Web Development Tools and Bioinformatics

Over the last few years I have been doing a lot of experimentation and development work (mostly unpublished) surrounding things like genomic pipelines and ways of managing and exploring genomic level data (focused on rare variant analysis in humans). While there are plenty of exceptional programs and tools out there for this (particularly pipelines), we bioinformaticians do like to tinker and re-invent the wheel a lot. Sometimes this is bad (I’ve been guilty of this in the past), and sometimes it isn’t. We all also tend to come at how to execute and configure things (again, particularly pipelines) in our own particular ways so sometimes even the best software can be a chore for us to use, because some early step just doesn’t seem right to us.

This is one reason why I think we should follow a trend that has become a bit of a trend in web design, which is the concept of microservices. I am by no means an expert, and suffice it to say that you can learn much more about microservices elsewhere, but the general idea is that instead of building monolithic programs we should build loosely coupled microservices that can work together to form your application. These microservives should speak to each other through APIs, meaning that you reduce the risk of internal changes to the service breaking other parts of the application. These services can also be re-used again and again in different applications. Microservices also should generally be small and focused. Do one thing, and do it well basically.

For me I think this is a worthwhile ideal in Bioinformatics, although I understand that it can sometimes be counter-productive from the sense of publishing. Of course we can always develop applications and frameworks as microservices and publish them together as a collection. The upside is that other people may want to only use selected services from your application instead of the whole application. Developing as microservices should make this easier and more straightforward.

Written on November 20, 2015