This article first appeared in redcedar. Also in a summarised version in Ellipse PRBB magazine.

It’s been almost a decade since the term “Open Science” first appeared in Wikipedia. The page was created by Aaron Swartz and initially redirected to the “Open Access” entry. Some years later this young activist committed suicide as a result of the pressure from the judicial charges against him after having uploaded many privative licensed articles to the Internet.

In a previous post I detailed how to set up a web-based streaming from a Raspberry Pi device. After having updated Raspbian to its latest stable version, jessie, I thought it could be a good moment for reconsidering the streaming approach I was using.

A few weeks ago I finally had my dissertation (PhD) defence. Below you can see the shown slides (in Catalan), trying to touch in around 3/4 hour many of the different involved works.

One of the mentioned topics was protein moonlighting (or multitasking), that is, the property that some protein molecules may have additional functions or roles apart from the one that is primarily annotated or known. As example, the group in which I worked during my PhD studies is actually keeping an exhaustive list of these cases.

This usage can be considered as a kind of metaphor of the original moonlighting term. As it can be read in Urban Dictionary, it refers to the fact of having an additional job, normally during moonlit hours (at night).

For a non-native English speaker it's always hard to know how popular certain words or expressions are. It was funny to learn that at least this word seemed to exist already during the 1970s in the USA. However, as we can see during a conversation of the main character of Taxi Driver, not all people may have been fully familiar with it.

Around one year and a half ago I started some testing with graph databases (Neo4j so far) and I used Gene Ontology and NCBI taxonomy datasets as sample cases. I explained my experience in this presentation by February 2015:

After a while, I finally found time to update my importing scripts and API Java extension so they could work with newer versions of Neo4J and Py2neo (2.2.3 and 2.0.7 at the time of writing).

Regarding Py2neo, I noticed that Neo4j REST API seems to rely more explicitly on Cypher queries that it did in the past. With the help of this article about multiprocessing in Python and Py2neo, and after several tries, I managed to get importing work within acceptable time.

As final tips, if you plan to use similar approaches with your own data, I would suggest to create nodes and populate their properties at the same time (keeping data in memory if necessary). I also noticed that trying to create relationships with multiple parallel processes fails, so keep only one worker for these steps.

I purchased a RPi Camera for Xmas, and I could not wait for testing it with my personal aquarium. Of course, if you browse the web, you'll see I'm not the first one to try it with their aquatic pets. In any case, below I share with you some notes that can be helpful for setting up a low-CPU consuming web-streaming using a domestic Raspberry Pi (with Raspbian in my case).

The resources I mostly followed:

These winter holidays I've been taking care of my home network and I finally found some time to set up a Raspberry Pi for my everyday Internet needs.

It's already almost 2 years that I wrote about the upcoming RESTful times in Bioinformatics. And well, it's already happening...
Just as curiosity, I will explain my recent experience using ENSEMBL REST API.

Since its beginning I liked Persona (also known as BrowserID), because it:

• technically supports a more decentralised Internet
• makes authentication easier for users

Shame on me, only just a few weeks ago I found time to play with this. As a proof of concept, I prepared an Express application that connects to MySQL so I could have a better understanding about how this authentication system actually works in practice (from a developer point of view).

For long time Softcatalà wiki used a MediaWiki AJAX rating extension, so we could have a rough idea of visitors feedback on the different applications we list in our software repository. Recently I migrated that wiki to a newer version, so before I had reviewed which extensions to use: basically I checked whether there was any update to the current MediaWiki version for every installed extension.

It's a long time since Molecular Biology data (from sequence strings to protein structural coordinates) are being released openly to the public, as it's the Web an interface for exploring and visualizing those data. Indeed, my first approaches to Bioinformatics and to, more or less, serious programing were preparing CGI points to command-line applications or to results of analysed data.