From 80134115699d2284fb3200decef51463526631f4 Mon Sep 17 00:00:00 2001 From: Vincent Rubinetti Date: Tue, 19 Dec 2023 14:15:31 -0500 Subject: [PATCH] Init (#1) --- .github/pull_request_template.md | 4 + .nojekyll | 0 README.md | 42 ++++- images/manubot.jpg | Bin 0 -> 33086 bytes index.html | 244 +++++++++++++++++++++++++ list.json | 102 +++++++++++ src/alpine.js | 43 +++++ src/grid.css | 179 +++++++++++++++++++ src/header.css | 89 +++++++++ src/share.jpg | Bin 0 -> 31847 bytes src/styles.css | 118 ++++++++++++ src/util.css | 75 ++++++++ src/viz.js | 297 +++++++++++++++++++++++++++++++ 13 files changed, 1192 insertions(+), 1 deletion(-) create mode 100644 .github/pull_request_template.md create mode 100644 .nojekyll create mode 100644 images/manubot.jpg create mode 100644 index.html create mode 100644 list.json create mode 100644 src/alpine.js create mode 100644 src/grid.css create mode 100644 src/header.css create mode 100644 src/share.jpg create mode 100644 src/styles.css create mode 100644 src/util.css create mode 100644 src/viz.js diff --git a/.github/pull_request_template.md b/.github/pull_request_template.md new file mode 100644 index 0000000..1399157 --- /dev/null +++ b/.github/pull_request_template.md @@ -0,0 +1,4 @@ +Submission/review checklist: + +- [] I have followed the submission guidelines in the `README.md`. +- [] I have looked at the preview link to verify that my changes appear correctly. diff --git a/.nojekyll b/.nojekyll new file mode 100644 index 0000000..e69de29 diff --git a/README.md b/README.md index 2b9388a..8c1c127 100644 --- a/README.md +++ b/README.md @@ -1 +1,41 @@ -# software-registry \ No newline at end of file +# CU DBMI Wall of Software + +The [Department of Biomedical Informatics (DBMI) at the University of Colorado](https://medschool.cuanschutz.edu/dbmi) investigates complex problems in medicine and biology using integrated computational technology. +This repository and website contains a non-comprehensive list of tools, packages, workflows, resources, and other software that have been developed by our diverse group researchers, scientists, developers, and collaborators in support of [our mission](https://medschool.cuanschutz.edu/dbmi/about-us). + +[⭐️⭐️ View the List ⭐️⭐️](https://CU-DBMI.github.io/wall-of-software) + +## Submit Your Software + +If you work for or with the department, you are eligible to submit your software here. +To start, [open a pull request in this repo](https://github.com/CU-DBMI/wall-of-software/pulls) with the following changes: + +- Add an _entry_ to **the top** of `list.json`. + - A short ~3-20 char name. + - A short ~20-60 char description. + - A link to a website or repo. +- Add a _web-friendly_ image to `/images`. + - Filename **must** be lowercase, kebab-case version of entry name, e.g. _Word Lapse_ → `word-lapse`. + - **Must** have extension `.jpg`. + - Roughly square. + - Enough margins for main content to fit nicely inside hexagon. + - Larger than ~400px × 400px , smaller than ~1000px × 1000px + - Better than ~80% jpeg compression level, smaller than ~50 kB. + +Shortly after opening a PR, a link should appear to a preview of the site with your changes. + +Entries are shuffled randomly on each page visit to not give preferential treatment! + +### Printed + +If you'd also like your image to be printed out and posted on the wall of the DBMI office (6th floor Anschutz Health Sciences Building), **also** include these changes: + +- Add a _printable_ image to `/images`. + - Filename should be lowercase, kebab-case version of entry name. + - Should have extension `.png`. + - Enough margins for main content to fit nicely inside hexagon. + - Conforms to the [4" × 4" hexagon template here](https://www.stickermule.com/uses/hexagon-stickers). + +### Help + +If you need help submitting software, you may [contact the Software Engineering Team](https://cu-dbmi.github.io/set-website/about/) for help. diff --git a/images/manubot.jpg b/images/manubot.jpg new file mode 100644 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zzmakL^GB3*{^j>3Unw21|M|-gpFjBepTG5=k^juVe`er6Gw`1o_ + + + + + + + + + + Wall of Software | CU DBMI + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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+ + + + Department of Biomedical Informatics +

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+ + + + + GitHub + + + + + + Submit + +
+ + + + + +

+ – (and counting) + tools, packages, workflows, resources, and other software + developed at or in collaboration with the + Department of Biomedical Informatics (DBMI) at the University of + Colorado. +

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+
+ + + + + + diff --git a/list.json b/list.json new file mode 100644 index 0000000..6505f5f --- /dev/null +++ b/list.json @@ -0,0 +1,102 @@ +[ + { + "name": "Manubot", + "description": "Manuscripts, open and automated", + "link": "https://manubot.org" + }, + { + "name": "Dolor Sit Amit", + "description": "Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor incididunt ut labore et dolore magna aliqua.", + "link": "" + }, + { + "name": "Lorem Ipsum", + "description": "Lorem ipsum dolor sit amet", + "link": "" + }, + { + "name": "Lorem Ipsum", + "description": "Lorem ipsum dolor sit amet", + "link": "" + }, + { + "name": "Lorem Ipsum", + "description": "Lorem ipsum dolor sit amet", + "link": "" + }, + { + "name": "Lorem Ipsum", + "description": "Lorem ipsum dolor sit amet", + "link": "" + }, + { + "name": "Lorem Ipsum", + "description": "Lorem ipsum dolor sit amet", + "link": "" + }, + { + "name": "Lorem Ipsum", + "description": "Lorem ipsum dolor sit amet", + "link": "" + }, + { + "name": "Lorem Ipsum", + "description": "Lorem ipsum dolor sit amet", + "link": "" + }, + { + "name": "Lorem Ipsum", + "description": "Lorem ipsum dolor sit amet", + "link": "" + }, + { + "name": "Lorem Ipsum", + "description": "Lorem ipsum dolor sit amet", + "link": "" + }, + { + "name": "Lorem Ipsum", + "description": "Lorem ipsum dolor sit amet", + "link": "" + }, + { + "name": "Lorem Ipsum", + "description": "Lorem ipsum dolor sit amet", + "link": "" + }, + { + "name": "Lorem Ipsum", + "description": "Lorem ipsum dolor sit amet", + "link": "" + }, + { + "name": "Lorem Ipsum", + "description": "Lorem ipsum dolor sit amet", + "link": "" + }, + { + "name": "Lorem Ipsum", + "description": "Lorem ipsum dolor sit amet", + "link": "" + }, + { + "name": "Lorem Ipsum", + "description": "Lorem ipsum dolor sit amet", + "link": "" + }, + { + "name": "Lorem Ipsum", + "description": "Lorem ipsum dolor sit amet", + "link": "" + }, + { + "name": "Lorem Ipsum", + "description": "Lorem ipsum dolor sit amet", + "link": "" + }, + { + "name": "Lorem Ipsum", + "description": "Lorem ipsum dolor sit amet", + "link": "" + } +] diff --git a/src/alpine.js b/src/alpine.js new file mode 100644 index 0000000..c1d116d --- /dev/null +++ b/src/alpine.js @@ -0,0 +1,43 @@ +// reactive render html + +document.addEventListener("alpine:init", async () => { + // init store + Alpine.store("store", { + title: [], + list: [], + cols: 1, + set(key, value) { + this[key] = value; + }, + }); + + // page title, split by word and char + let index = 0; + const title = "Wall of Software" + .split(" ") + .map((word) => word.split("").map((char) => ({ char, index: index++ }))); + + // set title + Alpine.store("store").set("title", title); + + // load list + const list = await (await fetch("list.json")).json(); + // shuffle + for (let i = list.length - 1; i > 0; i--) { + const j = Math.floor(Math.random() * (i + 1)); + [list[i], list[j]] = [list[j], list[i]]; + } + + // set list + Alpine.store("store").set("list", list); + + // set number of cols on window resize + function updateCols() { + Alpine.store("store").set( + "cols", + Math.min(10, Math.floor(window.innerWidth / 200)) + ); + } + updateCols(); + window.addEventListener("resize", updateCols); +}); diff --git a/src/grid.css b/src/grid.css new file mode 100644 index 0000000..87a9de4 --- /dev/null +++ b/src/grid.css @@ -0,0 +1,179 @@ +.grid { + --ratio: 1.1547; + --gap: 5px; + display: grid; + grid-template-columns: repeat(var(--cols), 1fr); + place-content: center; + width: 100%; + padding: 40px 60px; + gap: calc(var(--gap) / var(--ratio)) var(--gap); +} + +.cell { + display: flex; + position: relative; + align-items: center; + justify-content: center; + aspect-ratio: var(--ratio) / 1; + transform: translateX( + calc(var(--offset) * 25% + (var(--offset) * var(--gap)) / 4) + ); +} + +.cell:has(.hex:hover, .hex:focus) { + z-index: 1; +} + +.hex { + display: flex; + position: absolute; + flex-direction: column; + align-items: center; + justify-content: center; + aspect-ratio: 1 / var(--ratio); + width: 100%; + gap: 5px; + color: var(--white); + text-align: center; + overflow-wrap: anywhere; + animation: hex 1s var(--delay) both; + transition: opacity var(--fast); +} + +.grid:has(.hex:hover, .hex:focus) .hex { + opacity: 0.75; +} + +.hex:hover, +.hex:focus { + opacity: 1 !important; +} + +.hex::after, +.hex::before { + position: absolute; + bottom: calc(100% + 5px); + background: var(--dark); + color: var(--white); + opacity: 0; + pointer-events: none; + transition: opacity var(--fast), transform var(--fast); +} + +.hex::after { + width: 10px; + height: 10px; + transform: translateY(50%) translateY(-0.1px) translateY(0) rotate(45deg); + content: ""; + clip-path: polygon(200% 200%, 200% -100%, -100% 200%); +} + +.hex:hover::after, +.hex:focus::after { + transform: translateY(50%) translateY(-0.1px) translateY(-5px) rotate(45deg); + opacity: 1; +} + +.hex::before { + width: 175%; + max-width: max-content; + padding: 10px 15px; + border-radius: 5px; + content: attr(data-tooltip); +} + +.hex:hover::before, +.hex:focus::before { + transform: translateY(-5px); + opacity: 1; +} + +@keyframes hex { + from { + opacity: 0; + } +} + +.hex > * { + position: absolute; + width: 100%; + height: 100%; + inset: 0; +} + +.shape { + overflow: visible; + pointer-events: none; +} + +.stroke { + fill: none; + stroke: var(--dark); + stroke-width: 0.03; + stroke-dasharray: 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 0.01 + 0.01 0.01 0.01 0.01 0.01 1.5; + stroke-dashoffset: 1.84; + transform: scale(1.1); +} + +.hex:hover .stroke, +.hex:focus .stroke { + animation: stroke 1.25s linear; +} + +@keyframes stroke { + to { + stroke-dashoffset: 0.17; + } +} + +.fill { + fill: var(--mid); +} + +.image { + clip-path: polygon(0% 25%, 0% 75%, 50% 100%, 100% 75%, 100% 25%, 50% 0%); + pointer-events: none; +} + +.img { + position: absolute; + width: 100%; + height: 100%; + inset: 0; + object-fit: cover; + transition: opacity var(--fast), transform var(--fast), filter var(--fast); +} + +svg.img { + fill: currentColor; + text-anchor: middle; + dominant-baseline: middle; +} + +.hex:hover .img, +.hex:focus .img { + transform: scale(1.1); + opacity: 0; +} + +.text { + display: flex; + flex-direction: column; + align-items: center; + justify-content: center; + padding: 20px 10px; + overflow: hidden; + gap: 5px; + transform: scale(0.9); + font-weight: 600; + font-size: 1.1rem; + opacity: 0; + transition: opacity var(--fast), transform var(--fast); +} + +.hex:hover .text, +.hex:focus .text { + transform: scale(1); + opacity: 1; +} diff --git a/src/header.css b/src/header.css new file mode 100644 index 0000000..cbaa624 --- /dev/null +++ b/src/header.css @@ -0,0 +1,89 @@ +h1 { + display: flex; + flex-wrap: wrap; + justify-content: center; + gap: 0 20px; + color: var(--dark); + font-size: 2.5rem; + font-family: "IBM Plex Mono", monospace; +} + +@media (max-width: 400px) { + h1 { + font-size: 2rem; + } +} + +.word { + display: inline-flex; + flex-wrap: wrap; + justify-content: center; +} + +.char { + text-transform: uppercase; + animation: title1 0.5s var(--delay) both, title2 5s var(--delay) infinite; +} + +@keyframes title1 { + from { + display: none; + } +} + +@keyframes title2 { + 0%, + 10% { + color: var(--dark); + } + 5% { + color: var(--mid); + } +} + +h2 { + font-size: 1.2rem; + animation: subtitle 2s 1s both; +} + +h2 .icon { + position: relative; + top: 0.15em; + margin-right: 0.5em; + color: var(--dark); +} + +@keyframes subtitle { + from { + color: var(--light); + opacity: 0; + } +} + +.cursor { + animation: cursor 1s 2s infinite steps(1); +} + +@keyframes cursor { + 0%, + 100% { + opacity: 1; + } + 50% { + opacity: 0; + } +} + +canvas { + position: absolute; + width: 100% !important; + height: 100% !important; + inset: 0; + animation: canvas 3s 1s both; +} + +@keyframes canvas { + from { + opacity: 0; + } +} diff --git a/src/share.jpg 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line-height: 2; + text-align: justify; +} + +p a { + text-decoration-line: underline; +} + +p a:is(:hover, :focus) { + color: var(--mid); +} + +header { + display: flex; + position: relative; + flex-direction: column-reverse; + align-items: center; + justify-content: center; + padding: 150px 20px; + gap: 10px; + background: var(--light); + font-weight: 300; + text-align: center; +} + +header > * { + z-index: 1; +} + +footer { + display: flex; + flex-wrap: wrap; + align-items: center; + justify-content: center; + padding: 40px; + gap: 30px; + background: var(--dark); + color: var(--white); + text-align: center; +} + +footer a:is(:hover, :focus) { + color: var(--mid); +} diff --git a/src/util.css b/src/util.css new file mode 100644 index 0000000..53c0e73 --- /dev/null +++ b/src/util.css @@ -0,0 +1,75 @@ +.buttons { + display: flex; + flex-wrap: wrap; + justify-content: center; + gap: 30px; +} + +.button { + display: flex; + position: relative; + align-items: center; + padding: 10px 15px; + gap: 10px; + border-radius: 5px; + background: var(--dark); + color: var(--white); + transition: color var(--fast), background var(--fast); +} + +.button:is(:hover, :focus-visible) { + background: var(--light); + color: var(--dark); +} + +.button::after { + z-index: 1; + position: absolute; + inset: -7.5px; + border: dashed 2px transparent; + border-radius: 10px; + content: ""; + pointer-events: none; +} + +.button:is(:hover, :focus-visible)::after { + animation: button 1s ease-in-out; +} + +@keyframes button { + 0%, + 100% { + clip-path: inset(0 0 97% 0); + } + 25% { + clip-path: inset(0 97% 0 0); + } + 50% { + clip-path: inset(97% 0 0 0); + } + 75% { + clip-path: inset(0 0 0 97%); + } + 0%, + 100% { + border-color: transparent; + } + 10% { + border-color: var(--dark); + } + 50% { + border-color: var(--mid); + } + 90% { + border-color: var(--light); + } +} + +.icon { + flex-shrink: 0; + height: 1em; +} + +.icon path { + fill: currentColor; +} diff --git a/src/viz.js b/src/viz.js new file mode 100644 index 0000000..9de70c7 --- /dev/null +++ b/src/viz.js @@ -0,0 +1,297 @@ +// header background visualization + +import { + BufferGeometry, + CanvasTexture, + Clock, + Color, + Float32BufferAttribute, + PerspectiveCamera, + Points, + PointsMaterial, + Scene, + Vector3, + WebGLRenderer, +} from "three"; +import { LineMaterial } from "three/addons/lines/LineMaterial.js"; +import { LineGeometry } from "three/addons/lines/LineGeometry.js"; +import { LineSegmentsGeometry } from "three/addons/lines/LineSegmentsGeometry.js"; +import { Line2 } from "three/addons/lines/Line2.js"; +import { LineSegments2 } from "three/addons/lines/LineSegments2.js"; + +// helix props +const strandSize = 0.3; +const pairSize = 0.1; +const helixMinZ = -10; +const helixMaxZ = 10; +const helixRadius = 1.75; +const helixStep = 0.1; +const helixTwist = 1 / 15; +const helixTilt = 16; + +// particle props +const particleSize = 0.75; +const particleChars = ["0", "1"]; +const particleCount = 150; +const particleAcceleration = (position) => new Vector3(position.x * 0.5, 1, 0); +const particleDecay = 1; + +// 360 degrees +const tau = 2 * Math.PI; + +// rand between range +const rand = (min = 0, max = 1) => min + Math.random() * (max - min); + +// round to multiple +const round = (value, multiple) => multiple * Math.floor(value / multiple); + +// triangle +const ramp = (value, mid = 0.25) => { + if (value < 0) return 0; + if (value < mid) return value / mid; + if (value < 1) return 1 - (value - mid) / (1 - mid); + return 0; +}; + +// three js main objects +const canvas = document.querySelector("canvas"); +const renderer = new WebGLRenderer({ canvas: canvas, alpha: true }); +const scene = new Scene(); +const camera = new PerspectiveCamera(45, 1, 0.01, 100); +const clock = new Clock(); + +// resize/reset scene/camera +const reset = () => { + camera.aspect = canvas.clientWidth / canvas.clientHeight; + camera.position.set(0, 0, -15); + camera.lookAt(0, 0, 0); + camera.translateX(-5); + camera.updateProjectionMatrix(); + renderer.setSize(canvas.clientWidth, canvas.clientHeight); + renderer.setPixelRatio(window.devicePixelRatio); +}; +reset(); +window.addEventListener("resize", reset); + +// get color palette +const style = window.getComputedStyle(document.documentElement); +const mid = new Color(style.getPropertyValue("--mid")); +const light = new Color(style.getPropertyValue("--light")); + +// generate helix +const leftPoints = []; +const rightPoints = []; +const pairPoints = []; +const colors = []; +const pairColors = []; +for (let z = helixMinZ; z <= helixMaxZ; z += helixStep) { + // percent through length + const percent = (z - helixMinZ) / (helixMaxZ - helixMinZ); + + // position + const x = Math.sin(-helixTwist * tau * z) * helixRadius; + const y = Math.cos(-helixTwist * tau * z) * helixRadius; + leftPoints.push(x, y, z); + rightPoints.push(-x, -y, z); + + // color + const color = mid.clone().lerpHSL(light, percent); + colors.push(color.r, color.g, color.b); + + // connect strands with a pair at z integer intervals + if (Math.abs(z - Math.round(z)) < 0.001) { + pairPoints.push(x, y, z, -x, -y, z); + const { r, g, b } = color; + pairColors.push(r, g, b, r, g, b); + } +} + +// materials +const strandMaterial = new LineMaterial({ + color: 0xffffff, + linewidth: strandSize, + worldUnits: true, + vertexColors: true, +}); +const pairMaterial = new LineMaterial({ + color: 0xffffff, + linewidth: pairSize, + worldUnits: true, + vertexColors: true, +}); + +// left strand object +const leftStrandGeometry = new LineGeometry(); +leftStrandGeometry.setPositions(leftPoints); +leftStrandGeometry.setColors(colors); +const leftStrand = new Line2(leftStrandGeometry, strandMaterial); +leftStrand.name = "helix"; +leftStrand.rotation.x = tau / 4; +scene.add(leftStrand); + +// right strand object +const rightStrandGeometry = new LineGeometry(); +rightStrandGeometry.setPositions(rightPoints); +rightStrandGeometry.setColors(colors); +const rightStrand = new Line2(rightStrandGeometry, strandMaterial); +rightStrand.name = "helix"; +rightStrand.rotation.x = tau / 4; +scene.add(rightStrand); + +// get random point on strands +const getStrandPoint = () => { + const left = Math.random() > 0.5; + const strand = left ? leftStrand : rightStrand; + const points = left ? leftPoints : rightPoints; + const pointIndex = round(Math.random() * points.length, 3); + return strand.localToWorld( + new Vector3(...points.slice(pointIndex, pointIndex + 3)) + ); +}; + +// pairs object +const pairGeometry = new LineSegmentsGeometry(); +pairGeometry.setPositions(pairPoints); +pairGeometry.setColors(pairColors); +const pairs = new LineSegments2(pairGeometry, pairMaterial); +pairs.name = "helix"; +pairs.rotation.x = tau / 4; +scene.add(pairs); + +// particles +for (const char of particleChars) { + // draw char on canvas + const canvas = document.createElement("canvas"); + canvas.width = 100; + canvas.height = 100; + const ctx = canvas.getContext("2d"); + ctx.fillStyle = "black"; + ctx.fillRect(0, 0, 100, 100); + ctx.fillStyle = "white"; + ctx.font = "100px IBM Plex Sans"; + ctx.textAlign = "center"; + ctx.textBaseline = "middle"; + ctx.fillText(char, 50, 50); + + // use canvas as texture + const material = new PointsMaterial({ + size: particleSize, + alphaMap: new CanvasTexture(canvas), + alphaTest: 0.5, + transparent: true, + vertexColors: true, + }); + + // init buffer of points and colors + const points = Array(particleCount * 3).fill(0); + const colors = Array(particleCount * 3).fill(0); + const geometry = new BufferGeometry(); + geometry.setAttribute("position", new Float32BufferAttribute(points, 3)); + geometry.setAttribute("color", new Float32BufferAttribute(colors, 3)); + + // particle object + const particle = new Points(geometry, material); + particle.name = "particle"; + particle.userData = Array(particleCount) + .fill() + .map(() => ({ + life: rand(), + acceleration: new Vector3(), + velocity: new Vector3(), + })); + scene.add(particle); +} + +// render frame +const frame = () => { + // time since last tick + const delta = Math.min(0.1, clock.getDelta()); + + // for each element in scene + for (const child of scene.children) { + if (child.name === "helix") { + // spin + child.rotation.z += delta; + } + + if (child.name === "particle") { + // get buffers + const positionAttr = child.geometry.getAttribute("position"); + const colorAttr = child.geometry.getAttribute("color"); + + // loop through other "buffers" + for (let [index, particle] of Object.entries(child.userData)) { + // cast to number + index = +index; + + // get position + let position = new Vector3( + positionAttr.getX(index), + positionAttr.getY(index), + positionAttr.getZ(index) + ); + + // init position + if (!position.length()) position = getStrandPoint(); + + // increment life + particle.life += delta / particleDecay; + + // accelerate + particle.acceleration = particleAcceleration( + position.clone().normalize() + ); + + // increment velocity + particle.velocity.add(particle.acceleration); + + // increment position + position.add(particle.velocity.multiplyScalar(delta)); + + // interpolate color + const [r, g, b] = light + .clone() + .lerpHSL(mid, ramp(particle.life) / 1.25); + colorAttr.setXYZ(index, r, g, b); + + // respawn + if (particle.life > 1) { + position = getStrandPoint(); + particle.life = 0; + } + + // set position + const { x, y, z } = position; + positionAttr.setXYZ(index, x, y, z); + } + + // signal buffers to update + positionAttr.needsUpdate = true; + colorAttr.needsUpdate = true; + } + } + + // update scene + renderer.render(scene, camera); + + // run frame again + window.setTimeout(() => window.requestAnimationFrame(frame), 10); +}; + +frame(); + +// on mouse move +const mouse = (event) => { + // get x/y from -1 to 1 + const x = event ? -1 + 2 * (event.clientX / window.innerWidth) : 0; + const y = event ? -1 + 2 * (event.clientY / window.innerHeight) : 0; + + // tilt helix + for (const child of scene.children) + if (child.name === "helix") { + child.rotation.y = helixTilt + (tau / 4) * (x / 4); + child.rotation.x = tau / 4 + (tau / 4) * (y / 4); + } +}; +mouse(); +window.addEventListener("mousemove", mouse);