ideogram
genetic-origins-heatmap
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ideogram | genetic-origins-heatmap | |
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3 | 8 | |
277 | 4 | |
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9.2 | 0.0 | |
3 months ago | over 1 year ago | |
JavaScript | JavaScript | |
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.
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
genetic-origins-heatmap
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[OFFER] I will develop your desktop application or browser extension for just $40.
When I write a program I usually make it focused on a single thing that it's supposed to accomplish. For example, Calligrapher AI lets you type text and then "writes" the same text in human-like handwriting while you watch, and lets you save the image. Beep Knobs is just a board with knobs (albeit a fancy one) that lets you generate customized beeps. And Genetic Origins Heatmap does just what it sounds like, produces a world map indicating where your ancestors came from (using 23andMe DNA data, for example).
- Kosovar-Albanian Genetic Origins Heatmap
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Does anyone know a free genetic heat map that you can upload your data on
Here is an application I wrote that works the same, but is simpler to use. Currently it only accepts 23andMe data but I intend to update it to support AncestryDNA also. I will edit this comment when it's done.
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North Albanian Genetic Origins Heatmap
There's an additional flaw that I realize only in retrospect: A naïve heatmap will tend to exaggerate the significance of regions for which there are more datapoints, since they overlap and contribute to raising the temperature for that particular cluster. But this is a minor issue that doesn't fully explain the Switzerland thing. If any programmers would like to help resolve this, here is the source code on Github.
- Another use for your 23andMe raw data!
- Paint a heatmap of your ancestral origins — Python & PySciter
- Use your 23andMe data to paint a heatmap of your origins
What are some alternatives?
GoJS, a JavaScript Library for HTML Diagrams - JavaScript diagramming library for interactive flowcharts, org charts, design tools, planning tools, visual languages.
crossover-lite - 🎯 5mb crosshair overlay for Windows.
absurd-sql - sqlite3 in ur indexeddb (hopefully a better backend soon)
13andGene - A fun oracle for Eurogenes K13.
localForage - 💾 Offline storage, improved. Wraps IndexedDB, WebSQL, or localStorage using a simple but powerful API.
slidercards - Fun flash cards that slide across your screen!
rupy - HTTP App. Server and JSON DB - Shared Parallel (Atomic) & Distributed
SciterGamePOC - Remaking GameMaker with Sciter. Just a proof-of-concept!
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.
snappy - Helps you browse through and interpret your genotype data
fselect - Find files with SQL-like queries
sciter-js-sdk - Sciter.JS - Sciter but with QuickJS on board instead of my TIScript