#netcdf

Some 3D renderings of the Mandelbrot set.

As mentioned previous, using geometric algebra we can convert the iterative equation for the Mandelbrot set from complex number form \begin{equation} z \rightarrow z^2 + c, \end{equation} to an equivalent vector form \begin{equation} \mathbf{x} \rightarrow \mathbf{x} \mathbf{e} \mathbf{x} + \mathbf{c}, \end{equation} where \( \mathbf{e} \) represents the x-axis (say). Geometrically, each…

Got proficient in playing "La fille aux cheveux de lin". Started "Clair de lune". Plan to get proficient by the end of the new semester.

Finished the installation script. Got a new mission of finding out the mechanism of how OOI CI processes raw geo data from the ocean sensors.

Had some research on HDF and NetCDF, refreshed my memory of Hadoop and dynamic programming.

Need to read a 38 GB PBF (Pretty Big File) in any dimension in ~1 sec? You need to chunk the data. Check out netCDF-4 with its sub-sampling and discrete compression options.

So you got some mass spectra to analyze and you heard about xcms?  You also like to do everything in R like I am known to do. So you decide to follow instructions on installing xcms and execute the following in your R session 

source("http://bioconductor.org/biocLite.R")

biocLite("xcms")

This will most likely fail as you might not have the NetCDF libraries installed on your system. 

if you didn't you're all set, if you did get an error, read on to see how to make it work?

xcms is now distributed by bioconductor, an open source set of software for bioinformatics. As xcms depends on netCDF libraries, you need to do the following before installing R.

The instructions below are for Ubuntu (command to be executed are in bold)

1. install the libraries required by xcms to work

sudo apt-get install libnetcdf-dev build-essential 

This package includes all the libraries, you might also wish to install the netcdf-bin for programs that can read and write netCDF files.

2. You can install the programs with 

sudo apt-get install netcdf-bin

Now you're ready to install xcms under R.

3. download the xcms package source, it's available at http://www.bioconductor.org/packages/release/bioc/html/xcms.html

4. Start R as root

sudo R (to run it with root privileges in Ubuntu),

5. install xcms (make sure to give the full path to where you downloaded it)

install.packages("/path_to_xcms/xcms_*.tar.gz") 

the * is for version you downloaded, and you should be all set.