PROGRESS REVIEW Mike Langston

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PROGRESS REVIEW Mike Langstons Research
TeamDepartment of Computer ScienceUniversity
of Tennessee11 June 2003
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Team Members in AttendanceFaisal Abu-Khzam,
Nicole Baldwin, Rebecca Collins, Mahesh Dorai,
Mike Langston, Lan Lin, Jon Scharff, Pushkar
Shanbhag, Henry Suters Team Members
AbsentJohn Eblen, Xinxia Peng, Chris Symons
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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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Bioinformatics Short Course17 June to 11 July
University of TennesseeOrganized by Jay
SnoddyAttendees Nicole Baldwin, Rebecca
Collins, Jon Scharff, Xinxia Peng, Chris Symons
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Tutorial on Modern Concepts in Biology for
Mathematical and Physical Scientists 23 June to
3 JulyPrinceton UniversityOrganized by
BioMaPS/DIMACS Attendees Faisal Abu-Khzam,
Lan Lin
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Update for Faisal Abu-Khzam

• Working with Ottawa on Clustal XP portal
• Upgrading vertex cover codes
• Representing team at FPT workshop in Germany
• Transitioning to bioinformatics role with Jay
  Snoddy
• Co-chairing HICSS with Mike Langston
• Defending PhD thesis on 19 June ---- good luck
  Faisal!

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Update for Nicole Baldwin

• Working on new clique implementations
• - small cliques via direct algorithms
• - maximal and maximum cliques
• Use genomics and proteomics knowledge
• - applications include phylogeny,
• microarray analysis, motif finding
• and SELDI
• For details, see Nicole's Slides

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Update for Rebecca Collins

• Investigating Dinics algorithm for simple
  network flow (see Hochbaum)
• Incorporating it into our vertex cover
  kernelization suite
• Determining how it stacks up against Bill Cooks
  Linear Programming
• For details, see Rebecca's notes

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Update for Mahesh Dorai

• Some progress, some stumbling blocks
• For details, see Mahesh's report

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Update for John Eblen

• Investigating new clique implementations
• - medium-sized cliques
• - the independent set problem
• Examining the gene trolling problem
• Preparing to enter the PhD program this fall

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Update for Lan Lin

• Looking at interleaving, especially for vertex
  cover
• Studying dominating and dominated set
• Also considering gene trolling
• For details, see Lan's slides

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Update for Xinxia Peng

• Exploring 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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Update for Jon Scharff

• Working with Mike Langston and Mike Leuze on
  UT-ORNL summer internship
• Putting a front end on existing software
• Looking at the problem of adding a GUI
• Developing new motif finding algorithms and codes
• For details, see Jon's notes

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Update for Pushkar Shanbhag

• Assisting Faisal with vertex cover codes
• Maintaining and updating sequential versions
• Adding queue manager to parallel versions
• Defending PILOT -- good luck Pushkar!

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Update for Henry Suters

• Implementing crown decomposition rules
• Testing against kernelization alternatives
• Systematically exploring general utility
• For details, see Henry's write-up

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Update for Chris Symons

• Working on hitting set
• - new kernelization and branching rules
• - sequential and parallel implementations
• Serving as team expert for GRNs
• Participating in clique implementations
• Representing team at FPT workshop in Canada