Difference between revisions of "R Hackathon 1/Teleconferences"

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#** Internal data representation: Paradis, someone who does gene tree/species trees?, Luke Harmon might be good - his work w/ time slices might challenge the model
 
#** Internal data representation: Paradis, someone who does gene tree/species trees?, Luke Harmon might be good - his work w/ time slices might challenge the model
 
#** Documenters/testers: Clements, Sam Price, Amy, others?
 
#** Documenters/testers: Clements, Sam Price, Amy, others?
#* New list
+
#* New list (guesses by BCO preceded by ?)
 
#** Analysis holes: ?Luke Harmon, ?David Ackerly, ?Joe Felsenstein, ?Ted Garland, ?Gene Hunt, ?Aaron King, ?Marguerite Butler, ?Dan Rabosky, ?David Orme
 
#** Analysis holes: ?Luke Harmon, ?David Ackerly, ?Joe Felsenstein, ?Ted Garland, ?Gene Hunt, ?Aaron King, ?Marguerite Butler, ?Dan Rabosky, ?David Orme
 
#** Visualization:  Peter Cowan, Thibout Jombart, Damien de Vienne
 
#** Visualization:  Peter Cowan, Thibout Jombart, Damien de Vienne

Revision as of 17:57, 15 November 2007

1st Teleconference 11/16/2007

Agenda:

  1. Welcome, review of purpose and general objectives (TJV)
  2. Outline of planning schedule ahead (HL)
  3. Priorities and subgroups so far identified (SK, BCO) Note that this is preliminary...
    • Original list
      • Analysis holes: Purvis
      • Visualization: Peter Cowan, need others!
      • Interface w/ C/C++ (large data sets): O'Meara, Meade
      • R to NCL/NEXUS: ?
      • Interface w/ Mesquite: Wayne Maddison,
      • Interfacing w/ CIPRES: Swofford, Holder?
      • Interfacing w/ other C programs: Pagel
      • Internal data representation: Paradis, someone who does gene tree/species trees?, Luke Harmon might be good - his work w/ time slices might challenge the model
      • Documenters/testers: Clements, Sam Price, Amy, others?
    • New list (guesses by BCO preceded by ?)
      • Analysis holes: ?Luke Harmon, ?David Ackerly, ?Joe Felsenstein, ?Ted Garland, ?Gene Hunt, ?Aaron King, ?Marguerite Butler, ?Dan Rabosky, ?David Orme
      • Visualization: Peter Cowan, Thibout Jombart, Damien de Vienne
      • R to/from NCL/NEXUS: ?Todd Vision, ?Hilmar Lapp (maybe part of the data standard group? --Bco 16:55, 15 November 2007 (EST))
      • Interface w/ Mesquite: Wayne Maddison, Peter Midford
      • Interface w/ CIPRES: Mark Holder
      • Interface w/ others: Steve Kembel, ?Brian O'Meara [or to Nexus or internal rep groups]
      • Internal data representation: Emmanuel Paradis, Andrew Hipp, ?Ben Bolker (I think this is a main goal of the workshop we should settle early, so that any new code will not need to be re-coded and all can help craft the standard. A subgroup can then work on converting existing packages or creating a conversion function/package ----Bco 16:39, 15 November 2007 (EST))
      • Clocking trees: Peter Waddell, ?David Swofford, ?Chuck Bell
      • Documenters/testers: Clements, Sam Price, Amy Zanne, Mike Alfaro, Stacey Smith, Brian Sidlauskas


  1. Preparations (HL)
    • Lightning talks - purpose, topics, and presenters (These and bootcamps have been suggested, but have we decided to do them? Regarding lightning talks, my inclination would be for people to communicate that information (say, package overview, relevant package programming info, and package future) using the wiki: both the talks and the wiki are primarily text-based, so the info communicated could be the same, but the wiki 1) creates a permanent record of this information which we can refer to during the hackathon, 2) allows people to develop questions/start discussions over the course of weeks rather than 5 minutes, and 3) doesn't take time during the hackathon. But maybe we have decided to do lightning talks and I blocked it out? -- --Bco 14:53, 15 November 2007 (EST)) I think we should ask the participants tomorrow whether they think lightning talks and bootcamps would be useful to them or not --Sprice 15:19, 15 Nov. 07 EST
    • Bootcamps - purpose, needs, and presenters
    • Reading list - suggestions
    • Give list of functions, ideally with R-format help files, to be posted in the function spreadsheet. (Added by --Bco 14:57, 15 November 2007 (EST))
    • Converting data to internal formats using the datafiles available here, then posting this info to the wiki (Added by --Bco 15:00, 15 November 2007 (EST))
    • Other preparations we or others can facilitate or help with?
  2. Documentation & testing (SP, SK)
    • R vignette writing
      • Who has experience, and would be willing to help train the users? Examples to draw from?
      • Sweave - is it a good idea?
    • Collection of data for testing and validation
  3. Source code repository (or repositories) (HL)
    • Survey of current source code repository and versioning setup for participating packages
    • Assessing need for help with publicly accessible repository
    • Assessing need(s) for NESCent-run repository
    • Code branching needs
    • Other source code-related preparation needs
  4. IT logistics (HL)
    • Computers - will we need loaners?
    • Network access - will anyone need wired network?
    • File share needs
  5. Other homework?
  6. Q & A

1st Teleconference 11/16/2007

Note: I'm duplicating the agenda here so as to not interfere with the concurrent edits. I will later merge them, as needed, or break them out into separate pages. --Hlapp 16:42, 15 November 2007 (EST)

Agenda:

Note for participants: all of the items following the first two are topics posed for discussion, rather than decisions already made. We encourage you to voice any and all feedback, including that pursuing the topic is not desirable (if that is what you feel).

  1. Welcome, review of purpose and general objectives (TJV)
  2. Outline of planning schedule ahead (HL)
  3. Priorities and subgroups so far identified (SK, BCO)
  4. Preparations by participants (HL)
    • Presentations
      • Lightning (< 5-10mins) talks - purpose(s), topics, and presenters
      • Needs for full-length (> 15min) talks?
      • Brainstorming current or future challenges - useful topics, presenters?
    • Bootcamps - purpose, needs, and presenters
    • Compiling package-specific information on the wiki - e.g., overview, relevant programming info, future goals
    • Tabulating metadata across packages (as started by Brian O'Meara) - methods, supported formats and analysis methods, visualization capabilities
    • Describing internal representation of data from test files in each package on the wiki
    • Reading list - suggestions (both for possible gaps and for recommended reading)
    • Other preparations we or others can facilitate or help with?
  5. Documentation & testing (SP, SK)
    • R vignette writing - who has experience, and would be willing to help train the users? Examples to draw from?
    • Collection of data for testing and validation (such as tree files for testing)
  6. Source code repository (or repositories) (HL)
    • Survey of current source code repository and versioning setup for participating packages
    • Assessing need for help with publicly accessible repository
    • Assessing need(s) for NESCent-run repository
    • Code branching needs
    • Other source code-related preparation needs
  7. IT logistics (HL)
    • Computers - will we need loaners?
    • Network access - will anyone need wired network?
    • File share needs
  8. Other homework?
  9. Q & A

Attending:

Action Items: