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darthxaher edited this page May 21, 2012 · 33 revisions

Table of Contents

Timeline

Interim Period before Acceptance: April 7 - April 22

  • Become Familiar with Microbial Ecology Terms
  • Got mothur up and running with Xcode and Gfortran in my Mac OS X setup
  • Follow mothur tutorial from the wiki and get to know the workflow
  • Create a private git branch for mothur in Github
  • Take a closer look at the R implementation
  • Create the initial schematics for the command line programs that would be added to mothur ('train' and 'inquire')
  • Go through text books to make sure my knowledge of the classifier algorithms are clear once again

Week 1: April 23 - April 29 (Community Bonding Period Starts)

  • Register for Machine Learning Course at Coursera
  • Set up Wiki, Isssue Tracker and other stuffs in GitHub page
  • Determine Performance Evaluation Criteria - Issue #1
  • Prepare Datasets for The Random Forest Algorithm - Issue #2
  • Classification/Regression or Both! - Issue #3
  • Make a List of Reusable Classes/Functions from Mothur - Issue #4

Week 2: April 30 - May 6

  • Find Mothur's Common Practices - Issue #5
  • Find a Way to Merge 'train' and 'inquire' Commands Into One Single Command - Issue #6
  • Investigate Mothur's Multithreading/Multiprocessing API - Issue #7
  • Investigate The Possible Places of Parallelization in the Random Forest Classifier - Issue #8
  • Create Code Schematics/Pseudocode for the Random Forest Implementation - Issue #9
  • Investigate the Best Practices for Parameter Tuning/Estimation for Random Forest - Issue #10
Important Note: There has been some major revelations during this week. Following the discussion of Issue #3, we came to realize that the initial problem statement falls under neither Classification nor Regression but what we are seeking is actually a Feature Selection problem. Therefore, there will be a lot of changes in the project plan in the upcoming week as we might need to learn a lot of things and repurpose our timeline accordingly.

Week 3: May 7 - May 13

  • Create a shared folder in file sharing service like DropBox and share it with mentor Kathryn and Sarah, put all the papers/resources together that we come across.
  • Review the Literature of 'Parameter Selection' and Create a wiki Page to Document the Findings - Issue #11
* Track Upstream Mothur Branch and Update Our Master Branch from That - Issue #12

Week 4: May 14 - May 20

Milestone 1 Reached

Week 5: May 21 - May 27 (Start of Official Coding)

Week 6: May 28 - June 3

Week 7: June 4 - June 10

Milestone 2 Reached

Week 8: June 11 - June 17

Week 9: June 18 - June 24

Week 10: June 25 - July 1

Week 11: July 2 - July 8

Mid-term evaluation (from July 9 to July 13)

Status:

Week 12: July 9 - July 15

Week 13: July 16 - July 22

Week 14: July 23 - July 29

Milestone 3 Reached

Week 15: July 30 - August 5

Week 16: August 6 - August 12

August 13: Suggested ‘Pencils Down’

Status:

Week 17: August 13 - August 19

August 20: Firm ‘Pencils Down’

Status:

Final Evaluation

Status:

Further work after Google Summer of Code

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