gnomad-browser
haystack
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gnomad-browser | haystack | |
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15 | 55 | |
78 | 13,633 | |
- | 5.8% | |
9.7 | 9.9 | |
3 days ago | 4 days ago | |
TypeScript | Python | |
MIT License | Apache License 2.0 |
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
gnomad-browser
- All identified polymorphisms in a given gene, how to find?
- AskScience AMA Series: We're human genetics researchers here to discuss connections between people in different geographical regions. Ask us anything!
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Converting 23&Me raw data into a format usable by Admixtools 2
try one of these: GnomAD (https://gnomad.broadinstitute.org/) 1000 Genomes (http://browser.1000genomes.org) dbSNP (http://www.ncbi.nlm.nih.gov/snp)
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What is the maximum number of human?
Maybe you can ask the opposite question; what are the bounds of of a functional human being. https://gnomad.broadinstitute.org/ GnomAD is a aggregation of healthy human genetic sequences which was primarily built on the aggregated control groups of many genetic sequencing studies. There are studies of this data analysing the co-occurrence of variants in gnomAD which may help.
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Insights from personal sequencing data I can explore.
Maybe something like this? https://promethease.com/ Clinvar for variants that might be of clinical relevance. https://gnomad.broadinstitute.org/ for allele frequencies & some info about variants.
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What are some non-pathogenic alleles of the SNCA gene, or how do I find them?
You could look at aggregation databases such as gnomad https://gnomad.broadinstitute.org/ anything with a frequency incompatible with the disease is likely non pathogenic
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Ask HN: Who is hiring? (March 2022)
Broad Institute of MIT and Harvard | Cambridge, MA | Frontend Software Engineer | REMOTE or HYBRID (New England area)
We are hiring a frontend developer to help lead the next phase of the gnomAD browser, a web application for displaying the world's largest collection of human genome/exome sequences. https://gnomad.broadinstitute.org. Looking for applicants who are excited about data visualization and designing complex interfaces for scientific research.
Apply here: http://broad.io/cq7dw8
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Ask HN: Who is hiring? (February 2022)
Broad Institute of MIT and Harvard | New England | Software Engineer | REMOTE/HYBRID
Our team is focused on building the tools necessary to visualize and interpret massive data sets of human genetic variation and functional genomic information. We have developed gnomAD (https://gnomad.broadinstitute.org), the world’s largest public reference dataset of human exomes and genomes. gnomAD has become one of the most widely used resources in the field, and is now the default reference database for virtually all clinical interpretation pipelines, as well as a standard analysis resource for a wide variety of genetic and biological studies. We estimate gnomAD has contributed to the clinical diagnosis of over 2 million patients with genetic disorders.
Your role will be to maintain the gnomAD browser, our open source web application for exploring gnomAD and related datasets, and develop new scientific functionality as we continue to grow to over 1 million human samples. You will work with a team of software engineers, computational biologists and clinical and research users to develop new features and visualizations that incorporate user feedback. Software engineering skills and an interest in user interface design and data visualization are key. Basic familiarity with genomics and DNA sequencing data is preferred, but not required. Most importantly, the ideal candidate will have enthusiasm for playing a critical role in a team-oriented project and learning new domains.
Minimum Requirements
- Ask HN: How to be my own genetic disease researcher for my partner?
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How to check if a discovered mutation is novel or was discovered before ?
If you're talking about humans, start with gnomAD: https://gnomad.broadinstitute.org/
haystack
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Haystack DB – 10x faster than FAISS with binary embeddings by default
I was confused for a bit but there is no relation to https://haystack.deepset.ai/
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Release Radar • March 2024 Edition
View on GitHub
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First 15 Open Source Advent projects
4. Haystack by Deepset | Github | tutorial
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Generative AI Frameworks and Tools Every Developer Should Know!
Haystack can be classified as an end-to-end framework for building applications powered by various NLP technologies, including but not limited to generative AI. While it doesn't directly focus on building generative models from scratch, it provides a robust platform for:
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Best way to programmatically extract data from a set of .pdf files?
But if you want an API that you can use to develop your own flow, Haystack from Deepset could be worth a look.
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Which LLM framework(s) do you use in production and why?
Haystack for production. We cannot afford breaking changes in our production apps. Its stable, documentation is excellent and did I mention its' STABLE!??
- Overview: AI Assembly Architectures
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Llama2 and Haystack on Colab
I recently conducted some experiments with Llama2 and Haystack (https://github.com/deepset-ai/haystack), the NLP/LLM framework.
The notebook can be helpful for those trying to load Llama2 on Colab.
1) Installed Transformers from the main branch (and other libraries)
- Build with LLMs for production with Haystack – has 10k stars on GitHub
- Show HN: Haystack – Production-Ready LLM Framework
What are some alternatives?
webviz - web-based visualization libraries
langchain - 🦜🔗 Build context-aware reasoning applications
metamask-extension - :globe_with_meridians: :electric_plug: The MetaMask browser extension enables browsing Ethereum blockchain enabled websites
langchain - ⚡ Building applications with LLMs through composability ⚡ [Moved to: https://github.com/langchain-ai/langchain]
aioli - Framework for building fast genomics web tools with WebAssembly and WebWorkers
gpt-neo - An implementation of model parallel GPT-2 and GPT-3-style models using the mesh-tensorflow library.
Baserow - Open source no-code database and Airtable alternative. Create your own online database without technical experience. Performant with high volumes of data, can be self hosted and supports plugins
BentoML - The most flexible way to serve AI/ML models in production - Build Model Inference Service, LLM APIs, Inference Graph/Pipelines, Compound AI systems, Multi-Modal, RAG as a Service, and more!
FrameworkBenchmarks - Source for the TechEmpower Framework Benchmarks project
label-studio - Label Studio is a multi-type data labeling and annotation tool with standardized output format
threatbus - 🚌 Threat Bus – A threat intelligence dissemination layer for open-source security tools.
jina - ☁️ Build multimodal AI applications with cloud-native stack