My experience in the supercomputing with Calendula

 My experience in the supercomputing with CalendulaApril 19, 2013, published in Science, Technology, written by doctorGENoma
Picture of the outside of the supercomputer Calendula
After some attempt to prove the supercomputing for my PhD, I have finally been able to access the service provided by the Supercomputing Center Foundation of Castilla and Leon where I could enjoy giving commands to use some other core Calendula, so is called the "monster" in question.Picture of the inside of one of the Calendula computing clusters. Click for Larger.
Inside of one of the Calendula computing clusters. Click for Larger.
The course was metagenomics analyzes using supercomputing very subject addressed to use ultrasecuenciación. As I mentioned to the organizers, it's a shame that there is very poor information base in molecular biology researchers. Of the 19 present, I was the only one who knew typing instructions under UNIX. But surely, at least the audience, espabilarán. Almost all showed interest prove once any Linux distribution.
Turning to the core, the truth is that for a tech geek like me is a course highly recommended. A part of the title that gives you a not inconsiderable price of € 350 (more than adjusted to other bioinformatics courses offered on national issues), the experience of immersing themselves in the analysis of genomic and metagenomic sequences from different systems next generation as Roche 454 or Illumina HiSeq is exciting. Working in a practical manner all the steps like a real project opens her mind above all the work behind this style analysis. That and I am not alone in this freak of bioinformatics.There was a first part where Jesus Lorenzana, one of those directly responsible for Marigold, gave technical notions supercomputing system process installed in the CRAI-ICT of the University of León. Technical data for some but only serve to bore-stopping when you've spent years riding equipment.image layout and scheme of Supercomputer caracterísiticas Calendula.
Diagram of the layout and the Supercomputer caracterísiticas Calendula. Click for Larger.
After Lopez Mariví gave us the basics to manage in conditions in the Linux environment. Simple things, yes, but that even a self-taught as I come to remember from time to time. Many of the orders I have given through the terminal I typed the inertia without knowing specifically any of the attributes. But hey, they are also more than 12 years learning to brute force and it came great. Some commands which are then needed could not be given, but no problems since such orders were necessary later in another class that lack of time was not paramount and learned on the fly without problems.Image MobaXterm animations
Sympathetic animations SSH client to access MobaXterm. Click for Larger.
The afternoon of the first day was more relaxed after the "stress" morning Jesus A. Gómez-Ochoa made a very sensible introduction to bioinformatics wondering at first what was our experience and guidance provided in the talk.On the morning of the second day, Alexander Sánchez Pla systems introduced next-generation sequencing and showed us FastQC use in graphical mode, very important to understand and compare what lies ahead after passing our DNA for Illumina.Although all classes were enjoyable, in the time that it was time to chop commands to analyze data for real chaos was present. Possibly the professor in charge of the parts of RNAseq believed everyone had a background in linux using correct enough to not be thinking more about the order that given that the analysis itself, in steps. The execution of the scripts that is basic came as a cold shower for my teammates. And it is normal. Possibly in other editions shuffle give more gradual formation, leaving this part of RNAseq almost to the end. All too attached to it was the last class in the morning and lack of sugar raged.The afternoon sessions were later beginning with theoretical analysis using microarrays by Henry J. Andrew Galiana. A paper that, from my point of view, was very mathematical and which I felt quite lost.Features four pointers supercomputers worldwide.
Features four pointers supercomputers worldwide. Click for Larger.
Javier Tamames continued his part devoted to the analysis of microbial diversity and metagenomics explaining each and every one of the steps to follow for each type of experiment. With a website created for the course as a support for him and for students learning and accelerating properly, interspersed supercomputing applications via web tools for less demanding analysis. The repetition of the steps and the achievement of the following analysis these instructions caused a good assimilation of these studies were based on sequence analysis of 16S with 454 Roche systems.Practices with Dr. Tamames lasted until the last minute of the last day of class early-morning, after which we set out to visit the Calendula supercomputing system. Jesus reeled at the level understandable by all, both emergency systems and the technologies that make up the giant puzzle of supercomputing that until recently was among the top 500 worldwide.For notéis the feeling of being in the supercomputer, then I put the deafening sound recorded in situ. -> CLICK HERE to hear the sound of the supercomputer.Screenshot Calendula accessed from Android
Accessing Calendula from Android. Click for Larger.
Even after completing the course had not been able to assimilate the entire syllabus, availability downloaded everything taught and Calendula access for the next week (for me recently due to the proximity of Easter and I'm a little worried biologist ) causes that can make the most of the event. Although for me, a week I knew little. Hopefully, in the not too distant future, all disturbed by these analysis systems can be divided into different categories to satisfy minds. But today is a good experience that is beyond the reach of many. Yes, after seeing the guts of Calendula going to make any other small conventional computer system.Image of one of the days of the course.