Weekly Report for the DFG project: Algorithm Engineering for High Throughput Sequencing Data

Jul 2011

• 01. July 2011: Welcome AG ABI

week 04. - 0.8

• We: M.Sc. talk
• organizational stuff
• familiarization with SeqAn Project
  • overview of the project wiki
  • overview of important websites
  • novel SeqAn structure
  • code guidelines

week 11. - 15.

• notebook defect, rent AG ABI MacBook Air
• familiarization with Mac OS
• code refactoring: StringSet for journaled sequences
• Fr: graduation ceremony

week 18. - 22.

• create project plan
  • WBS and milestones
• literature research
  • Suffix Array construction algorithm
  • Kasai algorithm
  • Enhanced Suffix Arrays
• code Refactoring
• wiki maintanance

week 25. - 29.

• create project plan
  • WBS and milestones
• literature research
  • Suffix Array construction algorithm
  • creation of childtab
  • find suffixes affected by a modification
• Th: iMac has been delivered
  • went home earlier due to illness in family
• Fr: set up iMac

Aug 2011

week 01.08. - 05.08

• sign commencement of work for: David, Manuel, Chris, Björn, Jochen, Sabrina
• create project plan
  • WBS and milestones
• literature research
  • Suffix Array construction algorithm
  • dynamic update of SA: Salinger et al.
  • find suffixes affected by a modification
• code Refactoring

week 08.08. - 12.08.

• write eclipse tutorial
• create project plan
  • WBS and milestones
• literature research
  • dynamic update of SA: Salinger et al.
• develop concept of delta indices
• code refactoring Journal-Set

week 15.08. - 19.08.

• create project plan
  • WBS and milestones
• literature research
  • dynamic update of SA: Salinger et al.
• concept of delta indicies
• code refactoring Journal-Set

week 22.08. - 26.08.

• code refactoring Journal-Set
• tutorial to set up eclipse for seqan

week 29.08. - 02.09.

• code refactoring Journal-Set

Sep 2011

week 05.09. - 09.09.4

• code refactoring Journal-Set
• Knime: test plugin
• Workshop
  • Checking tutorials