Merging latest from JimHokanson's repo

GitAndGitHub.md

@@ -0,0 +1,5 @@
+## Git & Github: Tips & Notes ##
+
+This page is meant to be a place to put things related to working with Git and GitHub
+
+https://help.github.com/articles/github-flavored-markdown

Movement/ReadMe.md

@@ -1,3 +1,12 @@
-This folder and subfolders are meant to document aspects of the project which are related to movement.
+This folder and subfolders are meant to document aspects of the project which are related to **worm movement**.
 
-[features](features.md) - A description of features, such as time spent not moving, that can be used to compare the behavior of different worms.
+**[data sources](Data/MRC_HDF5.md)** - A description of movement data that we have access to
+
+**[features](features.md)** - A description of features, such as time spent not moving, that can be used to compare the behavior of different worms.
+
+
+**Other possible topics:**
+- Groups studying movement
+- worm movement data
+- worm movement explained
+- papers on worm movement

Movement/features.md

@@ -1,20 +1,62 @@
 ## List of Movement Features ##
 
 One source for features is listed at:
-http://www.nature.com/nmeth/journal/vaop/ncurrent/extref/nmeth.2560-S3.xlsx
 
-TODO: Eventually it would be nice to have a list and some illustration via data
+http://www.nature.com/nmeth/journal/v10/n9/extref/nmeth.2560-S3.xlsx
 
-A better list is available in the Nature Methods paper.
+A csv copy is availabe [here](features/nmeth.2560-S3.csv)
 
+NOTE: We are currently going through the information from Yemini et al and compiling the lists seen below.
+
+## TODOS ##
+- Eventually it would be nice to have a list and some illustration via data
+- Include other sources ...
+
+## Morphology Features ##
+- Length - (um) skeleton length
+- Width  - (um) average width of subsection in microns
+  - head, midbody, tail
+- Area - (um^2) # of pixels within contour converted to um^2
+- Area/Length
+- Width/Length
+
+## Posture Features ##
+- Bends
+- Bend Count
+- Eccentricity
+- Amplitude
+- Wavelength
+- Track Length
+- Coils
+- Eigen Projections
+- Orientation
+
+## Motion Features ##
+- Velocity
+- Motion States
+- Crawling
+- Foraging
+- Turns
+
+## Path Features ##
+- Range
+- Dwelling
+- Curvature
+
+## OLD LIST ##
+NOTE: Some of these still need to be included above ...
 A brief list (not yet exhaustive):
 - egg laying
 - omega bends
 - pirouettes
 - coiled shapes
 - defecation
-- morphology
-  - length and width at various locations
-  - area within its contour
-  - width/length
-  - area/length
+
+
+## Sources ##
+
+1. Yemini, E., Jucikas, T., Grundy, L. J., Brown, A. E. X. & Schafer, W. R. A database of Caenorhabditis elegans behavioral phenotypes. Nature methods (2013). doi:10.1038/nmeth.2560
+
+In particular see:
+
+http://www.nature.com/nmeth/journal/v10/n9/extref/nmeth.2560-S1.pdf