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Beam Knowledge Rep Sept 04

Difference between version 59 and version 50:

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- *** Participants: Steve Cox, David Chalcraft, Shawn Bowers, Bertram Ludaescher, Mark Schildhauer, Chad Berkley,
- Dan Higgins, Jianting Zhang ([jzhang@lternet.edu|mailto:jzhang@lternet.edu])
+ *** Participants: Steve Cox, David Chalcraft, Shawn Bowers, Bertram Ludaescher, Mark Schildhauer, Chad Berkley, Dan Higgins, Jianting Zhang
Removed line 174
-
At line 207 added 61 lines.
+ ** __Traits of Parts of Plants__: (note the important plant parts given by the trait categories)
+ *** Leaf Traits (Photosynthetic organ traits?)
+ **** Evergreen, deciduous (defined based on leaf longevity?)
+ **** Specific leaf area (Area/mass) or mass per unit area.
+ **** Water content or % dry mass
+ **** Many others ...
+ *** Root Traits
+ *** Stem Traits
+ **** Stem density
+ ***** Mass per unit volume
+ ***** Woody/nonwoody
+ **** Branching pattern
+ *** Seed Traits
+ **** Size
+ ***** Mass
+ **** Shape
+ **** Appendages/Fruits -- closely related to dispersal categories, often highly correlated with seed size.
+ ***** Fly through the air
+ ***** Stick to an animal
+ ***** Eaten and excreted
+ ***** Cached for later consumption
+ ***** Ballistic dispersal
+ ***** Floating
+
+ ** __Traits of Interactions__
+ *** Competitive ability
+ **** Measure how an individual suppresses the growth of a neighbor
+ *** Interaction strength
+ *** Effect on environment (ability to reduce resources) (Tilman)
+
+ ** __Experimental Methods__
+ *** Experiment
+ **** Field Experiment
+ ***** Observational/Empirical Experiment
+ ***** Manipulation
+ *** All field experiments have
+ **** Where (site, plots etc)
+ **** When (sampling regime)
+ **** What (properties of organism/population/community/system)
+ *** (An empirical experiment is a field experiment with no manipulation)
+ *** Manipulations have one or more Treatments
+ *** Treatment has
+ **** What was treated?
+ **** Strength (amount), can be positive (addition) or negative (exclusion)
+ **** Temporal extent
+ *** When defining a treatment, a scientist might describe a substance (nutrient, presence of an organism) as being manipulated, or describe the manipulation of a process.
+ *** Sampling Regime
+ **** Random
+ **** Stratified
+ **** Stratified random
+ **** Nested
+ **** Regular (uniform)
+ **** Haphazard
+ **** Random haphazard
+ *** Note that the choice of a sampling regime (and of plot layout?) constrains the possible statistical analysis techniques that can be applied.
+ *** Traits of Experiments
+ **** Balanced or unbalanced sampling
+ **** Replication
+ *** Traits of Treatment Regime
+ **** Factorial (all possible combinations of treatments) or not
+ **** Random factors (treatments along a natural gradient)
Removed lines 209-210
- * __Notes from workflow breakout__
- ** Workflow based on part of Steve and David's Jornada analysis
At line 212 added 33 lines.
+ * __Notes from workflow breakout__
+ ** Workflow based on part of Steve and David's Jornada analysis
+ ** [http://jornada-www.nmsu.edu/studies/lter/datasets/plants/nppqdbio/data/nppqdbio.htm]
+ ** General steps outlined:
+ *** Data Request
+ *** Quality Control and Assurance (if from different sites)
+ *** Data Integration
+ *** Quality Control and Assurance (of the integration)
+ *** Analysis
+ *** Capture result of analysis …
+ ** Workflow we examined:
+ [http://cvs.ecoinformatics.org/cvs/cvsweb.cgi/~checkout~/seek/projects/kr-sms/docs/beam_kr_sms_meeting_sept_04_workflow.png]
+ ** Useful Actors
+ *** List Summarizer
+ **** A set of values in a data column
+ *** List Comparator
+ **** Given two sets (lists), do they match?
+ **** Which ones in the first list aren’t in the second
+ **** Assign first list values to new values
+ *** Nested Transpose
+ **** (site, taxon, count)
+ **** {(A, x, 3), (A, y, 1), (B, y, 4), (C, z, 2)}
+ **** Transpose to:
+ ***** (site, x, y, z)
+ ***** {(A, 3, 1, 0), (B, 0, 4, 0), (C, 0, 0, 2)}
+ **** Notes about this from Bertram and Shawn after meeting:
+ ***** Given an annotated schema S, denoted S*. And a white-box actor q s.t. q(S*) -> S’. We want to “push through” the annotations to obtain S’*.
+ ***** The “nested” transpose is basically a combination of various lower-level algebraic operators, such as (theoretical) group-by, matrix transpose, projection, etc. So, given q as such a plan of operators, can we reason over the plan (white box-actor) q to obtain S*’? Using symbolic manipulation? Using the chase, e.g., for similar problems in integrity constraints?
+ ** Often-found pattern of computation
+ *** Can Kepler/Ptolemy efficiently and conveniently support the following pattern?
+ *** Given a data set, construct a scatter plot for pairs of variables, allow user to select a subset of the plots -or- pairs of variables of interest, return data subsets based on chosen pairs (with no extraneous variables)
+ *** Similarly, given data sets, an actor computes a set of regressions, the user is shown the results, the user selects the regressions of interest, and the workflow then proceeds using only those selected regressions
+ *** These "patterns" can be supported now (with lots of plumbing) using the browser actor. Can we also add functionality to better support/model these patterns?

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