2014.01.13 BIEN

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Last updated: Jan 13, 2014Version comment
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BIEN Planning Meeting

January 13, 2014

Participants

Brody, Jens, Naia, Ben Blonder, Aaron, Bob, Brad, Brian E, Brian M, Irena, Jeff Ott, Nathan Kraft, Peter J, Cyrill, Martha 

Agenda

Notes 

BIEN3 Update (Martha, Brad, Bob)

  • Performing the spot-checking validations and making necessary changes to the loading scripts has taken much longer than anticipated.
    • Changed the approach to loading data.
    • Still cumbersome.
    • Beta milestone in Jan
    • Still will need quantitative validations
  • Brad will ask what people want to see in denormalized views for doing analyses.
  • BM: Will abundance numbers be reliable in BIEN3
    • BB: Yes, but will always need to use them with caution
    • Brian M will help with early research to check reliability of the abundance aggregations.

Public release of BIEN2 and 3 data, and range maps

  • Start with trait data
  • Via website or iPlant
  • John sent a range modeling methodology paper to Naia. Hasn’t changed much since last spring. Now that Naia has finished her thesis, she has more time to help John move that manuscript along.
  • Range maps and phylogeny from BIEN 2 are available and people have requested to use them.
  • BB: As we make new data available, people won’t want to use the BIEN 2 data. However, it needs to be archived for those who have used it.
  • Recall that the two main problems with BIEN2 data reliability were:
  • Abundance data
  • Specimen data resulted in problems in range maps
  • Who wants to be part of a group to deal with issues associated with data release?
  • Brian M
  • Cyrill (trait)
  • Brad

sPlot and sDiv (Brody, Bob)

  • sPlot was founded in March to do focused study of vegetation along environmental gradients.
  • Trying to get plots that span the world rather than all the plots.
  • Doing species lists and cover values.
  • Moved from a focused science question to the need to build a database.
  • Ended up following the TRY example for being part of a consortium.
  • There were discussions about how sPlot and BIEN could
  • Do a vegetation extract from BIEN and send it to sPlot
  • It’s taking longer than anticipated for sPlot to get the database set up
  • sDiv has its schema and wants data to fit into it, so don’t want to use BIEN schema.
  • They would want summary data from BIEN on the abundance and biomass from each plot.
  • Brad unsure how to summarize with “cover” as the aggregator.

TRY (Cyrille)

  • Want to have a web link from BIEN website to TRY data.
  • TRY is moving more toward open access.
  • The link would be direct, could refresh TRY data, and download some.
  • Still need to write and request data.
  • Jens Kattich is ok with this.
  • Traits would be released first from BIEN.
  • TRY trait data could be open access.
  • e.g., for Kew data, can not serve the data on another website.
  • Would be the first official collab between BIEN and TRY.

U Kansas Bioinformatics group (Brian E)

  • Towne Peterson
  • Barbara and Brian were invited
  • Goal was same as BIEN’s to create vegetation db for Americas.
  • There is still a vast network of scientists who would like to be involved.
  • Also interested in predicting range maps under different climate scenarios.

BIEN app (Brian, Brody)

  • Greg would like to do this within a month.
  • Brody has had interactions with Greg.
  • There will be a trial period for the app before it goes on iTunes
  • Will be a free app

Funding sources

Luc Hoffman

  • Spoke with Josh
  • Meetings and post doc to work with fellows doing outreach to the conservation network in World Wildlife Fund.
  • Would need a champion within WWF.
  • Amazon
  • South Africa
  • IUCN
  • Would need conservation goals as well as bioinformatics goals.
  • Jens thinks the Amazonian work is a good fit with BIEN and he’s happy to help.
  • BB: IUCN status would have to be added externally when making the analytical views

OTS Costa Rica

  • Has high funding rate.
  • Barbara very interested
  • Opportunity to expand network in Central and South America.

Research Publications

  • Irena has a trait mapping study in the works and will set up a drop box.
  • Stephen Smith’s group was going to provide an updated phylogeny.
  • Haven’t heard from them.
  • Brian will ping them.

Jeff Ott

  • Would like to use…
  • BB: He came across a large scale effort in modeling vegetation across the Americas. Identified vegetation boundaries. Will pass along to Jeff.

Brian would like to hold monthly planning meetings at the same day/time if that works for everyone.