Project Summary

Computing for Structure is an NSF Funded Research Experience for Undergraduates, created and directed by the University of Miami Department of Computer Science and Center for Computational Science. The program ran from May 21 to July 27, 2018 with the following REU student researchers:

• Tate Bestwick, University of Kansas
• Michael Castellanos, University of Miami
• Nathan C. Fox, University of Miami
• Colin Jiang, Emory University
• Nancy Newlin, University of Florida
• Serena Nicholl, University of Minnesota Twin Cities
• Morgan Rosser, St. Lawrence University
• Jack Weissburg, University of Wisconsin-Madison
• Blake Williams, University of Vermont
• Joshua Zahner, University of Miami

The REU experience concluded with a poster presentation and closing ceremonies, on Friday, July 27, 2018. This presentation was held in the atrium of the Cox Science center, as was joint with the University of Miami Chemistry REU, PI'ed by Prof. Knecht as well as the Summer Undergraduate Research Fellowship Program (SURF).

See the ★ poster day brochure for all presentations. Below are the presentations funded by REU-CFS 2018.

• ★ Congratulations to Morgan Rosser for her presentation of her poster at the Research Experiences for Undergraduates Symposium, Alexandria, VA. October 28–29, 2018.

• The Effect of the StartReact Response on Gross Hand Function after Human Spinal Cord Injury, Morgan Rosser, Vance Lemmon, Monica A. Perez. (Selected presentation)
• Angular Orientation During Social Contact I, Blake Williams, Jack Weissburg, Laura Vitale, Daniel Messinger. (Selected presentation)
• Angular Orientation During Social Contact II, Jack Weissburg, Blake Williams, Laura Vitale, Daniel Messinger. (Selected presentation)
• Audio and Visual Synchronization for Data Visualization, Michael Castellanos, Jack Weissburg, Blake Williams, Laura Vitale, Michael Scordilis, Daniel Messinger.
• Reconstruction of Submesoscale Velocity Fields, Joshua Zahner, Rafael Goncalves, Mohamed Iskandarani.
• Exploring Image Recognition with Deep Neural Networks and the Effects of Normalization, Colin Jiang, Luis G. Sanchez Giraldo, Odelia Schwartz.
• COMB-PSO: Features Selection of Kinases for Prediction of Neurite Outgrowth, Nathan C. Fox, Hassen Dhrif, Hassan Al-Ali, Stefan Wuchty, Joh L. Bixby, Vance P. Lemmon.
• Robust GPU Based 3D Visualization of Algebraic Surfaces, Nancy Newlin, Joseph Masterjohn, Victor Milenkovic.
• Aiding the Discovery of Susceptibility Variants for Complex Phenotypes, Serena Nicholl, Timothy Mitchell, Athena Hadjixenofontos.
• Applying Machine Learning to Deep Eutectic Solvents, Tate Bestwick, Brian Doherty, Kun Yue, Orlando Acevedo.

The P.I. for the REU is Prof. Rosenberg of the Computer Science Department, but the real work went to the many mentors, listed as co-authors of the student presentations. These mentors were drawn from across the university, and volunteered to mentor the participants.

Please see last year's web page for a summary of prior REU's under the same grant.

Support for the program REU Site: Scientific Computing for Structure in Big or Complex Datasets is by the NSF grant CNS-1659144, program solicitation NSF 13-542, Research Experiences for Undergraduates (REU).

General Information

• Please check in at Mahoney-Pearson Residential College. Your rooms have been assigned.
• Our slack channel
• The bootcamp plan.
• Canecard form
• Wellness center and parking form
• Recruitment page 2018

Boot Camp:

The Boot Camp has two parts, where the first is a comprehensive introduction to data-python and unix scripting. That runs Monday to Thursday, May 21–24.

Following are topics in computational science including grid/cluster computing, neural nets, and GPU's, which are given on Friday, Tuesday and Wednesday, May 25 to 30th, excluding Memorial Day on Monday.

The morning sessions are 9:30am – 12:00pm and the afternoon sessions are 1:30pm – 4:00pm. Both sessions are at the Computer Science computer lab, on the 3ird floor of the Ungar Building.

• Atina's github
• Burt's github

Part I:

• Monday:
  AM: CLI Intro (Athina/Dawson);
  PM: Python programming (svn://simple/*.py) (Burt)
• Tuesday:
  AM: Python programming (svn://simple/*.py) (Burt);
  PM: Scripting and Textfile manipulation (Athina/Daswon)
• Wednesday:
  AM: Numpy and fast arrays (Burt);
  PM: Python for data analysis (Athina)
• Thursday:
  Project (cohort)

• Friday: Pegasus (Athina)
• Monday: Memorial Day (day off)
• Tuesday: Deep learning (Luis)
• Wednesday:
  AM: CUDA with the K80 (Burt);
  PM: Mentor meetup

Professional Development Workshop

In coordination with the REU at the Chem Dept, we had a series of weekly workshops to help new scientist develop in their field and understand their future options.

Date and time: 3pm–5pm Fridays, either in the Cox science building, next to Ungar, or downtown on the Medical Campus, at the Gautier building. (excel format: spreadsheet)

But note underlined exceptions! E.g. time for June 8.

Friday, 1 June

Life as a Graduate Student, Panel discussion. Cox 166.

Friday, 8 June

Reading and Critiquing Scientific Literature, OGPS Pane. Gautier 118. 4pm–5:30pm.

Friday, 15 June

Graduate School Opportunities, Dr. Captain, Dr. Salas, Knecht and Deo. Gautier 118.

Friday, 22 June

Diversity and Inclusion in the Sciences, Dr. Symes, Gautier 118.

Friday, 29 June

Destination - Passion. My road to a Career in Academia. Dr Sophia George, Gautier 118.

Friday, 6 July

Research Outside of Academia: Industry, Dr. Sur, Gautier 118.

Tuesday, 10 July

Tips for an Effective Research Presentation, Dr. Emre Dikici. Gautier 118.

Friday, 13 July

Transitioning to an Independent Academic Career, Dr. Rai. Cox 166.

Friday, 20 July

Research Outside of Academia: Government, Dr. Li, Gautier 118.

Friday, 27 July

Research Symposium and Luncheon. 9:30am–3:00pm Cox Atrium.

Nature of Science Lecture Series / Research Seminars

A series of Wednesdays afternoon lectures with a historical or conceptual viewpoint of the development or practice of science. Some lectures in the series were devoted to an overview of specific research topics, relevant to the REU theme, by active researchers in those fields. On Thursdays at 3:30, in Ungar 300.

Thursday, 28 June

Prof. Ogihara, Computer Science. Humanities and Computation

Thursday, 5 July

Prof. Acevedo, Chemistry. Chemistry and Computation

Thursday, 12 July

Prof. Rosenberg, Computer Science. Truth, Knowledge, and Computation

Thursday, 19 July

Prof. Kirtman, Marine Sciences (RSMA). Climate and Computation

Mentorships

Computational Chemistry

Prof Acevado

Cryptography

Prof. Rosenberg

Neural Networks

Prof Schwartz

Luis Gonzales

Neuroscience

Prof Uddin

Prof Lemmon

Ocean Science

Prof Iskandarani

Protein Networks

Prof Wuchty

Psychology

Prof Messinger

Laura Vitale

Visualization

Prof Milenkovic

Genomics

Dr. Hadjixenofontos

With help and guidance from:

High Performance Computing

Joel Zysman

Kalan Dawson

Administration

Julie Garcia, Project Administration and Manager CSC
Prof. Sutcliffe, Chair Computer Science

Sponsored by the National Science Foundation

The NSF has set up the REU program in order to involve students in meaningful ways in ongoing research programs so as to attract talented students into careers in science and engineering.

The full title of this program is REU Site: Scientific Computing for Structure in Big or Complex Datasets and it is NSF grant CNS-1659144. The REU program is described in program solicitation NSF 13-542, Research Experiences for Undergraduates (REU).