Submission

Submission details coming soon — reach out to the instructor when you have a working tool

Deliverable

Submit a working browser automation tool that:

Automates the submission of draft jobs on AlphaFold Server
Handles the multi-step submission flow (Continue → Preview → Confirm → Submit)
Can process multiple drafts in sequence
Includes basic documentation for installation and use

This route is worth 8 regular routes. It's a significant engineering challenge.

Mission checklist

Analyzed the AF3 Server submission flow
Identified DOM elements and click targets
Built working automation (extension, script, or other)
Tested on real draft jobs
Documented installation and usage

Exercise 3: Build and Test

Build your automation tool. Options include:

Chrome Extension — most robust, can be scheduled
Bookmarklet — simpler, runs on demand
Selenium/Playwright script — if you're comfortable with browser automation frameworks

Requirements

Your tool must:

Submit N drafts in sequence (where N is configurable or reasonable)
Wait appropriately between steps (the server needs time to respond)
Not break if a job fails
Work on the actual alphafoldserver.com interface

Testing

Test on a small number of real drafts (2-3) before running on larger batches. Jobs count against your daily quota, so test carefully.

Exercise 2: Reverse-Engineer the Flow

Before you can automate, you need to understand exactly what happens when you submit a job manually.

The submission flow

When you click on a draft job, you go through:

Draft page → Click "Continue"
Preview page → Click "Preview Job" (or similar)
Confirmation page → Click "Confirm" or "Submit Job"
Job starts running

Your task

Open Chrome DevTools (F12)
Go through the submission flow manually for one draft
Identify the button elements at each step (use Inspector)
Note any delays or loading states between steps
Document the CSS selectors or XPaths for each button

Hint: Look for button elements, data-* attributes, or class names that identify the submit/continue buttons.

Questions to answer

How long should you wait between clicks?
How do you know when a page has fully loaded?
What happens if you click too fast?

Exercise 1: Understand the Problem

The pain point

AlphaFold Server's batch upload creates drafts, not running jobs. To actually submit each job, you must manually:

Click on the draft
Click "Continue"
Click "Preview Job"
Click "Confirm and Submit"

For 30 jobs, that's 120+ clicks. Every day. This is exactly the kind of tedious task that computers should handle.

Your challenge

Build a browser automation tool that submits draft jobs automatically. Your tool should:

Navigate the multi-step submission flow
Handle multiple drafts in sequence
Wait appropriately between actions (don't break the server)
Ideally, handle failed jobs gracefully

How you implement this is up to you. Analyze the AlphaFold Server interface and figure out how to automate it.

Exercise 0: Setup

Prerequisites

Familiarity with browser DevTools (Inspector, Console)
Basic JavaScript knowledge
An AlphaFold Server account with some draft jobs to test on

Useful background

If you've never built a browser extension or automation tool, start here:

Chrome Extension Getting Started Guide
MDN: Browser Extensions
Or ask your chatbot: "How do I build a simple Chrome extension that clicks a button on a webpage?"

Approach options

Approach	Complexity	Pros	Cons
Chrome Extension	High	Full control, can schedule, persistent	More setup, manifest files
Bookmarklet	Low	Simple, no installation	Manual trigger each time
Selenium/Playwright	Medium	Powerful, scriptable	Requires local Python/Node setup

Choose based on your comfort level. A working bookmarklet is better than an unfinished extension.

Intro

In Routes 37A and 37B, you submit jobs to AlphaFold Server manually. For a handful of jobs, this is fine. But what if you needed to submit hundreds?

The AlphaFold Server interface requires multiple clicks per job:

Upload JSON → creates drafts
Click each draft → Continue → Preview → Submit

This is tedious and error-prone. Real research labs running large-scale AF3 campaigns have built automation tools to handle this.

Your challenge: Build a tool that automates AF3 Server job submission.

This is a real engineering problem. There's no single right answer. You'll need to:

Analyze a web interface
Understand DOM structure
Write code that interacts with a live website
Handle timing and error cases

Why this matters

Browser automation is a valuable skill beyond this specific use case:

Web scraping and data collection
Automated testing
Repetitive workflow automation
Building browser-based tools

Route 037C: AF3 Server Automation Widget

RouteID: 037C
Wall: Protein-Protein Interactions (W10)
Grade: 5.13d (Extra Credit — worth 8 routes)
Routesetter: Adrian
Time: Variable (significant project)
You'll need: Chrome browser, DevTools, JavaScript knowledge, AF3 account with test drafts