The return of the X-files

A classic of TV shows about conspiracies, aliens and the like is returning this year. The X-files was one of the most viewed TV show in the nineties and lasted 9 seasons. Just last night the first episode of this tenth season was aired. This will be a short season miniseries consisting of 6 episodes.The same main characters are back, played by same actors; Dana Scully (Gillian Anderson) and Fox Mulder (David Duchovny). In this season, it appears that plot will float around the idea that all the previous investigation carried by Scully and Mulder was in fact a manipulation to lead them to believe and make public the idea of an alien intervention on Earth. Now, the protagonists realize that there is in fact a global human conspiracy that experimented on abducted humans with discovered science from a captured alien in Roswell in 1947.

I must say that I found this first episode not very good, but I do really hope that the next episodes get better. And finally I must say also that Gillian Anderson, despite her years, is still very beautiful and attractive!!!

X-Files: The Complete TV Series and Movie Collection

The X-Files: I Want To Believe

TV series: FlashForward

Recently I have seen a TV series called FlashForward. This was a typical TV show that lasted just one season. The reason? well, I think it was too scientific/technical for most people? in almost every episode of this show there are references to Quantum mechanics concepts. Since I like this kind of "nerd" stuff, I liked almost every episode of this show. OK ok.. it is not perfect, some explanations of things are kind of Deus ex-machina from a QM concept, but anyway, I appreciate the attempt.
A popular TV series that many scientist that I know use to see is "The Big-Bang theory" (I will not even put a link here). Honestly, I really dislike that show because they try to make a "funny parody" with scientific concepts, without even achieving that (in my humble opinion). Instead, FlashForward tries a bit more serious science fictional explanation of events.

This TV show also combines some lines of conspiracy, suspense and thriller. If you like this mix, do not miss this show.

SQL or not SQL?

So much propaganda I have read in the Web about the so-called NoSQL databases that I would like here to say something about this. I will assume that the reader have knowledge of relational databases.

In general, every piece of data needs a non-random structure, otherwise it can hardly represent useful information (worth to be stored and then retrieved for some human purpose). Considering the client-server paradigm, the structure can be imposed to data in the client, in the server or both. Relational databases have the ability to relate data within tables and these can be related to other tables within the same database (server). However, the relational schema can have a minimal relation description of a key-value class. For example, we can define single documents into relational databases by creating a table like this (assuming a maximum document length of 8 kilobytes, which of course can be extended):

CREATE TABLE docs (id INTEGER PRIMARY KEY, docdata VARCHAR(8192))

and then we can store XML or JSON documents into the docdata field, which can be interpreted in the clients of the respective database. Therefore, relational databases can be perfectly used as document-oriented database, provided an appropriate schema. Unfortunately, this quite obvious application of relational databases is normally omitted by proponents of the so-called NoSQL databases, promoting a lot of misunderstanding of what a relational database can or can not do.

On the other hand, the wrongly-termed NoSQL or document-oriented databases can store documents in such a way that the SQL language is avoided, and also providing sometimes automatic parsing or processing of the XML or JSON content. These document formats have become very popular among web developers and other computer-programming enthusiasts and thus there are many software packages that can be used to process these formats. 

In conclusion:

1. NoSQL databases should be called “client-side structured databases” because the interpretation of the structure of the data is usually left as a task for the client, not the database itself (server) 
2. In SQL databases the structure of the data is explicit on the database itself (in the form of relations of formal first-order logic, with SQL as the query language). In NoSQL databases the structure is less formally (and thus more flexible) defined in document formats like XML or JSON that are normally parsed or processed by the client
3. Relational databases can also be used to store/retrieve formatted documents (e.g. XML and JSON)
4. The real and tangible advantages of NoSQL databases comes from the consequence of storing unstructured data, which can be more easily distributed among servers. Also, that the structure is left to be interpreted to the client in most cases, makes these more scalable. However, relational databases are much more secure for the integrity of the data. 

Using SQLite

TV series: Damages

I know this is outdated, but I just recently saw the season 1 of Damages and I must say that I had missed an excellent show, in the perfect line of content that I enjoy, which is psychological thriller. The performances of Glenn Close , Rose Byrne and Ted Danson are outstanding, in fact all of them received important nominations and awards.

In the series, each season is about a lawsuit against a big company, or a multi-billionaire, as in the case of the first season. During each episode flash-forwards images from the season finale somehow announce a fatal outcome, with a horrific music making one to think how in Earth things got to that point.

Grasping inspiration

Inspiration is an interesting word. It ultimately comes from the Latin word inspirare, and this from spiro.. both being related to the effect of breathe or carrying air into your lungs, although it was also related to live, in general, or to fill the body with something that allows one to live. Related words are spirit for example, normally used as synonym of ghost in modern language.

Religious people can say that God is a matter of inspiration. Well, even when I am not a religious person, I can believe this. Take for example one marvelous piece of music, the "Miserere mei, Deus" written by Allegri more than 300 years ago. It has been said that the pope at the time asked Allegri to write this piece for exclusive performance within the Sistine Chapel only. Nobody listened this beautiful polychoral composition outside this chapel, until the fourteen years old Mozart attended this service and re-wrote it entirely by memory!

Nice story, formidable inspiration...
More information about this can be found here.

File formats of bioinformatic programs

In bioinformatics we face the problem of manipulating huge volumes of data and most bioinformatic programs still use plain text as output. Each time a new program is released a new output format is created and new computer parsers should be programmed on every place the program is to be used. Using XML for storing outputs has started to be common in some well-known programs but it is not the best solution (for bioinformatic programs) available today. Here I show how to use SQLite in a very basic bioinformatic example.

Complete document: http://zdruid.blogspot.com/p/on-file-formats-of-bioinformatic.html

Homeland S05E08 today...

Today is "Homeland day".

Homeland is an american TV show that has been aired on Sundays in Showtime.

It is currently on the fifth season (each having 12 episodes) and today it will be aired the eight episode.

This is a really good show about spies, geopolitics and the like. Unlike some other shows about politics and spies, the protagonist here is a woman (Carry Mathison), played by the great Claire Daines.

Other great shows arguably in this line and that I have enjoyed are Rubicon, The shadow line, The Honourable Woman.