gnomad-browser
FrameworkBenchmarks
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gnomad-browser | FrameworkBenchmarks | |
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15 | 366 | |
78 | 7,384 | |
- | 1.2% | |
9.7 | 9.8 | |
3 days ago | 3 days ago | |
TypeScript | Java | |
MIT License | GNU General Public License v3.0 or later |
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/
FrameworkBenchmarks
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Why choose async/await over threads?
Neat. Thanks for sharing!
Interestingly, may-minihttp is faring very well in the TechEmpower benchmark [1], for whatever those benchmarks are worth. The code is also surprisingly straightforward [2].
[1] https://www.techempower.com/benchmarks/
[2] https://github.com/TechEmpower/FrameworkBenchmarks/blob/mast...
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Ntex: Powerful, pragmatic, fast framework for composable networking services
ntex was formed after a schism in actix-web and Rust safety/unsafety, with ntex allowing more unsafe code for better performance.
ntex is at the top of the TechEmpower benchmarks, although those benchmarks are not apples-to-apples since each uses its own tricks: https://www.techempower.com/benchmarks/#hw=ph&test=fortune&s...
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A decent VS Code and Ruby on Rails setup
Ruby is slow. Very slow. How much you may ask? https://www.techempower.com/benchmarks/#hw=ph&test=fortune&s... fastest Ruby entry is at 272th place. Sure, top entries tend to have questionable benchmark-golfing implementations, but it gives you a good primer on the overhead imposed by Ruby.
It is also not early 00s anymore, when you pick an interpreted language, you are not getting "better productivity and tooling". In fact, most interpreted languages lag behind other major languages significantly in the form of JS/TS, Python and Ruby suffering from different woes when it comes to package management and publishing. I would say only TS/JS manages to stand apart with being tolerable, and Python sometimes too by a virtue of its popularity and the amount of information out there whenever you need to troubleshoot.
If you liked Go but felt it being a too verbose to your liking, give .NET a try. I am advocating for it here on HN mostly for fun but it is, in fact, highly underappreciated, considered unsexy and boring while it's anything but after a complete change of trajectory in the last 3-5 years. It is actually the* stack people secretly want but simply don't know about because it is bundled together with Java in the public perception.
*productive CLI tooling, high performance, works well in a really wide range of workloads from low to high level, by far the best ORM across all languages and back-end framework that is easier to work with than Node.JS while consuming 0.1x resources
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The Erlang Ecosystem [video]
Although that seems to have improved in recent years.
https://www.techempower.com/benchmarks/#hw=ph&test=json§...
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Ruby 3.3
RoR and whatever C++ based web backend there is count as a valid comparison in my book. But comparing the languages itself is maybe a bit off.
On a side note, you can actually compare their performance here if you’re really curious. But take it with a grain of salt since these are synthetic benchmarks.
https://www.techempower.com/benchmarks
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API: Go, .NET, Rust
Most benchmarks you'll find essentially have someone's thumb on the scale (intentionally or unintentionally). Most people won't know the different languages well enough to create comparable implementations and if you let different people create the implementations, cheating happens. The TechEmpower benchmarks aren't bad, but many implementations put their thumb on the scale (https://www.techempower.com/benchmarks). For example, a lot of the Go implementations avoid the GC by pre-allocating/reusing structs or allocate arrays knowing how big they need to be in advance (despite that being against the rules). At some point, it becomes "how many features have you turned off." Some Go http routers (like fasthttp and those built off it like Atreugo and Fiber) aren't actually correct and a lot of people in the Go community discourage their use, but they certainly top the benchmarks. Gin and Echo are usually the ones that are well-respected in the Go community.
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Rage: Fast web framework compatible with Rails
There is certainly a lot of speculation in Techempower benchmarks and top entries can utilize questionable techniques like simply writing a byte array literal to output stream instead of constructing a response, or (in the past) DB query coalescing to work around inherent limitations of the DB in case of Fortunes or DB quries.
And yet, the fastest Ruby entry is at 274th place while Rails is at 427th.
https://www.techempower.com/benchmarks/#hw=ph&test=fortune&s...
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Node.js – v20.8.1
oh what machine? with how many workers? doing what?
search for "node" on this page: https://www.techempower.com/benchmarks/#section=data-r21
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Strong typing, a hill I'm willing to die on
JustJS would like a word https://www.techempower.com/benchmarks/#section=data-r20&tes...
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Rust vs Go: A Hands-On Comparison
In terms of RPS, this web service is more-or-less the fortunes benchmark in the techempower benchmarks, once the data hits the cache: https://www.techempower.com/benchmarks/#section=data-r21
Or, at least, they would be after applying optimizations to them.
In short, both of these would serve more rps than you will likely ever need on even the lowest end virtual machines. The underlying API provider will probably cut you off from querying them before you run out of RPS.
What are some alternatives?
webviz - web-based visualization libraries
zio-http - A next-generation Scala framework for building scalable, correct, and efficient HTTP clients and servers
haystack - :mag: LLM orchestration framework to build customizable, production-ready LLM applications. Connect components (models, vector DBs, file converters) to pipelines or agents that can interact with your data. With advanced retrieval methods, it's best suited for building RAG, question answering, semantic search or conversational agent chatbots.
drogon - Drogon: A C++14/17 based HTTP web application framework running on Linux/macOS/Unix/Windows [Moved to: https://github.com/drogonframework/drogon]
metamask-extension - :globe_with_meridians: :electric_plug: The MetaMask browser extension enables browsing Ethereum blockchain enabled websites
django-ninja - 💨 Fast, Async-ready, Openapi, type hints based framework for building APIs
aioli - Framework for building fast genomics web tools with WebAssembly and WebWorkers
LiteNetLib - Lite reliable UDP library for Mono and .NET
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
C++ REST SDK - The C++ REST SDK is a Microsoft project for cloud-based client-server communication in native code using a modern asynchronous C++ API design. This project aims to help C++ developers connect to and interact with services.
threatbus - 🚌 Threat Bus – A threat intelligence dissemination layer for open-source security tools.
SQLBoiler - Generate a Go ORM tailored to your database schema.