2010 Bio-Grid REU Participants
Baur, Brittany
Affiliation: Manhattanville College
Major: Biology/Mathematics
Brown, Colin
Affiliation: Manchester Community College
Major: Computer Science
Chowdhury, Rifat
Affiliation: University of Connecticut
Major: Computer Science and Engineering
Kulzer, Lindsay (*)
Affiliation: Siena College
Major: Computer Science/Mathematics
Luciano, Claire
Affiliation: University of California – San Diego
Major: Computer Science/Bioinformatics
Mochan, Ericka
Affiliation: Western New England College
Major: Biomedical Engineering
Ngu, Huy
Affiliation: Tufts University
Major: Computer Science
Nkounkou, Brittany
Affiliation: University of Connecticut
Major: Computer Science and Engineering
Su, Kevin
Affiliation: University of Pennsylvania
Major: Computer Science
Wong, Elisabeth
Affiliation: Bowdoin College
Major: Biology/Mathematics
2010 Program Info
** 5/31 (Mon, 7:00AM-11:00PM, Rome Commons) Check-In
** 7/24 (Sat, 8:00AM-12:00PM, Rome Commons) Check-Out
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Week 1
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Orientation
6/1 (Tue, 10:00AM, ITE 360)
Orientation and Program Overview
Research Seminars
6/2 (Wed, 10:00AM-12:00PM, ITE 360)
Applying Molecular Dynamics Simulation to Detection of Protein Misfolding (Smith)
6/3 (Thr, 10:00AM-12:00PM, ITE 360)
Application of Multi-Class Sequential Linear Discriminant Analysis to Biological Data (Lee)
6/4 (Fri, 10:00Am-12:00PM, ITE 360)
Intractability and Approximation in Computational Biology
Responsible Conduct of Research (RCR) Seminar Series (All REU Sites)
6/1 (Tue, BPB 131)
The Basis of Research Ethics (Aggison, 2:30PM-3:15PM)
Scientific Record Keeping (Collisson, 3:15PM-4:00PM)
6/2 (Wed, BPB 131)
Ethics in the Use of Humans in Research (Andrews, 5:30PM-6:15PM)
Ethics in the Use of Animals in Research (Washington, 6:15PM-7:00PM)
6/3 (Thr, BPB 131)
Conflict of Interest (Aggison, 5:30PM-6:15PM)
Ethics in Mentoring and Training Relationship (James, 6:15PM-7:00PM)
6/4 (Fri, BPB 131)
Misconduct of Research (Taigen, 5:30PM-6:15PM)
Ethics in Publications and Authorship (Taigen, 6:15PM-7:00PM)
6/5 (Sat, BPB 131)
RCR Symposium: Case Studies (All Students, 9:00AM-12:00PM)
Reception (12:00PM)
Social Activities (All REU Sites)
Ice-Cream Social
6/1 (Tue, 4:30PM, Swan Lake)
Cook-Out
6/5 (Sat, 5:00PM, Prof. Amy Howell’s house)
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Week 2
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Discussion Sessions
6/7 (Mon, 10:00AM) LK, HN
6/8 (Tue, 10:00AM) EM, KS
6/8 (Tue, 1:00PM) BN, CB
6/9 (Wed, 10:00AM) BB, EW
6/9 (Wed, 1:00PM) RC
(CL to be scheduled)
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Week 3
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6/16 (Wed, 11:00AM, Physics Building Room P-121)
Special Computational Science Seminar
Title: Cyber Infrastructure — From the Campus to the World
Speaker: Dr. Dan Fraser, Production Coordinator, Open Science Grid
6/17 (Thr, 2:00PM, ITE 336)
Special Computational Science Seminar
Title: Scientific Computing at Extreme Scale
Speaker: Dr. Rob Ross, Argonne National Lab
Discussion Sessions
6/14 (Mon, 10:00AM) (LK,) HN
6/15 (Tue, 10:00AM) EM, KS
6/16 (Wed, 10:00AM) BB, EW
6/16 (Wed, 1:00PM) RC
6/17 (Thr, 10:00AM) CL
6/17 (Thr, 1:00PM) BN, CB
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Week 4
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6/23 (Wed, 12:00-1:00PM, ITE360)
Informational Session on Proposal Preparation
Individual Group Discussion Sessions
6/21-6/24
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Week 5
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6/30 (Wed, 1:00PM-3:00PM, ITE 360)
Bio-Grid Mini-Symposium: Proposal Presentations (All Bio-Grid Students)
1:00-1:20 Speakers: Baur, Brittany and Wong, Elisabeth
On Tools for Network Motif Finding
1:20-1:40 Speakers: Brown, Colin and Nkounkou, Brittany
Application of Multi-Class Sequential Linear Discriminant Analysis to Biological Data
1:40-1:55 Speaker: Chowdhury, Rifat
Multi-core Programming with OpenMP for Matrix-Based Computations
1:55-2:10 Speaker: Luciano, Claire
Network Motifs and Transcriptional Regulation in Model Organisms
2:10-2:30 Speakers: Mochan, Ericka and Su, Kevin
Modeling Transcription Factor Binding Sites with Supervised Learning
2:30-2:45 Speaker: Ngu, Huy
Performance Analysis for Molecular Dynamics Simulation on an SGI Altix Supercomputer
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Week 6
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7/8 (Thr, 10:00AM-11:00AM)
Informational Session on Technical Report Writing
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Weeks 7 & 8
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7/19 (Mon, 9:30AM-10:30AM, BPB 131)
Diversity Forum: Challenges and Choices in Higher Education
Hosted by Chemistry, CSE, NEA and PNB
7/23 (Fri, 1:00PM-4:40PM, ITE 360)
Bio-Grid REU Student Symposium
1:00-1:10 Opening Remarks
1:10-1:40 Speaker: Ngu, Huy
Performance Analysis for Molecular Dynamics Simulation on an SGI Altix Supercomputer
1:40-2:10 Speakers: Mochan, Ericka and Su, Kevin
Modeling Transcription Factor Binding Sites with Supervised Learning
2:10-2:40 Speaker: Luciano, Claire
Network Motifs and Transcriptional Regulation in Model Organisms
2:40-3:00 Break
3:00-3:30 Speaker: Chowdhury, Rifat
Multi-core Programming with OpenMP for Matrix-Based Computations
3:30-4:00 Speakers: Brown, Colin and Nkounkou, Brittany
Application of Multi-Class Sequential Linear Discriminant Analysis to Biological Data
4:00-4:30 Speakers: Baur, Brittany and Wong, Elisabeth
On Tools for Network Motif Finding
4:30-4:40 Closing Remarks
2010 Reports
Wong, Elisabeth and Baur, Brittany
On Tools for Network Motif Finding
Nkounkou, Brittany and Brown, Colin
Application of Multi-Class Sequential Linear Discriminant Analysis to Biological Data
Su, Kevin and Mochan, Ericka
Modeling Transcriptional Factor Binding Sites with Supervised Learning
Ngu, Huy
Performance Analysis for Molecular Dynamics Simulation on an SGI Altix Supercomputer
Chowdhury, Rifat
Multi-Core Programming with OpenMP for Matrix-Based Computations
Luciano, Claire
Network Motifs and Transcriptional Regulation in Model Organisms