Notes on John Donoghue's work (BIEN2)

Page Contents

Presentations from BIEN 2012 meeting (login required)

• Range Modeling Update (Tuesday session)
• Geographic Range Size Methodology (Tuesday session)
• Range Area Methodology Breakout Update (Wednesday session)

Range model methods manuscript (login required)

• JD_Range_Size_MS_V3_NMH (17 January 2014)

Documentation on iPlant wiki

Hi Brad,

Below is what I found on the iPlant wiki. Do pay attention to the last date the pages were edited. The range models were computed twice. The first time (ultimately) Edwin and Sangeeta ran them in Oct 2011. The second time John ran them in fall 2012. I've ordered things (in what I consider) most useful to less useful.

Let me know if you have any questions.

Martha

---------------------

Documentation on iPlant wiki

• Most recent and probably most useful is this doc John prepared for a meeting on 6.25.2012:
  • https://pods.iplantcollaborative.org/wiki/download/attachments/8405617/12-06-25+iPlant+BIEN+Range+Modeling+Documentation.pdf?version=1&modificationDate=1341277022000
• Martha's periodic update notes to iPlant (high level overview), 2011-12:
  • https://pods.iplantcollaborative.org/wiki/display/sciplant/SciPlant+Updates+on+Range+Maps
  • Read from the bottom up. 
• Links to meetings about the second run in 2012:
  • https://pods.iplantcollaborative.org/wiki/display/iptol/Meetings+Range+Maps
• Using the parametric launcher, July 2012:
  • https://pods.iplantcollaborative.org/wiki/display/SOT/BIEN+Range+Modeling+Output+Files
  • Brad, you may not use the parametric launcher since the APIs to run jobs at TACC are now available. 
• Workflow, Aug. 2011: 
  • https://pods.iplantcollaborative.org/wiki/display/SOT/BIEN+Range+Modeling+Workflow
• File structure on iPlant Data Store (iRODS), Aug. 2011:** https://pods.iplantcollaborative.org/wiki/display/SOT/BIEN+Range+Modeling+File+Structure
• Output files, Oct. 2011:
  • https://pods.iplantcollaborative.org/wiki/display/SOT/BIEN+Range+Modeling+Output+Files

Tips and Notes (from emails)

There's limited info of use in the emails. Martha flagged the few possibly useful ones in her mailbox. Most messages are back and forth when John needed help doing something.

• John's second run scripts and data were archived to Ranch (tape which is slow to access) at TACC.
• Look for things in /jdonoghu/bien/
• Beware of the graphic package dependency
  • From Edwin: maxent.jar requires access to X libraries due to this error: 
    • Error in .jcall(mxe, "S", "fit", c("autorun", "-e", afn, "-o", dirout,  : 
    •   java.lang.NoClassDefFoundError: Could not initialize class sun.awt.X11GraphicsEnvironment
    • Calls: computeSDM_Spatial ... maxent -> maxent -> .local -> .jcall -> .jcheck -> .C