Hey Chemists! Planetary Forge Twitter Bot

[mattodd]

I'm asking for advice, and potential solutions, for a twitter bot that is able to tweet out pictures of molecules to catch the eyes of chemists who may own related structures or know how to make them.

This is intended to contribute to solving the matchmaking problem of open source drug discovery: connecting projects that need molecules with those people (individuals or companies) who may be able to provide them.

Context

I gave a talk recently where I was describing how easy it is to miss relevant scientific work that is taking place elsewhere in the world (slide below). I was telling the story of how I had been scrolling through my Twitter feed and I'd screeched to a halt when I noticed a picture from one of the SGC's open lab notebooks. The structures were remarkably similar to structures we were looking at in OSM Series 3. One thing led to another and we and the SGC co-evaluated each others' molecules, but the point about the story is that I could so easily have missed it. I suspect I'm missing things all the time.

What we need is the magic bot that automatically connects people working in the open on similar molecules, SCINDR, that we've proposed (and just need 50K to implement). But we don't have that yet. Nor yet do we have a good Molecular Craigslist solution.

As I said in the talk "Finding people working on relevant things shouldn't rely on scrolling through pictures on Twitter". But then I added "although actually a bot that tweets out pictures of molecules isn't a terrible idea."

The need

We humans respond well to pictures, and we chemists respond particularly well to pictures of chemical structures. We understand them quickly and can place them in context well: Do I have that structure? Have I read about them recently or do I know someone looking at these? How would I make that?

In open source drug discovery projects we have openly available sheets of molecules that accumulate as the projects progress. These sheets contain SMILES/InChI strings. Here are examples from malaria, TB and mycetoma.

What we need is a bot that takes a random entry from one of these sheets, renders a nice chemical structure, and tweets out the picture of the molecule along with a link to where the interested person might find more info (e.g. the relevant project's landing page) as well as a chemical string (to make the tweet useful to other bots). So the idea is to attract the attention of human chemists, and make it easy for those interested people to connect to the project to see if they can help further.

This could be done with molecules that have been made already, or molecules that are needed next in a project.

Here's a mocked-up tweet, and I used the hashtag #planetaryforge to try to get across the underlying vision. It's a little like the Molecular Craigslist concept, but made specifically to catch the attention of human chemists.

The request

Anyone want to try this out by making a prototype bot? We can call it The Germinator.

[greglandrum]

I'd be happy to talk about it. Looks like it might not be that much work to put something together if we can agree on what it should do. :-)

[miike]

I'd be happy to talk about it. Looks like it might not be that much work to put something together if we can agree on what it should do. :-)

Happy to help out here as well!

A few questions:

• Is it worth thinking about syndication e.g., publishing across multiple social platforms?
• Should posts require human approval before being automatically published? (structure sanity check)

[mattodd]

Hi @greglandrum @miike Belated thanks for questions and enthusiasm.

1. Bot knows to look once each day at a certain spreadsheet(s). It picks a random row.
2. It takes a string and renders the structure as a picture for humans
3. It formulates a post that includes the pic, the string and some pre-arranged hashtag(s).
4. It includes a URL where the molecule is featured or required. That URL is already in the spreadsheet, so it's just coping and pasting, not thinking.
5. It spits out a tweet or equivalent, so that the output looks roughly like the above example.

Publishing across multiple platforms - very good, though the "thoughtlessness" of it fits better with Twitter than e.g. Linkedin. Sanity check: ideally not needed.

What do you think? Anything in that workflow missing?

[miike]

1. That should be easy enough - do we need a mechanism for preventing it picking the same row again (or should it have a cool-off period before it can pick that row again?)
2. That should be fine
3. I'm guessing the hashtags can be defined in the sheet?
4. That should also be easy enough

I don't think we'll run into any character limits (280) though we may get close if we're posting InChI + SMILES.

Publishing across multiple platforms can probably be done with a social media management tool - which would make having things like queues / scheduling a little bit easier.

[mattodd]

Nice @miike ! I think we needn't worry about duplicates, i.e. the bot picking the same molecule. Twitter's a waterfall. Yes, hashtags could be in the sheet I guess. Would need to think how. Let's say someone comes along and says "I have a sheet of 100 molecules we need for my open science project, could you please have the Planetary Forge Twitterbot look at it every now and again" then we could ask that person to provide a hashtag in a certain place, or a certain column. I wonder whether on a per-sheet or per-row basis.

[mattodd]

Real example, to test this out. Let's say we have this molecule

which is OCC@HCOC1=CC2=NC=C3C(NC4=C3C=CC(C#N)=C4)=C2C=C1OC
and SEJTVQTXSCTJDG-LBPRGKRZSA-N

The molecule is derived from this page: https://github.com/mattodd/SGC_Sandbox
So let's say all this is in one row of some spreadsheet somewhere and there's also a column of that sheet where (in this row we're talking about) there is a hashtag #kinase and the bot auto-adds in (each time) the hashtag #planetaryforge (let's say). Is that enough for the tweet to render?

I'm assuming that the tweets would need to come from a dedicated account we set up for that purpose?

[mattodd]

Hey @alintheopen I bet the above pic from @miike reminds you of that Wanted posted you made for Series 1 and which drew in @PatrickThomson's expertise.

[miike]

@mattodd Yes, we'll need a separate / dedicated Twitter account to render this from.

I've mocked up a proof of concept (without hashtags, as the sheet doesn't have them at the moment) to demonstrate here - https://opensourcemalaria.github.io/render.html

Refreshing the page should generate a new molecule.