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Scientific Computing

A blog about computational biology

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Scientific Computing | webappl.blogspot.com Reviews

https://webappl.blogspot.com

A blog about computational biology

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1

Science Notes: July 2014

http://webappl.blogspot.com/2014_07_01_archive.html

Sunday, July 6, 2014. How to create a Perl Module for code reuse? José's Guide for creating Perl modules. Http:/ www.perlmonks.org/? Http:/ www.perlmonks.org/? Thursday, July 3, 2014. What is principal component analysis? A really good post by Lior Pachter. Http:/ liorpachter.wordpress.com/2014/05/26/what-is-principal-component-analysis/. Print specific column of a text file. To print the second last column of a tab delimited file,. Awk -F ' t' '{print $(NF-1)}' file. Tail -q -n 2 file1 file2 file3.

2

Science Notes: February 2015

http://webappl.blogspot.com/2015_02_01_archive.html

Wednesday, February 25, 2015. Extract rRNA and tRNA features from UCSC Browser. Credit to Matthew Speir. In the Table Browser, you can use the following steps to get the coordinates for tRNA genes, with all of the tRNA pseudogenes filtered out:. 1 Select your assembly and tracks. Assembly: Feb. 2009 (GRCh37/hg19). Group: Genes and Gene Predictions Tracks. Output: GTF - gene transfer format. Output file: enter a file name to save your results to a file, or leave blank to display results in the browser.

3

Science Notes: Installing lapack on ubuntu

http://webappl.blogspot.com/2010/07/installing-lapack-on-ubuntu.html

Monday, July 26, 2010. Installing lapack on ubuntu. 1 Download lapack.tgz from www.netlib.org. 2 Unpack the archive. 3 Copy the appropriate make.inc.xxx file from the install directory into make.inc in the main directory. 4 Edit the make.inc and Makefile when appropriate. 6 In cases of getting error blas Linux.a: no such file or directory, type: make blaslib testing. Subscribe to: Post Comments (Atom). Install Sun Grid Engine (SGE) on Ubuntu Server 11.04. Installing lapack on ubuntu. Installing lapack on...

4

Science Notes: Set Up an MPICH2 Cluster With Ubuntu Server 11.04

http://webappl.blogspot.com/2011/05/setting-up-mpich2-cluster-with-ubuntu.html

Tuesday, May 17, 2011. Set Up an MPICH2 Cluster With Ubuntu Server 11.04. This is a short note of setting up MPI cluster with Ubuntu system. Assume four machines named ub0-3, with ub0 being the master node. They are connected through private local network. At the time of writing this note, the operating system of these machines is Ubuntu Server 11.04. 1 Define hostnames in /etc/hosts. Edit /etc/hosts like this (change IP address accordingly):. 192168.133.100 ub0. 192168.133.101 ub1. User@ub0: $ sudo user...

5

Science Notes: October 2013

http://webappl.blogspot.com/2013_10_01_archive.html

Sunday, October 27, 2013. How to recover sudo if /etc/sudoers file is invalid? If /etc/sudoers file is damaged/changed so that sudo command cannot be invoked, the best method of saving the world is to call utility 'pkexec':. Pkexec command to run. For example, to edit the /etc/sudoers file is simply. Tuesday, October 1, 2013. Some useful PBS/Maui commands. Showq Show a detailed list of submitted jobs. Showbf Show the free resources (time and processors available) at the moment. Subscribe to: Posts (Atom).

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