Open Science Student Projects

We’re launching a new kind of student project in synthetic organic chemistry. The idea is this: any student anywhere in the world can join in, provided all data are posted openly online. We aim to publish the research with all participants.

What we’re looking for are students who can actually carry out practical experiments in a lab and upload data. This project is ideally suited to being run as part of a formal undergraduate laboratory course, but any student can join in. We’ve just started this at The University of Sydney this year – one undergraduate, Clara, is working on the project, and she will be joined by others later in semester. Our first partner to sign up is Stanford University, where lab director Charlie Cox has run the project as an option in third year undergrad lab. A few people have contacted me informally about running the project at their own universities, and we’re going to try to secure some money to help run the project in some universities in Africa.

This post opens up the project to the rest of the world. If you’re reading this, and would like to join in, then yes, you can.

The project concerns the optimization of our resolution of praziquantel. Though the route is easy to perform, and efficient, we’re looking for ways to improve the route still further to bring the cost down.

There are a number of things we can look at. We will need to set up some online forums where the project can be discussed. If you have any questions now, you can post them below, or on the Friendfeed room, or get an account on Labtrove (our open source ELN) and post things here, or tweet me, or comment on The Synaptic Leap. There’s also email, which I’m trying to discourage, but please use this if you don’t want to discuss possible involvement in the project in the open.

The relevant online lab notebooks to which you’d contribute if you took part are here.

Any student contributing data can then take part in writing the resulting research paper, which is here. Once you’ve contributed an experiment, add your name to the paper, and start making changes to the manuscript. For undergraduates this is exciting because they can take part in real research, generating new data, rather than repeating experiments with known outcomes. This way we also aim to generate a real research publication – very useful for students interested in a career in research.

Some very important points:

1. All data generated by students are to be deposited openly on the web. Please don’t take part and not share all data – no point in doing that. Use the ELN like a real lab book – don’t leave things out.

2. We’ll publish when we’ve reached a significant milestone. What that is depends on what people do, so we can decide this later.

3. Students who contribute experimental data can be authors and can edit the paper.

4. All reagents ought to be inexpensive and generally available – this is kind of the point. The starting material itself, praziquantel, is ironically not that cheap from most commercial suppliers. At the outset of the project, we can provide PZQ to labs wanting to take part – we’ll just mail you some. We’re looking for a longer-term solution to this once things get going.

5. I/my group are starting this up and, for convenience, hosting it, but we don’t own it. If other people work on this project so much they start taking it over and leading the science, that’s perfect. Leadership in open projects is fluid. Thus anyone who takes part works for the project, certainly not “for” me or my group. There is no other incentive to taking part than getting the job done and finding a route to this enantiopure drug that’s viable for scale-up.

If you’re a student who wants to take part, go hassle your lab director/PI. If you’re a lab director reading this, please consider having a cohort of students try this lab. This is a real optimization of a real process involving a real drug that affects millions of people.

Background to the science involved can be found here. There’s a pdf there that describes some of the chemistry. Essentially, though: the resolution is several steps, and each needs improvement. There’s an initial hydrolysis of the drug, synthesis of resolving agents, the resolution itself, and then the re-isolation and purification of enantiopure drug. Each step works, but needs to be better. There are lots of very nice crystalline solids throughout. We can’t use chromatography. We need inexpensive reagents, and environmentally benign solvents. We need high yields, and effective recycling strategies. And so on.

There are other examples of distributed student involvement in science. William Scott and Martin O’Donnell began a related project in 2009 called D3, and there were some papers describing this excellent work. The difference here is that our project is open, in the sense that anyone can participate and all data are freely available as they are acquired. That may make it more chaotic. It may also make it more effective. Part of the innovation here for people taking part is working that out.

It’s also fitting that this project is being launched during the International Year of Chemistry. We’re trying to use the web not just to share data, but actually to collaborate on a real research question in experimental lab science. If you’ve an interest in trying to solve this problem, you’re free to join a worldwide effort. There’s an interesting “crowdsourcing” experiment being run by the RSC that concerns measuring the pH of water worldwide. In our project we’re not asking for a measurement, we’re actually asking students to perform synthesis, but then also to think about what experiments to try next, and to help write the paper – the full gamut of aspects of a full research project. This is pretty demanding. It’s more reminiscient of the wonderful Biobricks competition, with the difference that our project here is open and web-based, rather than a competition in a specific location.

What’s the hope here? I hope that students can get excited about working together on a real research problem, and can get a taste for what a mind-bending exercise real research is – research where you’re not even sure what question to ask at the outset, let alone how to answer it. What I’m hoping for is that students can help solve an important problem as a group. I recently went to a meeting organised by a student cohort committed to lobbying universities to take part in research in tropical diseases without necessarily seeking patents and profits, UAEM. The guy then in charge of the group, Ethan Guillen, said at the start: “Students are great allies to have if you’re a professor”. Amen to that.