Embedded Files
Journal Club
Journal Club
Name: Daniel D. Ferrante, PhD
Title: Atlas AI: Drug Discovery at the Speed of AI
Abstract: In an era when the costs and timelines of pharmaceutical R&D have escalated — now exceeding $2 billion and requiring upwards of a decade to bring an average new drug to market — the industry confronts substantial obstacles. These challenges range from isolated data repositories and incompatible analytical pipelines to the protracted periods required for human-centric manual analysis. Addressing these pressing issues, we introduce Atlas AI, a revolutionary product developed through a strategic partnership between NVIDIA and Deloitte. Leveraging state-of-the-art NVIDIA GPUs and software such as BioNeMo, NeMo large language models, and the DGX Cloud, Atlas AI embodies a scientific data-centric and AI-first methodology to fundamentally transform the drug discovery landscape. It facilitates seamless integration of both proprietary and open-source multimodal life sciences research data, breaking down data silos that hamper cohesive analysis.
Notes
Notes
Serverless environment potentially via https://www.nvidia.com/en-us/clara/bionemo
NVIDIA NIMs https://www.nvidia.com/en-us/ai
converting genAI into GrapthQL :-O
AlphaFold 3 predicts the structure and interactions of all of life’s molecules: The AlphaFold3 blog post
Hackathon
Hackathon
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HeatCluster update (Lorena)
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Yjs update (Praful)
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Stop at 11:00
Stop at 11:00
Analyzing Cancer Data from the CRDC in the Google Cloud with the ISB-CGC Cancer Gateway in the Cloud
Analyzing Cancer Data from the CRDC in the Google Cloud with the ISB-CGC Cancer Gateway in the Cloud
Date: Wednesday, May 22, 2024, 11:00 a.m.–12:00 p.m. ET
Location: Virtual
Register
Meeting Link
The ISB-CGC (Cancer Gateway in the Cloud) hosts data from programs such as The Cancer Genome Atlas (TCGA) and Clinical Proteomic Tumor Analysis Consortium (CPTAC) in Google BigQuery, where it can be quickly analyzed using simple SQL or loaded into R and Python. As a cloud initiative and part of the Cancer Research Data Commons, ISB-CGC provides many resources and funding to start processing and analyzing your own data in the cloud.
Presented By:
David Pot, ISB-CGC
Fabian Seidl, ISB-CGC
Data Commons
Data Commons
Preparing for our own CRDC hackathon, maybe with thyroid cancer as the first exploratory .
Context:
Context:
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Bob: https://pubmed.ncbi.nlm.nih.gov/36878917
Sci Data
2023 Mar 6;10(1):120. doi: 10.1038/s41597-023-02029-x.
Ten lessons for data sharing with a data commons
Robert L Grossman
Recall reference implementation: https://gen3.org
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CRDC: https://pubmed.ncbi.nlm.nih.gov/38488510
Review Cancer Res
2024 May 2;84(9):1404-1409. doi: 10.1158/0008-5472.CAN-23-2730.
NCI Cancer Research Data Commons: Lessons Learned and Future State
Erika Kim # 1, Tanja Davidsen # 1, Brandi N Davis-Dusenbery 2, Alexander Baumann 3, Angela Maggio 4, Zhaoyi Chen 1 5, Daoud Meerzaman 1, Esmeralda Casas-Silva 1, David Pot 6, Todd Pihl 7, John Otridge 7, Eve Shalley 8; CRDC Program; Jill S Barnholtz-Sloan # 1 9, Anthony R Kerlavage # 1
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