Summer Institute Schedule and Presentation Materials, 2013

(Activity type): Pres=Presentation; Actv=Activity; Disc=Discussion; Tech=Technical Session; Tutl=Tutorial; GP=Group Project; Lect=Lecture

[Instructor]:  JA= Juliann Aukema; BB=Ben Bolker; FD=Frank Davis; SH=Stephanie Hampton; MJ=Matt Jones; JR=Jim Regetz; MS=Mark Schildhauer

 

Wednesday, 19 June

Collaboration and Communication

08:30 - 09:00 (Pres) NCEAS welcome, logistics, etc
09:00 - 09:30 (Pres)About the course, context, NCEAS Institute plans, "around the room" 30 sec introductions  [SH] 
09:30 - 10:00 (Actv) Survey + Break
10:00 - 10:45 (Actv) "Thinking preferences" activity
10:45 - 11:30 (Pres) Social aspects of collaboration - characteristics of high-performing groups, policy documents (authorship, collaborators, data), ground rules [SH]
11:30 - 12:00 (Actv) Facilitating group discussions
12:15 - 01:30 * Lunch * John Parker seminar: Sociology of scientific collaboration
01:30 - 03:15 Group projects launch; groups meet to start to refine projects, etc [SH]
03:15 - 03:45 (Pres) Introduction to the message box  [SH, Ben Halpern] 
03:45 - 04:45 (Activ) Small group work on message box
04:45 - 05:15 Small group presentations of message box - 3 min presentation, 1 slide
05:15 - 05:30 Overflow


Thursday, 20 June

Computing, Unix, and Virtual Collaboration

08:30 - 08:45 (Disc) Feedback/thoughts on previous day
08:45 - 09:15 (Tech)  Computers, servers, and networks [MJ]
09:15 - 10:15 (Tutl) Intro to the *nix command line [JR] 
10:15 - 10:30 * Break *
10:30 - 12:00 (Tutl) Regular expressions , Text editors [JR] 
12:00 - 01:00 * Lunch *
01:00 - 02:00 (Pres/Disc) Virtual collaboration modalities  [JR, MJ]
02:00 - 20:30 (Pres/Tutl) Intro to Redmine (with EVOS case study)  [MJ]
02:30 - 05:00 GP: get up and running in Redmine, start entering content
05:00 - 05:15 "The view from the balcony"  [SH, JA]


Friday, 21 June

Data Management, Metadata, and Data Repositories

Readings: Borer et al. (2009);  Reichman et al. (2011)Wolkovich et al. (2012)

08:15 - 08:30 (Disc) Feedback/thoughts on previous day
08:30 - 09:15 (Lect) Data Management
09:15 - 10:15 (Actv) Scientific data repositories: Data discovery and contribution
10:15 - 10:45 * Morpho Install and Break *
10:45 - 11:45 (Tutl) Documenting and Sharing data with Morpho
12:00 - 01:00 Lunch Social media with Jai and Jarrett in NCEAS lounge: Bik and Goldstein (2013)
01:00 - 02:00 GP: Data sharing policies
02:00 - 02:45 (Disc) Report and discussion: Data sharing policies
02:45 - 03:00 * Break *
03:00 - 05:00 GP: Locating, organizing, documenting project data
05:00 - 05:15 Open

 

Monday, 24 June

Open Science, R, Version Control

08:15 - 08:30 (Disc) Feedback/thoughts on previous day
08:30 - 09:00 (Lect) Open source software and open science
09:00 - 10:00 (Tutl) Working with R  / Finding help on R [JR] 
10:00 - 10:15 * Break *
10:15 - 11:45 (Lect)  rOpenSci  [Karthik Ram]
12:00 - 01:00 * Lunch *
01:00 - 02:00 (Tutl) Version control and Git in particular
02:00 - 05:00 (Actv) GP: start to populate Git repo
05:00 - 05:15 "The view from the balcony" - [Brittany, Alison]

 

Tuesday, 25 June

R, Wrangling Messy Data from Different Formats

08:15 - 08:30 (Disc) Feedback/thoughts on previous day
08:30 - 09:30 (Lect)  Best practices for managing digital (data) resources [MS] (materials coming soon)
09:30 - 10:00 (Actv)  DataONE R client  (examples) [MJ]
10:00 - 10:15 * Break *
10:15 - 12:00 (Actv) Wrangling heterogeneous data formats, structures [JR]
12:00 - 01:00 * Lunch *
01:00 - 02:00 (Actv) Data summarization, visualization, QA/QC, cleaning
02:00 - 02:45 GP updates
02:45 - 04:15 GP: data, data, data
04:15 - 05:00 Messy text, character encoding, and other thorny topics
05:00 - 05:15 "The view from the balcony" - [Holly, Steve]

 

Wednesday, 26 June

Tabular Data

08:15 - 08:30 (Disc) Feedback/thoughts on previous day
08:30 0- 9:00 (Lect) Data models, esp the relational model [MS] (materials coming soon)
09:00 - 10:15 (Tutl) SQL, PostgreSQL (via psql) [MJ]
10:15 - 10:30 * Break *
10:30 - 11:00 (Tutl) Interfacing R and PostgreSQL [JR]
11:00 - 12:00 (Tutl) Emulating SQL with core R functions (filt, join, agg), tables in R (sqldf, reshape, data.table) [JR]
12:00 - 01:00 * Lunch *
01:00 - 02:00 Overflow or participants' choice?
02:00 - 05:00 GP
05:00 - 05:15 "The view from the balcony" - [Cristian, Jill]

 

Thursday, 27 June

Geospatial Data and Tools Galore

08:30 0- 8:45 (Disc) Feedback/thoughts on previous day
08:45 - 09:15 (Lect)  Geospatial data concepts (data representation, CRSes, etc) [JR]
09:15 -0 9:45 GDAL utilities: inspecting, converting, manipulating data [JR]
09:45 - 10:30 JTS/GEOS, PostGIS: SQL + spatial; interfacing from QGIS [JR]
10:30 - 10:45 * Break *
10:45 - 12:00 R Spatial (sp, rgdal, rgeos, maptools, raster, ...?) [JR]
12:00 - 01:00 * Lunch * and Mark Schildhauer: Aristotle to OWL in the Lounge
01:00 - 02:00 (Overflow from morning)
02:00 - 04:30 GP - be sure policy documents are complete for your project and uploaded to Issues
04:30 - 05:15 (demo)  GRASS GIS [JR] 
05:15 - 05:30 "The view from the balcony" - [Shalene, Michelle M]

 

Friday, 28 June

Workflows

08:15 - 08:30 (Disc) Feedback/thoughts on previous day
08:30 - 09:30 (Lect) Workflow concepts, benefits
09:30 - 10:15 (Actv) Diagram workflow(s) from your GPs
10:15 - 10:30 * Break *
10:30 - 11:30 (Lect) Kepler, provenance, distributed execution, and other SWF apps
11:00 - 12:00 (Disc) Scripting versus dedicated workflow apps
12:00 - 01:00 * Lunch *
01:00 - 04:30 GP: (possibly architect and flesh out project workflows)
04:30 - 05:00 GP updates
05:00 - 05:15 "The view from the balcony" - [Jennifer, Narcisa]

 

Monday, 1 July

Statistical Paradigms and Approaches

Homework for Monday: read Breiman 2001

until 12:30 GP + lunch
12:30 - 01:00 Mid-course survey
01:00 - 02:00 (Lect)  Goals of analysis; statistical/analytical cultures; model assessment [BB]
02:00 - 03:00 Discussion and activities: choosing analytical approaches
03:00 - 05:00 Visualization (+ lab?)
05:00 - 05:15 "The view from the balcony" - [Isabella, Michelle L]

 

Tuesday, 2 July

Algorithmic Approaches

08:15 -0 8:30 (Disc) Feedback/thoughts on previous day

08:30 - 09:30

(Lect) Intro to algorithmic approaches: CART [Sapna Sharma] 
09:30 - 09:45 * Break *
09:45 - 12:00 (Actv) Lab on CART etc.; more on visualization; more on model diagnostics
12:00 - 01:00 * Lunch *
01:00 - 04:00 (Actv) GP Revisit message boxes - are there issues that haven't been addressed that could be better articulated?
04:00 - 05:00 (Lect)  The linear model and extensions [BB]
05:00 - 05:15 "The view from the balcony" - [Dave, Erika]

Parking lot: (Lect) Frameworks for model comparison and uncertainty assessment (classical, likelihood, Bayes, information-theoretic ...)  [BB]


Wednesday, 3 July

Multi-level modeling, systematic reviews

08:15 - 08:30 (Disc) Feedback/thoughts on previous day
08:30 - 09:30 (Lect) Mixed models
09:30 - 09:45 * Break *
09:45 - 12:00 Lab (mixed models)
12:00 - 01:00 * Lunch *
01:00 - 03:45 (Actv) GP
03:45 - 04:15 GP updates
04:15 - 05:00 (Lect) Systematic reviews [Chris Lortie] 
05:00 - 05:15 "The view from the balcony" - [Sarah, Sigrid]

 

Friday, 5 July

Space

08:15 - 08:30 (Disc) Feedback/thoughts on previous day
08:30 - 10:00 (Lect) Spatial analysis
10:00 - 10:15 * Break *
10:15 - 12:00 Lab: spatial analysis
12:00 - 01:00 * Lunch *
01:00 - 04:00 (Actv) GP
04:00 - 05:00 Parameterizing models, model reduction
05:00 - 05:15 "The view from the balcony" - [Antonin, Shirley]

 

Monday, 8 July

Group projects! Publications and such

08:15 - 08:30 (Disc) Feedback/thoughts on previous day
08:30 - 12:00 GP
12:00 - 01:00 * Lunch *
01:00 - 04:15 GP
04:15 - 05:00 Preparing the message box [Nancy Baron]
05:00 - 05:15 "The view from the balcony" - [Jon, Kristen]

 

Tuesday, 9 July

Communicating results

08:15 - 08:30 (Disc) Feedback/thoughts on previous day
08:30 - 09:15 (GP) Prep for presentations
09:15 - 09:30 Break
09:30 - 11:00 Message box Final presentation and discussion [Nancy Baron] (Two minutes to impress)
11:00 - 12:00 GP
12:00 - 01:15 * Lunch * with NCEAS residents - "speed dating" science conversations
01:15 - 02:15 Wrangling text with regular expressions
02:15 - 05:00 GP
05:00 - 05:15 "The view from the balcony" - [Iain, Sharon]

 

Wednesday, 10 July

Wrapping up

08:15 - 08:30 (Disc) Feedback/thoughts on previous day
08:30 - 12:00 GP - submit project Summary and plan for completion to NCEAS
12:00 - 01:00 * Lunch *
01:00 - 02:00 The magical Vim text editor
02:00 - 02:50 (GP) individual feedback on GP summaries, refinements as necessary, wrap up
02:50 - 03:20 Plenary wrap-up session, GP message boxes before/after
03:30  Final survey (submit by 3:30pm)
03:20 - 05:15 reflections and loose ends
05:15 Adjourn!

 

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