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