Using Desktop Data in Kepler

Using Desktop Data in KeplerDan Higgins – NCEAS

Prepared for:

Ecoinformatics Training for Ecologists

LTER (Albuquerque)

January 8-12, 2007

http://www.kepler-project.org

http://seek.ecoinformatics.org

http://www.kepler-project.org/

http://seek.ecoinformatics.org/

Viewing a Dataset – Text Editor1999 Sevilleta LTER NPP Quadrat Sampling Data

Text Editor view ofdata from a web page

Includes both data anddocumentation (metadata)In a single text document

727 KB file

Viewing a Dataset - Excel 1999 Sevilleta LTER NPP Quadrat Sampling Data

Excel View

Data and column header only

Can be saved in various formats

SevilletaData.xls – 1489 KBSevilletaData.csv – 369 KBSevilletaData.txt – 369 KBSevilletaData.xlm – 5863 KB

Only some formats are easily readable by other applications!*.csv - comma separated values ; *.txt - tab separated values(Cutting & Pasting from Excel results in tab separated columns)

Viewing a Dataset – Morpho1999 Sevilleta LTER NPP Quadrat Sampling Data

Morpho view

Shows data and emlmetadata

Viewing a Dataset – Kepler1999 Sevilleta LTER NPP Quadrat Sampling Data

Kepler view(using KNB MetacatEcogrid query)

Can view formattedEML metadata

Default configurationshows a port foreach column in thedata table

Viewing a Dataset – Kepler1999 Sevilleta LTER NPP Quadrat Sampling Data

Kepler view(using KNB MetacatEcogrid query)

Data source actor canbe configured to displaythe data by running asimple workflow.

Viewing a Dataset - Kepler

Kepler view(using local EML2 Dataset actor)

Depends on properformat of link fromMetadata (eml) tothe local data file(not yet workingwith local Morphofiles)

Kepler – ReadTable Actor1999 Sevilleta LTER NPP Quadrat Sampling Data

Kepler view(using the R-basedReadTable actor)

Read local file andprovide metadatasuch as separator,file name, headerpresence, etc.



Result of executingworkflow



Text display from theReadTable actorafter adding ‘dim(df)’and ‘summary(df)’ commands

Row and Column count

Data Summary



Result of creating aBoxPlot of data inthe 9th column (the‘height’ column)

Kepler – ReadTable Actor


Dataframe createdby the ReadTableactor can be passedTo another actorfor further processing

Kepler – ReadTable Actor


Result of furtherdataframe processing:

Species vs countBoxPlots

Acknowledgements•This material is based upon work supported by:

•The National Science Foundation under Grant Numbers 9980154, 9904777, 0131178, 9905838, 0129792, and 0225676.

•Collaborators: NCEAS (UC Santa Barbara), University of New Mexico (Long Term Ecological Research Network Office), San Diego Supercomputer Center, University of Kansas (Center for Biodiversity Research), University of Vermont, University of North Carolina, Napier University, Arizona State University, UC Davis

•The National Center for Ecological Analysis and Synthesis, a Center funded by NSF (Grant Number 0072909), the University of California, and the UC Santa Barbara campus.

•The Andrew W. Mellon Foundation.

•Kepler contributors: SEEK, Ptolemy II, SDM/SciDAC, GEON

Using Desktop Data in Kepler

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