ideogram
absurd-sql
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ideogram | absurd-sql | |
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3 | 24 | |
277 | 4,057 | |
- | - | |
9.2 | 2.5 | |
3 months ago | 9 months ago | |
JavaScript | JavaScript | |
GNU General Public License v3.0 or later | MIT License |
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.
ideogram
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New CRISPR-based map ties every human gene to its function
> Where are the polished, powerful design tools for biology
User interfaces for biology have drastically improved over the last 10 years.
Domain-specific tools like genome browsers, protein viewers, or phylogenetic explorers [1-3] almost all look and feel a lot better than they did in 2012.
The biggest exception here is UCSC Genome Browser, which has an old-school design and web technology stack. That said, it's steadily added features over the years, has substantially sleekened UX in its periphery, and remains widely used.
There are also bespoke visual design resources for biology applications that are good and getting better, like BioRender and PhyloPic [4-5]. There are multi-tiered packages like Dash Bio that wrap biology components together. There's Blender biology community, too!
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1. Genome browsers and components: https://jbrowse.org/jb2/, https://www.ncbi.nlm.nih.gov/genome/gdv, https://igv.org/app, https://eweitz.github.io/ideogram
2. Protein viewers: https://pymol.org/, https://nglviewer.org/ngl/
3. Phylogenetic explorers: https://clades.nextstrain.org/
4. https://biorender.com/
5. http://phylopic.org/
6. https://github.com/plotly/dash-bio, https://dash.gallery/Portal/?search=[Pharma]
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Why IndexedDB is slow and what to use instead
I'm more interested in read speeds than write speeds. I have about 2 MB of data that I fetch, then parsed and transformed into a heavily nested object for easy look-up by various types of keys.
In my brief experiment, it was 12% faster to read from the web Cache API, re-parse and re-transform that heavily nested object than to read the fully transformed object via IndexedDB. That surprised me! My understanding is that IndexedDB does a structured clone as part of the read, which I suspect is the main cause of slowness of IndexedDB relative to the Cache API approach in my use case.
Related commits to reproduce that finding are in [1], specifically [2].
[1] https://github.com/eweitz/ideogram/pull/285
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Ask HN: What are some tools / libraries you built yourself?
I created Ideogram.js, a JavaScript library for chromosome visualization [1]. Ideogram supports drawing and animating genome-wide datasets, enabling a variety of genomic views [3].
[1] https://github.com/eweitz/ideogram
[2] https://eweitz.github.io/ideogram
absurd-sql
- Absurd-SQL: sqlite3 in ur indexeddb (hopefully a better back end soon)
- What If OpenDocument Used SQLite?
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WASM SQL database recommendations wanted
Not really, but I'm aware of absurd-sql. Note that this requires IndexedDB and thus a browser environment.
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Best local database that works on all platforms including web?
I don't need SQL capabilities, so I didn't look into those options (there's also absurd-sql, which ports sqlite to the browser on top of IndexedDB).
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SQLite WASM in the Browser Backed by the Origin Private File System
Ironically I was just about to drop in absurd-sql [1] to a project, which uses indexeddb to back SQLite. This seems better.
[1] https://github.com/jlongster/absurd-sql
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Irmin in the Browser (OCaml/MirageOS)
There is also absurd-sql that is sqlite3 in wasm using IndexDB as storage and it’s faster than IndexDB itself
[1]: https://github.com/jlongster/absurd-sql
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Postgres WASM by Snaplet and Supabase
Offline data: running it in the browser for an offline cache, similar to sql.js or absurd-sql.
- WordPress WASM
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Learn PWA
We are very close to having WASM SQLite with persistence in the web platform. Until now SQLite compiled to WASM was in memory and you had to write the whole database out as a binary array to save changes. There is absurd-sql (https://github.com/jlongster/absurd-sql), which builds a virtual file system on top of IndexedDB for sqlite, its incredible, but a bit of an ugly hack.
However, the new file-access apis (https://developer.mozilla.org/en-US/docs/Web/API/File_System...) that are landing in browsers will fix this. One of the things it does is enable very efficient block level read/write access to a privet sandboxed filesystem for the websites origin, perfect for persistent sqlite. There is more here: https://web.dev/file-system-access/#accessing-files-optimize...
- Learn Postgres at the Playground
What are some alternatives?
genetic-origins-heatmap - Use your DNA data (e.g. from 23andMe) to paint a global heatmap of your origins.
lovefield - Lovefield is a relational database for web apps. Written in JavaScript, works cross-browser. Provides SQL-like APIs that are fast, safe, and easy to use.
GoJS, a JavaScript Library for HTML Diagrams - JavaScript diagramming library for interactive flowcharts, org charts, design tools, planning tools, visual languages.
crdt-example-app - A full implementation of CRDTs using hybrid logical clocks and a demo app that uses it
localForage - 💾 Offline storage, improved. Wraps IndexedDB, WebSQL, or localStorage using a simple but powerful API.
dolt - Dolt – Git for Data
rupy - HTTP App. Server and JSON DB - Shared Parallel (Atomic) & Distributed
realtime - Broadcast, Presence, and Postgres Changes via WebSockets
lowdefy - The config web stack for business apps - build internal tools, client portals, web apps, admin panels, dashboards, web sites, and CRUD apps with YAML or JSON.
donutdb - Store and query a sqlite db directly backed by DynamoDB.
fselect - Find files with SQL-like queries