ideogram VS GoJS, a JavaScript Library for HTML Diagrams

> 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]

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

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

Have spent six figures yearly on ads, mostly for reach for the developer-focused diagram library GoJS (https://gojs.net)

> Each experiment will need ~$500 and 2 weeks

I would add a zero if you want serious data. I would also double the timescale. $5,000 over 4 weeks

I second the uselessness of Google Display, it might look like conversions numbers are good but they are 100% too good to be true. As soon as you look into them you find the sources are things like "ad from HappyFunBabyTime Android app". You have to ruthlessly prune daily for months to get anything real, and even then I'm skeptical of value. For a developer tool with very strict conversion metrics!

But I disagree on Google Search:

> Good for conversion, bad for awareness.

Before we were popular it was excellent for awareness. Post popularity its much more arguable.

Creating the Halogen components would be simple enough if one takes inspiration from gojs-react. The issue is that there are no PureScript bindings for the GoJS types themselves, but GoJS does provide .ts.d declarations, which means I could use purescript-read-dts, but that library's maturity/usability seems somewhat ambiguous, according to an author's post from 3 years ago.

used goJS in one project and konva in another

I built GoJS, which is one of the most popular commercial JS diagramming libraries: https://gojs.net

I built carefulwords, a very fast thesaurus and quote site for inspiration, used by... tens of people a day. Eg: https://carefulwords.com/gift https://carefulwords.com/solitude

I mostly made it for myself, me and my wife use it all the time. I am slowly editing down the thesaurus to managable size.

I built a 12x16 "Goose Palace" barn out of local pine timbers, which taught me timber framing, and taught my tiny baby who turned 2 years old while doing it that this is just the kind of thing that people normally do, build barns in their driveway. Some context: https://simonsarris.substack.com/p/the-goose-palace

Some photos of building it with the baby: https://twitter.com/simonsarris/status/1584169368203956225

I designed my house, and have been writing extensively about that. Maybe this is the most impactful, since photos of it are all over Pinterest and other sites, now. The first post on that: https://simonsarris.substack.com/p/designing-a-new-old-home-...

I am not sure what is most impactful. Maybe ultimately it is building my family.

I made a pull request for GoJS (https://gojs.net)

I have been building this canvas-based graphing library since 2011, and it contains a good number of features around customization and interactivity that are not found in other libraries. It is commercial for non-academic use however.

in one project we use konva, in another we used gojs. Any of them or some other library needs some training and introduce own limitations but it still way way way better than handing all the coordinates, calculations, routing etc on your own.

I am really surprised by this guy's opinion. I make GoJS (https://gojs.net/), a diagramming library written in TypeScript. The project began in 2011 and we converted it to TS in 2018. It's been a huge plus. The sole downside was the initial time it took during conversion, but even in doing so we caught bugs with incorrect input types, documentation mistakes, etc.

On our end, it enforces type safety better than the Google Closure Compiler. There has scarcely been a problem with type complexity that was not ultimately our fault. Just a couple minor things that TS amended later. For that matter the TS experience has only gotten better, generally.

On our users end, we can now give them a .d.ts file that's much richer and easier for us to produce to aid their autocompletion. And we can use that .d.ts file to ensure that all the methods we intended to expose/minify are getting exposed. The advantages with the .d.ts and documentation make it feel almost essential to me for library developers to consider TS.

TypeScript has only made debugging easier, much easier since it catches errors at time of typing unlike the closure compiler. The sole exception is that debugging is a bit slower since I have to transpile instead of just refreshing the browser. But I have tsc set to compile a relatively unminified version of the JS. But if the slowness gets to me, I can just edit the JS output until I solve the issue, and then carry those edits over to the TS. This has never felt like a problem, though maybe his library is significantly more complicated.

Feel free to ask me anything if you have questions about library design + TS.

GoJS might work for you: https://gojs.net

Although the focus of the library is interactivity and not setting up sequences of animation, but that is possible too.

My livelihood has been primarily building a Canvas diagramming library since 2010 (https://gojs.net), if anyone has any questions about 2D Canvas use in the real-world I'd be happy to answer them.

roundRect is great. Though you don't need 4 arcTo in order to make a rounded rect, you can use bezier instead (we do). Their example is also 1% amusing because they set the `fillStyle` but then call `stroke` (and not `fill`). I'll have to do some performance comparisons, since that's the operative thing for my use case (and any library author).

text modifiers are very welcome. It's crazy how annoying measuring still is, especially if you want thinks to look perfectly consistent across browsers. Though the chrome dominance is making things easier in one way, I guess.

context.reset is kinda funny. Most high-performance canvas apps will never want to use it. For that matter you want to set all properties as little as possible, especially setting things like context.font, which are slow even if you're setting it to the same value. (Or it was, I haven't tested that in several years).

I'm sure most users know this by now, but generally for performance the fewer calls you make to the canvas and the context, the beter. This is even true of transforms: It's faster to make your own Matrix class, do all your own matrix translation, rotation, multiplication, etc, and then make a single call to `context.setTransform`, than it is to call the other context methods.

I have some problem with gojs(https://gojs.net/),