San Diego Supercomputer Center High
School Volunteer Summer 2012 Internship Opportunities
For the third year, SDSC launches an exciting volunteer
internship program for high school students entitled Research Experience
for High School Students (REHS). As part of this program, students will
be paired with an SDSC mentor and will work as part of a research team
dedicated to a particular area of computational research.
Please
review the research opportunities listed below and submit a
separate application for each opportunity that may interest you.
Students may apply for up to three opportunities. All applications must
be submitted via US Mail no later than March 30,
2012.
San Diego Supercomputer Center, UC San Diego June 25- August 10, 2012
(seven weeks). Internship hours will be coordinated with your mentor and can
range from 15 to 25 hours per week.
Please note that
students applying for this opportunity must be 16 years of age on or before June
24, 2012 per UCSD volunteer and employee
requirements.
High School Volunteer Summer
Research Opportunities
Project Title: Exploring the Uncanny Valley
Project Overview Artificial agents such as humanoid robots and animated 3D characters are actively being developed for use in various domains such as entertainment, retail, education, and healthcare. But how should artificial agents be designed? It may seem like a good idea to make artificial agents look as human-like as possible, especially if they will be used in social settings. However, we soon encounter a phenomenon called the “uncanny valley”: As an agent’s appearance is made more human-like, people’s reactions to it becomes more positive and empathetic, until a point at which the increasing human-likeness leads to the agent being considered repulsive, disturbing, or “zombie-like”. For example, many viewers found the film Polar Express creepy, whereas Avatar received more positive evaluations. Despite significant anecdotal evidence, there is little scientific data to characterize the uncanny valley. In our lab we are exploring the uncanny valley using various different methods such as perceptual experiments, physiological recording (GSR, heart rate), and neuroimaging.
Activities: We have internships available for a small group of motivated and technically skilled high school students. Internship tasks include:
- Finding, digitizing and editing images and movie clips of normal and “uncanny” characters.
- Creating animations of normal and “uncanny” characters.
- Setting up and analyzing online questionnaires and experiments (e.g., present pictures or movies on the web and collect responses).
- Recording and analyzing heart rate and galvanic skin response.
Internship Hours Per Week:
15-20 hours Project Mentor: Ayse P. Saygin, Department of Cognitive Science, Neuroscience Program, Calit2, UCSD
Download Detailed Project
Overview
Project Title: Defining Privacy Consent Directives for Reusing Data from iDash Research Repositories
Project Overview The purpose of IDASH is to facilitate the integration of data for analysis, anonymization, and sharing. With this project we aim to contribute to IDASH’s aim by developing and evaluating a taxonomy of privacy consent directives that will allow facilitating the reuse and sharing of existing research data (medical records and biosamples) obtained through patient’s informed consent.
There are no pre-requisites for this research project. During this project the participating student will be trained and supervised to develop a myriad of research skills.
Internship Hours Per
Week: Flexible up to 20 hours Project Mentor: Drs. Adela Grando and Aziz Boxwala, UCSD Download
Detailed Project Overview
Project Title: Developing a Biological Web Search Engine
Project Overview With the growth of biological data in volume and heterogeneity, web search engines become key tools for researchers. However, general-purpose search engines, like Google or Yahoo, are not specialized for the search of biological data. We have recently developed IntegromeDB (www.integromedb.org), a prototype for a biological web search engine based on the Semantic Web technologies. Currently, it enables to retrieve gene- and protein-centered knowledge; specifically, data on gene regulation, gene expression, protein-protein interactions, pathways, metagenomics, mutations, diseases, and other gene- and protein-related data that are automatically retrieved from publicly available databases and web pages using biological ontologies. The engine queries the in-house database that integrates thousands of data sources. The goal of this project is to further develop this search engine, making it faster, error-free, and also disease and drug-centered.
Internship Hours Per Week: 20-25 hours Project Mentor: Dr. Michael Baitaluk, Senior Scientist at SDSC, NIH PI
Download Detailed Project Overview
Project Title: Predictive Analytics Center of Excellence Research Assistant
Project Overview Uniquely positioned as an honest broker among industry, academic and
governmental organizations, Predictive Analytics Center of Excellence
(PACE) educates, promotes, develops standards and provides research and
services in the field of Predictive Analytics, Data Mining and Machine
Learning. PACE combines the next-generation supercomputing power of
Gordon‹the world¹s fastest supercomputer using flash memory‹with large
data repositories to create answers that will bridge the gap
and empower industry, education, and government. Since the Center is in its inception the tasks will include a wide range of activities from software installation and parallelization to administrative, educational and organizational work.
Internship Hours Per
Week: 15-20 hours Project Mentor: Dr. Natasha Balac, San Diego
Supercomputer Center, UCSD Download Detailed
Project Overview
Project Title: SCAlable National
Network for Effectiveness Research (SCANNER)
Project Overview The SCANNER project will develop a distributed network infrastructure for comparative effectiveness research that provides participating sites the means for flexibility in data sharing. This flexibility will be implemented by allowing codification of data sharing policies, where each institution will specify its own policies. SCANNER will connect diverse healthcare delivery settings with secure infrastructure that utilizes data collected at the point of care. Policies for data sharing will range from sharing of de-identified records to sharing aggregate results. The network will have a main node that manages policies, distributes queries, aggregates results, and maintains trust and security (authentication, authorization, auditing, etc). Each site will maintain a node that contains data from that site. The network will support retrospective analyses, prospective observational studies, clinical trials, and feedback to point-of-care users. Near real-time collection, analysis, and dissemination of results and feedback to the clinician will be enabled by an infrastructure that allows data to be exchanged according to policies specified by individuals and institutions.
Internship Hours Per Week:
20 hours Project Mentor: Dr. Michele Day, San Diego Supercomputer Center,
UCSD Download Detailed Project
Overview
Project Title: Summer Computing and Science Academy Assistant
Project Overview Do you love working with students in a fun and informal setting? Do you like learning about new software programs? Then this summer opportunity is for you! Help the San Diego Supercomputer Center (SDSC) with its summer workshops and learn new skills in the process. We are offering a variety of workshops from geoscience to digital illustration and art to computer security, programming and much more. We need you to be a course assistant, helping the instructor by helping the students with questions and project help. Students will work either at SDSC or at another location on the UCSD campus. Learn new skills in leadership, while learning new programming languages and scientific methods.
Internship Hours Per
Week: 10-20 hours Project Mentor: Ange Mason, San Diego Supercomputer
Center, UCSD Download Detailed Project
Overview
Project Title: Using data mining to uncover user behavior patterns
Project Overview The effect of the scheduler on the users is ignored in virtually all performance evaluations. Very little research has been done to understand user behavior since it involves live experiments and understanding psychology. It has been shown that it is possible to uncover the effect from the traces of the system. However job size, and batch jobs were not taken into consideration. We attempt to use a fresh angle in investigating the user behavior by analyzing the traces using data mining tools. Work involved for the student may include data gathering, learning to use Weka- a data mining tool, and help with designing a poster. The student participant will also be mentioned in any publication based on the outcome of the research. We encourage students working in the field of computer science or statistics to apply to work in this research.
Internship Hours Per Week:
15-20 hours Project Mentor: Subha Sivagnanam, Kenneth Yoshimot and Dr. Natasha Balac, UCSD School of Medicine, San Diego Supercomputer Center
Download Detailed Project
Overview
Project Title: Visualization of Earthquake Simulation
Project Overview This year’s project is to develop an easy-to-use scripting tool for visualizing velocity outputs from seismic wave propagation simulations. The primary objective of this REHS project is to provide an opportunity for highly motivated High School student to gain first-hand experience in Earth Sciences application development, and provide an intuitive way for student(s) to understand the simulation results, and validate the correctness accordingly. This year’s project targets to develop an easy-to-use scripting tool for visualizing velocity outputs from seismic wave propagation simulations. The visualization will aid in testing and validating the results and gain scientific insight by providing instructional material on earthquake phenomena to the public. The model will be simulated on an in-house built GPU cluster, the emergence of GPU as an alternative to conventional general-purpose processors has led to significant interest in these architectures.
This year’s project targets to develop an easy-to-use scripting tool for visualizing velocity outputs from seismic wave propagation simulations. The visualization will aid in testing and validating the results and gain scientific insight by providing instructional material on earthquake phenomena to the public. The model will be simulated on an in-house built GPU cluster, the emergence of GPU as an alternative to conventional general-purpose processors has led to significant interest in these architectures.
Internship Hours Per Week:
15-20 hours Project Mentor: Yifeng Cui, High Performance GeoComputing Laboratory (HPGeoC), San Diego Supercomputer Center, UCSD Download Detailed Project
Overview
Project Title: An encyclopedia of MHC binding sites in 4D
Project
Overview This project provides an unprecedented opportunity to learn from and collaborate with the leading experts in the fields of immunology and computational biology and to contribute to the further development of the Immune Epitope Database (IEDB) funded by the National Institute of Health. IEDB (www.iedb.org ) is the largest database collecting information about immune epitopes. The goal of this project is to develop an encyclopedia of experimentally solved 3D conformational ensembles of peptide binding sites in MHC molecules, using the ICM technology (http://en.wikipedia.org/wiki/ICM-Browser ), which is wildly used in an academia and industry for screening protein binding drugs. Made accessible within IEDB, the encyclopedia will instantly become a useful tool for researchers working on design of vaccines, therapeutics, and adjuvants (vaccine boosters). The student will become familiar with two major biological databases, IEDB and PDB, and ICM technology; learn about protein structure visualization; learn how to programmatically mine data in a database, build a database, and conduct computational research. The student will also learn about immunology and protein structure from the leading experts in the fields.
Internship
Hours Per Week: 20-25 hours Project Mentor: Dr. Julia Ponomarenko, NIH PI,, San Diego Supercomputer Center, UCSD Download Detailed Project Overview
Project Title: Integration of Workflow Management System (WfMS) and Enterprise Service Bus (ESB)
Project Overview This project takes on the challenge of investigating the integration possibilities between two application integration frameworks widely used in software development. Modularity and reusability are key issues in the development of any reasonably sized application, but general-purpose programming languages don’t provide complete support at this level. WfMS and ESB make it possible to tackle these problems head-on in object-oriented components. They allow the implementation of integrated applications by defining connections between the pieces being controlled and well defined. The integration logic that can be expressed in WfMS and ESB are different but they can be used interchangeably. This makes the integration of independent components a conceptual problem rather than a low-level algorithmic complexity issue. The student will work on the formalization of this problem using different integration primitives such as messages, connections and components. The overall goal is the development of a comparative study between two complementary technologies requiring conceptual and application development efforts.
Internship Hours Per Week: 20
hours Project Mentor: Ustun Yildiz, PhD. San Diego Supercomputer Center, UCSD
Download Detailed Project
Overview
Project Title: Linking PDB structural data to IEDB
Project
Overview The specific aims of this project are the following: (1) Develop and encode an approach at identifying the structural coverage of IEDB epitopes, antigens, antibodies, MHC molecules and T-cell receptors at different levels of sequence homology; (2) Develop and encode the presentation of structural information on the IEDB web site; and (3) Develop a procedure to automatically calculate the coverage to keep current to IEDB and PDB’s weekly updates.
Students will become familiar with two major biological databases, IEDB and PDB; learn how to programmatically mine data in these large databases, extract knowledge from scientific data and conduct computational research. Students will have an opportunity to learn technical aspects of database design, data management and data mining and will be exposed to the best programming practices applied in scientific research. They will also learn a lot about immunology and protein structure from the leading experts in the fields. Internship Hours Per
Week: 20 hours Project Mentor: Dr. Julia Ponomarenko, NIH PI, San Diego Supercomputer Center, UCSD
Download
Detailed Project Overview
Project Title: StudentTECH Portal Community Facilitation and Analysis
Project Overview The SDSC StudentTECH Program is a new program of workshops, seminars, and outreach events intended to make science and technology fun and easy for students of all ages. To help facilitate and nurture an every-growing community of actively-engaged learners we are creating the StudentTECH Portal. Developed with the Joomla content management system, the StudentTECH portal will serve as a central repository for active learning tools, resources, news, and events. Since, by definition, the REHS Student Intern will be a model of the prototypical portal user, they will serve in a central role providing insights and feedback on all things of current interest to STEM learners. The REHS Student Intern will be introduced to all aspects of the StudentTECH Community Portal, including administration, maintenance, design, development, and upgrading. A survey of student interest in specific areas of science, technology, engineering, and math will be administered with the assistance of the intern to provide additional important feedback for SDSC StudentTECH workshops and seminars. A database of reference material will be assembled with the intern’s assistance as well. The student will also have the opportunity to help with development and evaluation of interactive educational models and simulations. Internship Hours
Per Week: 10-15 hours Project Mentor: Jeff Sale and Ange Mason
San Diego Supercomputer Center, UCSD
Download Detailed Project Overview
Project Title: New QM/MM Approaches for
High Performance Molecular Dynamics Simulations of Condensed Phase Biological
Systems
Project Overview This REHS
opportunity is set up to be an integral part of our ongoing effort to develop an
extensible interface for mixed quantum mechanical/molecular mechanical (QM/MM)
molecular dynamics (MD) simulations that combines the AMBER
(http://www.ambermd.org) MD software engine with quantum chemistry programs like
ADF (http://www.scm.com), GAMESS (http://www.msg.chem.iastate.edu/gamess/) and
TeraChem (http://www.petachem.com). The availability of such an interface
improves the accuracy and range of applicability of MD simulations that are
available to researchers that are using the AMBER MD software package. This will
support research into the reaction paths of condensed phase enzymes having
benefits across multiple fields including drug design, protein engineering and
biofuel research. The REHS intern will contribute at various stages during the
project including software development, testing of the implementation and
validation calculations on local compute resources including GPU clusters, the
Triton compute resource (http://tritonresource.sdsc.edu/) and a variety of
TeraGrid (http://www.teragrid.org) supercomputing platforms. Internship Hours Per Week: 10- 15 hours Project Mentor:
Professor Ross C. Walker and Dr. Andreas W. Goetz , San Diego Supercomputer
Center, UCSD Download Detailed Project
Overview
The Application Process –
How to Apply
Once you have reviewed the projects listed above and
taken care to consider all of the prerequisites, then it is time to complete the
application form. Remember, if you are applying for more than one internship,
you will need to submit a separate application for each one. Multiple
applications may be submitted in the same envelope. Download Research Experience for High School Students Application
Form
Selected applicants will be contacted by San Diego Supercomputer
Center personnel to arrange a personal interview no later than April 20,
2012.
Questions?
If you have any questions
about the application process, please contact Ange Mason, SDSC Education and
Outreach, via phone at 858 534-5064 or email at amason@ucsd.edu .
