Tag Archives: SQL

Software Carpentry. A great resource to learn scientific computing.

Software Carpentry is a volunteer organization founded in 1998, whose mission is to enhance scientists’ productivity by teaching them basic computer skills. From January 2012, Software Carpentry joined the Mozilla galaxy, to become part of Mozilla Science Lab in June 2013. The organization provides workshops in several parts of the word and free online lessons. Their focus is to teach the basics of some very useful in silico methods to scientists, such as structured programming (Python and R), numerical programming (NumPy), version control (Git, mercurial and SVN), unit testing and automated tasks in Unix, regular expressions and relational databases (SQL).

Most likely, you have heard about them, but I still take some time to report their amazing work. After a long experience in this, guys at Software Carpentery have developed a very simple deal with their customers: short courses at an affordable price. You pay them accommodation, put yourself in the mood to become more efficient and dedicate a couple of days to learn very useful scientific computing stuff. As they affirm on their website, courses must be short to meet better the needs of very busy researchers, and the workshop represent the most efficient way to learn. efficiency is actually the thing they care the most, and you may consider its importance in your work.

The truly amazing thing is that they really operate worldwide. So, I think you may consider surfing their website and get to know this long- established and very useful project.


The 6 books you must consider for your very first steps into databases.

Basically one would really avoid this. Biology is already quite hard to keep in mind, and you don’t really need of informatics to keep your brain busy. But, by definition, a bioinformatician is someone who match the two subjects and the best thing to do is to do it the best you can. Learning a powerful programming language such as Python, Ruby or Perl, getting used with markup- languages (XML and derivates) and learning databases are the three things a biologist must do to call himself bioinformatician.

Yes, ok, but how to do it? The standard procedure a computer scientist would enthusiastically prospect you is to find all the information for free and on the web. And he would be right. After all, the hacker philosophy is pretty clear about that: take all the free information you can find, even if this can be quite hard. But, since many of us are romantically devoted to books, and since not everybody is willing to spend time in a fight to the death against information entropy, sometimes release few money for a book it is not that bad idea.

Here are reported some books that can be useful to deepen into the world of databases. Building a database is a really boring thing you might really need. Handling big information is needed for the majority of genomics and structural studies. Building a database, beeing able to build querys or developing scripts to reason with the major genomic or protein databases out there could be really useful and time- saving.

Introduction to Database and Knowledge-base Systems
By S. Krishna

With this book you’ll learn the basics of database theory. Very easy to read and exhaustive.

SQL in a Nutshell A Desktop Quick Reference
By K. Klein

Maybe the best guide to understand Structured Query Language.

SAMS Teach Yourself SQL in 10 Minutes
By B. Forta

A concise guide to SQL. The text is organized into lessons. Easy to read and exhaustive.

MySQL Cookbook
By P. DuBois

900 pages to have a very complete overview on the open source DBMS MySQL. Maybe the best MySQL book around.

Instant PostgreSQL Starter
By D. K. Lyons

Move your first steps in the world of the open source DBMS PostgreSQL.

Database Annotation in Molecular Biology: Principles and Practice
By A. M. Lesk

A very exhaustive guide to Biological databases. Useful for database curators and users.

If you know more, please comment this.