2003 SUMMER KICKOFF MEETING Mike Langston

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2003 SUMMER KICKOFF MEETING Mike Langstons
Research TeamDepartment of Computer
ScienceUniversity of Tennessee15 May 2003
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Team Members in AttendanceFaisal Abu-Khzam,
Nicole Baldwin, Rebecca Collins, Mike Langston,
Lan Lin, Xinxia Peng, Pushkar Shanbhag, Henry
Suters, Chris SymonsTeam Members AbsentMahesh
Dorai, John Eblen, Jon Scharff
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Major Research Thrusts

• Basic Research
• - Algorithm Design and Analysis
• - Fixed-Parameter Tractability
• - Novel Tools and Techniques
• Applied Research
• - Bioinformatics Toolchains
• - Computational Grids, Parallel Architectures
• and Hardware Acceleration
• - Highly-Scalable Implementations

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Topics of General InterestCrash Course on
FPT19-21 May, Organized by Chris
SymonsBioinformatics Short Course17 June to
11 July, Organized by Jay Snoddy
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Summer Tasks for Faisal Abu-Khzam

• Work with Ottawa on Clustal XP portal
• Upgrade vertex cover codes
• Represent team at FPT workshop in Germany
• Transition to bioinformatics role with Jay Snoddy
• Co-chair HICSS with Mike Langston
• Defend PhD thesis -- good luck Faisal!

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Summer Tasks for Nicole Baldwin

• Work on new clique implementations
• - small cliques via direct algorithms
• - all maximal as well as a maximum clique
• Use genomics and proteomics knowledge
• - focus on problems of impact
• - help others play meaningful roles
• - best examples thus far include
• phylogeny, microarray analysis, motif
• finding and SELDI

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Summer Tasks for Rebecca Collins

• Investigate Dinics algorithm for simple network
  flow (see Hochbaum)
• Incorporate it into our vertex cover
  kernelization suite
• Determine how it stacks up against Bill Cooks
  Linear Programming

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Summer Tasks for Mahesh Dorai

• Get the Pilchard branching code working
• Get the Pilchard branching code working
• Get the Pilchard branching code working
• Get the Pilchard branching code working
• Get the Pilchard branching code working
• Get the Pilchard branching code working
• Get the Pilchard branching code working
• See above

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Summer Tasks for John Eblen

• Investigate new clique implementations
• - medium-sized cliques
• - the independent set problem
• Prepare to enter the PhD program this fall

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Summer Tasks for Lan Lin

• Look at interleaving, especially for vertex cover
• Study exact and approximate algorithms for
  dominating set
• Investigate the nonblocker problem

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Summer Tasks for Xinxia Peng

• Explore opportunities for graph algorithms in the
  context of important problems of bioinformatics
• Possibilities include pattern recognition, data
  mining, and general operations of interest on
  data organized along the lines of GeneKeyDB
• A theme worth pursuing is GRN homology

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Summer Tasks for Jon Scharff

• Work with Mike Langston and Mike Leuze
• on UT-ORNL summer internship
• Put a front end on existing software
• Look at the problem of adding a GUI
• Develop new motif finding algorithms and codes

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Summer Tasks for Pushkar Shanbhag

• Assist Faisal with vertex cover codes
• Maintain and update sequential versions
• Add queue manager to parallel versions
• Defend PILOT -- good luck Pushkar!

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Summer Tasks for Henry Suters

• Implement crown decomposition rules
• Test against kernelization alternatives
• Systematically explore general utility

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Summer Tasks for Chris Symons

• Work on hitting set
• - new kernelization and branching rules
• - sequential and parallel implementations
• Serve as team expert for GRNs
• Participate in clique implementations
• Represent team at FPT workshop in Canada