REU Program 2010 | Bio-Grid

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
——————
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