Fourteenth Week Update in Valum

The 0.2.0-beta has been released with multiple improvements and features that were described in the preceeding update. It can be downloaded from GitHub as usual or installed from the Docker image.

The documentaion has been nicely improved with more contextual notes to put emphasis on important points.

The framework has reached a really good level of stability and I should promptly release a stable version in the coming week.

There’s a couple of features I think that could be worth in the stable release:

• listen to multiple sources (socket, file descriptor, )
• listen to an arbitrary socket using a descriptive URL

I have implemented a lookup function for cookies which finds a cookie in the request headers by its name.

var cookie = Cookies.lookup ("session", req.headers);

Mirdesign

I started working more seriously on the side project as I could meet up with Nicolas Scott to discuss what kind of web applications will be developed with Valum.

Mirdesign HIV prototype built with Semantic UI.

But first, let me briefly introduce you to his work. He works on µRNA simulations using a modified version of an algorithm that performs matches between two sets: µRNA and genes (messaging RNA) from a cell line.

He developed a language that let one efficiently describe and execute simulations. It does not have a name, but the whole thing is named Mirdesign, “Mir” standing for µRNA.

The web application will become a showcase for his work by providing specific testcases his language can actually describe. It consists of two layers:

• an API written with Valum and backed by a worker pool, memcached, MySQL and JSON documented here with Swagger
• a client written with Semantic UI that consumes the API

As of now, we decided to go on with a HIV testcase that would let one select a cell line, the amount of µRNA to pour and some extra genes that could be specified or extracted from a FASTA file.

If it works well, other testcases will be implemented to cover yet unexplored aspects of Mirdesign.

There’s still a couple of things to work out:

• parsing the FASTA file (fasta will be used)
• generating a Mirdesign word from user input
• exposing (partially) the MySQL database through the web API
• change the processing backend (TORQUE or other cluster)