #bioinformatics #opensource #genomics 🧪 🖥️🧬

OpenCRAVAT mouse

Need variant annotation fast? OpenCRAVAT makes it easy—whether you're analyzing one variant or thousands. Free, flexible, and built for discovery. Try it today at opencravat.org 🧪🖥🧬

OpenCRAVAT Integrates All of Us Dataset for Variant Annotation At ACMG 2025, Dr. Moez Dawood announced a groundbreaking initiative: the global democratization of deidentified allele count and frequency data from the first ~250,000 short-read Whole Genome…

🧬 🖥OpenCRAVAT will integrate the All of Us dataset. That's BILLIONS of gene variation annotations for better understanding our DNA.
Check out the blog: www.opencravat.org/opencravat-i...

Preprint coming soon from @moezdawood.bsky.social

The cat is out of the bag! We are excited to be a part of this collaboration. Global democratization of deidentified allele count + frequency data with population breakdown from the first ~250k short-read WGS in All of Us designed to plug straight into clinical workflows.🖥️🧪🧬

🖥️ New to OpenCRAVAT? Explore our Vignettes—tutorials designed for easy genomic variant analysis! 🧬

📖 Learn to:
✅ Annotate variants
✅ Interpret results for clinical & research
✅ Utilize powerful analysis tools

Start here: karchinlab.github.io/oc_vignettes/

#Genomics #VariantAnnotation #OpenSource

🧬 We Want Your Feedback! 🧬\

Do you use variant annotation software? We’re gathering insights from the genomics community to improve OpenCRAVAT and understand what features matter most to you.💡 Take this quick survey (it takes less than 2 minutes!): https://shorturl.at/iOvMt

OpenCRAVAT mouse

Have you seen our updated website? Head over to opencravat.org and check it out! 🖥🧪

Do you have research goals for 2025!? We'd love to hear them! #annotation #OpenCRAVAT #2025 🧪🖥