Blog de Toni Hermoso Pulido

Toni Hermoso Pulido

Open Science: not only a matter of outcomes, but also of processes


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 Sciencefirst 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.

Are you moonlighting?

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.

Using Neo4j with NCBI taxonomy and Gene Ontology datasets

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.

Chrono Trigger — 20 anys després

L'11 de març de 2015 van complir-se 20 anys del llançament del que molts consideren millor videojoc de la història, Chrono Trigger. El joc, un RPG japonès desenvolupat per l'empresa Square (després Square Enix), relata la història d'uns personatges d'una realitat que recorda l'Edat moderna europea, que viatgen al llarg del temps per salvar el món d'un futur apocalíptic. Es va comercialitzar per a la consola Super Nintendo el 1995 primer a Japó i pocs mesos després als Estats Units. Malauradament, no va arribar a distribuir-se mai a Europa (com tampoc a la resta del territori PAL).

Script per recórrer categories de la Viquipèdia

Per tal de preparar la Viquimarató de Bioinformàtica que tindrà lloc el proper divendres 27 de febrer de 2015 a Barcelona, una de les coses a fer és tenir preparat un llistat d'articles (inicial aquí) que suggerirem als participants perquè hi puguin treballar (sigui tant ampliant-los com creant-los de bell nou).

Aplicació per al registre a esdeveniments amb correu electrònic

Fa una setmana, a l'acte de DebatCatDigital de Palafrugell, comentava que hi ha molts casos d'ús, actualment relativament simples a nivell tècnic, com ara xats, que acabem emprant en serveis externs i on potser llavors esdevenim carn de dades quan aquests se'ns ofereixen de forma gratuïta.

Video streaming with a Raspberry Pi, Gstreamer and Nginx

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:


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