iPlant portal 04-04-2014d1354

2015-06-19

iPlant portal 04-04-2014d1354
plant bioinformatics
first heard about this from Josh

a platform that lets you run a certain amount of computer instances for free
-first heard about this from a presentation from Josh Richer about a Big Data conference

other possibly similar platforms
{
    Distributed European Infrastructure for Supercomputing Applications (DEISA), integrating eleven European supercomputing centers
    Enabling Grids for E-sciencE (EGEE)
    National Research Grid Initiative (NAREGEGI) involving several supercomputer centers in Japan from 2003[8]
    Open Science Grid - a distributed computing infrastructure for scientific research
    Extreme Science and Engineering Discovery Environment (XSEDE) - the TeraGrid successor

}

How good are the computers on iPlant?
{
-Not bad at all 08-26-2014d1711
--I did a test comparing my HP desktop computer and a 4 CPU iplant Ubuntu instance.  Here is the result of the comparison.
{
home desktop computer took from 12:04:01 to 12:05:44
-total time: 1 min 43 seconds
iplant 4 cpu computer took from 20:38:22 to 20:39:16
-total time: 54 seconds
}
}

iPlant images
-EpitopeAnalysis_2
--This comes with blast, the meme suite, clustal omega, and Java all pre-installed.  Note that the programs are already recognized from the command line.
-EpitopeAnalysis_1
--This comes with blast, the meme suite, clustal omega, and Java all pre-installed
--run the following two commands to get everything going
{
export PATH=${PATH}:/usr/local/bin/meme_4.10.0/src
export PATH=${PATH}:/usr/local/bin/ncbi-blast-2.2.29+/bin
}

-Troubleshooting
--[VNC problems on iplant atmosphere 09-04-2014d0926]

Questions
-How can I get vnc working on iPlant? 05-24-2015d1313
--You can click access by vnc on the webpage while connected to a university network, then the vnc seems to work sometimes (after you activate Java).  If it doesn't work, I think this can be solved by terminating the instance and creating a new one.  Once you are connected to a university network, you can also connect with realvnc.  This allows for easier file transfer.  Note that when you try to connect with realvnc, you need to put a ":1" after the ip address to connect.
-How to get Java project setup in Windows to work on a Linux computer on iPlant Atmosphere.  When you download a project file setup on Windows, the folder structure changes on the Linux system.  You can get the code running by importing the project when you find a location that lets you import a project, manually importing the jar files you need (you can delete the other ones that don't have proper paths now), and importing all the source files.

Some items
-[pr_old iplant instances 05-24-2015d1312]

---------------
See also
-[pr_iPlant user accounts 09-05-2014d1518]
-[vnc portal 05-21-2015d0934]

azim58wiki: