REU Program 2010

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

Bio-Grid Poster 2010

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
———-
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)

———-
Week 3
———-
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

———-
Week 4
———-
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
———-
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
———-
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