San Diego Supercomputer Center High School Volunteer Summer 2012  Internship Opportunities
June 25-August 10, 2012 - La Jolla, California
Submission Deadline - March 30, 2012

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.

High School Volunteer Summer Research Opportunities

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 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 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 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 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, prigramming 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 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 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 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 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 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 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

The Application Process - How to Apply

For detailed internship opportunity descriptions and to download an application, please visit
http://education.sdsc.edu/teachertech/index.php?module=ContentExpress&func=display&ceid=37
Selected applicants will be contacted by SDSC personnel to arrange a personal interview no later than April 26, 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.