Linxe's eye

Multi-tasking? A PhD must have ... From: http://www.phdcomics.com/

Last day, le Jacou asks me about the GenBank format, because he is writing a parser for this to integrate in his super-shining-colorfull-visual man-see annotation interface, so he needs a parser to split the file by sequences, each one will be in a separate HTML file. Later he show me his code in C# and after I think how it can be translate in Perl, I suggest: #!/usr/bin/perl -w # parseGBK2HTML.pl # Juan Caballero @ 2008 $ARGV[0] or die "Usage: parseGBK2HTML \n"; use CGI qw(:standard); use BIO:SeqIO; my $file_in = shift @ARGV; my ($seq_in, $seq_out, $file_out, $seq, $features); $seq_in = Bio::SeqIO->new(-format=>'genbank', -file=>$file_in); while ($seq = $seq_n->next_seq() ) { $file_out = $seq->accession_number; $file_out .= '.html'; $features = $seq->get_SeqFeatures; open OUT, ">$file_out" or die "Cannot open $file_out"; print OUT header, start_html("$file_out"); print OUT p($features); pri...

From here: http://www.freesoftwaremagazine.com/columns/bizarre_cathedral_4

This weeks had been a transition, new home, new work, new projects. All things are a little different, this week finally I got a computer to work and it's a Mac, its name is Broadcast. Many times I had used the Mac, specially from OS X, now I need to use it every day. The Unix inside is working great, all is simply and pretty, and the best is the 24" screen, larger than my old TV, my software selections are: Web browser: Mozilla Firefox Multichat: Adium Text edit: jEdit RSS reader: Vienna Seqs Tools: eBioX CHM Reader: Chmox FTP Client: Fetch Screensaver: Tron/RedPill I miss Linux, but many server and clusters are Linux-based, so I use my Mac to connect with it. Maybe later I try Xcode to develop some application for Mac.

In this part we'll install and configure the other nodes, in the master node we have a DHCP server and a PXE network boot which serves the netboot system, so we just need to connect the net cable, a keyboard and a monitor to the node, turn on and wait to install the base system. Options include partition of the hda disk, we use the defaults and put all the system in a partition and default swap size. We add the general user named beagle and after rebooting, login, become root, change the password and install the SSH server: sudo su - passwd apt-get install openssh-server Repeat this for all the nodes. The next steps will be only from the master node. SSH access You need to create a pair of keys for each user to access any node without a password, first we create it in the general user beagle : ssh-keygen cp .ssh/id_pub .ssh/authorized_keys Root also need this keys, but we don't export the root's home, after you created the keys, you need to copy to all the nodes. This st...

This time I want to show how to build a HPC ( High Performance Computing ) cluster using Ubuntu Linux. Before to begin My Institute (Cinvestav - www.ira.cinvestav.mx) ask me to build a small cluster to general works and it'll be a learning system for bioinformatic. The cluster name is Beagle, they put the hardware and my friend LuisD and I the hard job. The design includes a master node to access, to check status and to send jobs, and 10 slaves nodes with /home exported with NFS, a job queque created with Sun Grid Engine, Ganglia is user to monitor the systems and also include MPI support. Hardware Master Node : AMD Athlon 64 X2 4200+, 2 Gb RAM, 1 hard disk IDE 80 Gb (hda), 1 hd SATA 320 Gb (sda), 1 external USB hd 1 Tb (sdb), network card nForce 10/100/1000 (eth1), network card PCI Realtek 10/100 (eth2). Slave Nodes X10 : AMD Athlon 64 X2 4200+, 2 Gb RAM, 1 hard disk IDE 80 Gb, network card nForce 10/100/1000 (eth0). Network Switch : 24 ports 10/100/1000. Many meters of network c...

Bienvenido a este Blog, en él tratare de narrar mis experiencias y otras situaciones que inquietan mi mundo, no hay psicólogo más barato según me recomendaron. Los temas a tratar varían, desde cosas científicas hasta plenamente cotidianas, pueden esperar temas de bioinformática, genómica, genética, biología de sistemas, cómputo, programación y clústers en Linux y más.