Protein crystals are an essential part of X-ray crystallography, the method CSIRO uses to figure out the molecular structure of proteins. CSIRO is interested in the molecular structure of proteins because it is essential for our biotechnology research.
In order to find a protein crystal, CSIRO must set up thousands of experiments. Less than 1% of the experiments have crystals, and to find them we need to look at every experiment. CSIRO developed Cinder so we can crowd source our search for experiments with crystals.
Cinder is an easy app to use, swipe right for crystals. Your classification of each experiment is pushed back to CSIRO so we can use it to develop search algorithms in our scientific software.
What is it? Cinder is a crystal-image classification tool developed for mobile platforms. It is used to score crystallization experiment images based on four categories: Clear, Precipitate, Other and Crystal.
Why develop it? A few reasons, all linked to speeding up the protein crystallization process. The ultimate goal is to have computer software classify images so that we no longer need to trawl through 1000s of images, and for that we need an easy way to let many people score a training set (enter Cinder). With enough development support we will release a client specific version of Cinder, an alternative to desktop applications. This will make it easier for more people to score more often, and we can capture an ever growing data set.
How does it work? Conceptually it has some similarity to the mobile dating application Tinder, however we needed more granularity than “keep” (a hit) or “discard” (everything else), so included vertical swipes on top of the horizontal. Why? Precipitation and Other events can be helpful to guide an optimisation strategy failing any indication of a crystal. For naive users we’ve got a help tool called CinderKinder, which lets you know how good you are at classifying pre-scored images. CinderSolo allows scoring of your own images by logging in using your See3 credentials
How do we get it? From the links above.
The latest cinder App update adds functionality to allow scientists with accounts at CSIRO’s C3 facility to view and score there own images on the go! To do this just select the “Cinder Solo” option. This presents users with there own images in a randomised order. Simply swipe (or tap) to score. These scores will then be uploaded to the database and available for viewing via our See3 viewing software.
CinderKinder is a list of pre-scored crystallisation images that you are asked to score. Each time you swipe, your score is compared to the score given by a crystallographer to that same image. A brief explanation of why the score was assigned is also displayed. The purpose of this is to train novice users to look at a crystallisation image as a crystallographer would. If you would like to submit images for the CinderKinder training set please use the form below or email us.
Left: The standard screen, waiting for you to score. Centre: Cinder Kinder, our help tool. Right: Zoomed in to see the detail of an experiment (micro-crystal).