2017 Projects

UCSD REHS Application Information

Please read before applying: REHS Program Information

Apply here: REHS 2017 Online Application

UCSD REHS Important Dates to Remember

  • Application Deadline:  March 15, 2017
  • Latest Date for Notification: May 1, 2017
  • Period of Internship: June 19- August 11, 2017

Summer 2017 Research Project Descriptions

Molecular Mechanisms of Diseases: cancer, autism, Alzheimer’s disease
Dr. Igor Tsigelny, Dept. of Neurosciences, SDSC
View Description


Autistic Spectrum Disorders (ASD)

ASD is a neurodevelopmental disorder that includes social impairments, restrictive and repetitive behavioral patterns, and communication difficulties. Scientists have not found the cause for autism, however ASD is associated with both genetic and environmental factors. Autism is predicted to be caused by genetic mutations in critical neurological areas of the genome due to its etiological heterogeneity and likelihood in siblings. Specific genes and genomic loci have been located and implicated in ASD development. We study these genes interactions with the transcription factors that activate them and to find the spots of possible drug administration, molecular modeling and molecular dynamics simulations.

Alzheimer’s

Alzheimer’s Disease is a neurodegenerative disorder that affects a variety of the brain’s functions, starting with short term memory loss, and eventually progressing to mood swings, disorientation, depression, and even loss of bodily functions. It is responsible for 60-70% of all dementia cases, and is the sixth leading cause of death in America. It is characterized by a buildup of β-amyloid plaques in the brain. There is no known cure for the disorder today, but recently, the amyloid hypothesis has been heavily researched as the mechanism of the disease. The amyloid precursor protein (APP) is cut by two enzymes, β-secretase and γ-secretase, and β-amyloid, the toxic form of the protein, is one of the segments that remains. Since the marker of Alzheimer’s is the buildup of this plaque in the brain, there is potential for slowing the progression of the disease if production of this protein is inhibited. We study existing drugs inactions with the target proteins and try to find methods to improve their action.

Cancer

Cancer is the second leading cause of death in the United States, and responsible for 580,350 deaths in 2013, it has become ever more imperative that researchers focus their attention in this field. Ingenuity Integrated Pathway Analysis (IPA) program is used to build and explore transcriptional networks, microRNA-mRNA target networks, phosphorylation cascades, and Protein-Protein or Protein-DNA interactions. We try to identify regulatory effects that lead from signaling events to transcriptional events for causal network analysis and to construct a comprehensive chart of diseases and functions associated with target genes so as to elucidate gene functionality and possible points of drug administration.

  1. Number of Students to be supported: 3
  2. Name of Lead person: Dr. Igor Tsigelny, Dept. of Neurosciences, SDSC

The students will be a part of the research team working on the larger scale project that includes the project described here. They will attend the group meetings and communicate with the team members using other methods of communication. The student will work closely with the lead person and the other personnel involved.

  1. No parallel internship in other organizations are permitted.
  2. Student Prerequisite

We are looking for a student who is interested in both biology and computation.

  1. Number of hours per week: 15-20 hours
  2. Relevant link:|
    San Diego Supercomputer Center: http://www.sdsc.edu

Memory analysis of HPC Applications Intern
Dr. Laura Carrington, CI-RED, San Diego Supercomputer Center, UCSD
View Description

Research project: This project involves analyzing how each data structure within an HPC application moves data. The analysis is to investigate whether the upcoming Intel 3DXpoint technology could benefit the application and if so what would be the optimal data layout. The analysis will involve using the PMaC Memory Analyzer to capture the data movement within the application along with some data movement cost models. The work will involve:

  • Learning how to use the PMaC Memory Analyzer
  • Learning how to compile and run HPC applications
  • Graphing the output of the tools and drawing conclusions
  • Software engineering to improve the output of the tool using either existing scripts or choice of own scripting language (e.g. Python, Perl, etc.)

Number of Students: 1-2

Project Lead: Laura Carrington, PMaC Lab

Prerequisites: Familiar with Linux OS, computer programming, and a graphing program (e.g. GNU Plot, Excel, etc.)

Hours per week: 15-25

Relevant Link: http://www.sdsc.edu/pmac/research-areas/memory-analysis.html

Visualizing University Locations
Dr. Amit Chourasia, Visualization Services, San Diego Supercomputer Center, UCSD
View Description

Research project: This project involves analyzing how each data
There are several universities in the world. Some of them are very well known, while others not known beyond their local region. The goal of this project is to gather information about universities and create a well-defined list of their attributes along with their location. Then embark on creating visualization based on this data. Through visualization we hope to see how universities are distributed around the world. Thereafter, associate these universities with over 100,000 proteins registered in the Protein Data Bank. Finally package all this work as a website such that can be easily filtered and searched by the public.““““

Number of students: 2

Name of lead person: Dr. Amit Chourasia, Visualization Services,

Plan to integrate students into the group activity

This new project and the students will have an opportunity to contribute towards a larger effort on this work.

Student Perquisites

To apply for this project, you should be comfortable using the command line for Linux, MacOS, or Windows, and have some script programming knowledge, such as for shell scripts, Python, Java. Experience with Javascript, HTML, CSS is a plus, but optional. An interest in computing and visualization is encouraged.

Number of hours per week: 20 hours

Relevant Link: http://www.sdsc.edu/pmac/research-areas/memory-analysis.html

Data Mining and Analyses
Dr. Paul Rodriguez, Scientific Computing Applications, San Diego Supercomputer Center, UCSD
View Description

The past few years has seen a large increase in using analytic techniques to understand large datasets of scientific measurements, collections of text, socio-cultural collections, internet activity, and many other domains.   The analytics techniques come from a variety of subfields in statistics and computer science, such as machine learning, artificial intelligence, computer vision, inferential and exploratory statistics. However, they all have in common that one is generally interested in finding meaningful and useful relationships between elements of a dataset.

I have several projects spread across these subfields that involve using analysis tools with original code that prepares data, and post-processes data in order to get the best use of these tools. For example, we are processing 171,000 depression era photos and detecting faces (using open source tools in python) but we would like to expand that to other features such as human bodies or gender. This project involves developing code to run these feature extractors, testing parameters that work well, producing accuracy counts, post-processing to improve accuracy (if possible). Another project involves OCR of handwritten script for early 20th century mug shots, where the overall coding and processing steps are similar to the previous example. Other projects, for example, may involve using predictive analytics tools to explore how variables are related to outcomes, as a contrast to traditional statistical analysis in scientific or social science data.

  1. Number of Students to be supported: 1
  2. Name of Lead person: Dr. Paul Rodriguez, San Diego Supercomputer Center, UCSD
  3. Plan to Integrate Student into Group Activity

The student will be connected with a small group of researcher working in this area. Projects are typically run by 1 lead person who will be the primary mentor.

  1. Student Prerequisite

Ideally, the student will have some combination of programming knowledge (e.g. he/she is comfortable with at least one programming language such as Python, C, Java, or R) and has some comfort level with basis statistics.

  1. Number of hours per week: 15-20 hours
  2. No parallel internships in other organizations are permitted.
  3. Relevant link:
    San Diego Supercomputer Center: http://www.sdsc.edu

Auto-Correlation in Seismology Research
Dr. Pietro Cicotti, Dr. Dawei Mu, San Diego Supercomputer Center, UCSD
View Details

Analysis and correlation of patterns in seismic data can improve our ability to recognize pattens and anticipate events of interest. SDSC developed an auto-correlation program that detects repeated seismic signals without traditional template recognition preprocessing; this program is still in development and needs to be profiled and optimized.

Depending on background and interest, the successful applicant will work on various components of this software and will be involved in activities that include benchmarking,  profiling performance on CPU and GPU systems, test optimizations, and visualize results.

  1. Number of Students to be supported: 1
  2. Name of Lead person: Dr. Pietro Cicotti, Dr. Dawei Mu, San Diego Supercomputer Center, UCSD
  1. Plan to Integrate Student into Group Activity

The student will be a part of the research team working on the larger scale project that includes the project described here. He or she will attend the group meetings and communicate with the team members using other methods of communication. The student will work closely with the lead person and the other personnel involved.

  1. Student Prerequisite

The applicants should be interested in computer science and engineering. Some programming experience is desirable.

  1. Number of hours per week: 15-20 hours
  2. Relevant link:

San Diego Supercomputer Center: http://www.sdsc.edu

Metabolic Profiles for Cancer Diagnostics
Dr. Igor Tsigelny, Dept. of Neurosciences, SDSC
View Description


Cancer is the second leading cause of death in the United States, and responsible for 580,350 deaths in 2013, it has become ever more imperative that researchers focus their attention in this field. Ingenuity Integrated Pathway Analysis (IPA) program is used to build and explore transcriptional networks, microRNA-mRNA target networks, phosphorylation cascades, and Protein-Protein or Protein-DNA interactions. We try to identify regulatory effects that lead from signaling events to transcriptional events for causal network analysis and to construct a comprehensive chart of diseases and functions associated with target genes so as to elucidate gene functionality and possible points of drug administration.

  1. Number of Students to be supported: 1
  2. Name of Lead person: Dr. Igor Tsigelny, Dept. of Neurosciences, Moores Cancer Center, SDSC
  3. Plan to Integrate Student into Group Activity

The student will be a part of the research team working on the larger scale project that includes the project described here. He or she will attend the group meetings and communicate with the team members using other methods of communication. The student will work closely with the lead person and the other personnel involved.

  1. Student Prerequisites

We are looking for a student who is interested in both biology and computation.

  1. Number of hours per week: 15-20 hours
    No parallel internships in other organizations are permitted.
  2. Relevant link:
    San Diego Supercomputer Center: http://www.sdsc.edu

Neuroscience Gateway Software Intern
Subha Sivagnanam, and Amit Majumdar, San Diego Supercomputer Center, UCSD
View Description

The Neuroscience Gateways (NSG – www.nsgportal.org) provides access to supercomputing resources for computational neuroscientists. Through a simple web-based portal, the NSG provides user-friendly environment for uploading models, specifying supercomputing job parameters, querying running job status, receiving job completion notices, and storing and retrieving output data.  The NSG distributes user jobs to appropriate supercomputing resources. We are interested in students who are proficient in scripting languages  to be able to develop a code that will automatically submit various neuroscience modeling tools to supercomputing resources and test the NSG software infrastructure. Required skills include python or perl programming, exposure to Linux systems.

  1. Number of Students to be supported: 1-2 – for web development
  2. Name of Lead person: Subha Sivagnanam, Amit Majumdar, and Kenneth Yoshimoto, San Diego Supercomputer Center, UCSD
  3. Plan to Integrate Student into Group Activity

The student will be a part of the research team working on the larger scale project that includes the project described here. He or she will attend the group meetings and communicate with the team members using other methods of communication. The student will work closely with the lead person and the other personnel involved.

  1. Student Prerequisite

Knowledge of web technologies such as javascript, MySQL database, HTML, & XML, Prior knowledge of using supercomputing resources is desirable but not required, Keen eye for detail

  1. Number of hours per week: 10-15 hours
  2. Relevant link:
    San Diego Supercomputer Center: http://www.sdsc.edu/

Digital Oceanography Research Intern
Dr. Dave Nadeau, Visualization, San Diego Supercomputer Center, UCSD
View Description

The Scripps Institution of Oceanography (SIO) and the San Diego Supercomputer Center (SDSC) are collaborating on new digital techniques to survey large areas of shallow ocean habitats, such as coral reefs. Is the reef healthy? What species are present and how diverse is the reef? How do species vary in size? What types of seafloor do different species prefer? And at what depths and water temperatures?

Prior efforts to answer these questions have used scuba divers making careful measurements by hand of small parts of a reef. But this approach is hard to do over a large area, and small scale data is difficult to use to reliably answer questions about the reefs as a whole and how their health and biodiversity are changing. As coral reefs are increasing threatened by the effects of climate change, we need to know what is happening. We need more data and a faster way to process it.

SIO and SDSC are collaborating on new custom equipment that is towed behind a boat that zig-zags across a large part of a reef. As the boat moves, the equipment photographs the seafloor in high resolution and measures water characteristics such as temperature and saltyness. Later, computers are used to automatically analyze thousands of images and try to identify each coral species present. This is hard, but we hope this new data will help us answer new large-scale questions about coral reefs. We want you to help.

This project is looking for two or more student interns working on two separate projects. The other project is described separately.

Project Description:
You will work together with scientists and computing experts to analyze images of coral reefs collected recently off a tropical island in the South Pacific. This analysis will use desktop or laptop computers, and possibly supercomputers, and aim to develop and tune specialized image processing algorithms to recognize coral species. You will learn how our current algorithms work, and how they look for important characteristics of corals, sponges, and other invertebrates. You will also be encouraged to experiment and implement your own ideas for analyzing these images. As you test ideas, you will collect data, plot it, look for trends, and make decisions about how to change the processing to get better results. And then you will make these changes and repeat the analysis to gradually refine the approach and get a good characterization of the health and biodiversity of the reef. At the end of the summer, you will create a poster explaining your approach, the problems you encountered, and your results. You will also be featured in the project video created in task 1.

All work will be done at the San Diego Supercomputer Center at UC San Diego The projects will begin with a tour of SIO where students will meet the scientists involved in this research, see their labs, and learn more about coral reefs and new ways to study them.

Number of Students to be supported: 2 or more

Name of lead person: Dr. Dave Nadeau, Visualization Services, San Diego Supercomputer Center, UC San Diego

Student Prerequisite:
To apply for this project, you should be comfortable using the command line for Linux, MacOS, or Windows, and have some script programming knowledge, such as for shell scripts, Perl, PHP, or Python.  C++ programming ability is a plus, but optional. An interest in oceanography is encouraged.

     Number of hours per week: 20 hours per week

     Relevant link:
San Diego Supercomputer Center: http://www.sdsc.edu

Science Communications Writer Intern
Jan Zverina, Division Director of External Relations, San Diego Supercomputer Center, UC San Diego
View Description


SDSC’s External Relations group is seeking high school students who having an interest in basic journalism along with a focus on learning more about effectively communicating results of scientific research or ongoing initiatives that benefit science and society. Candidates should have a strong desire to learn more about how to communicate such research through both the written word as well as video interviews and graphics, and to make it understandable to a general audience without diminishing the scientific work of the researcher or research team. As a result of this internship, students will come away with a better understanding of how computational science is conducted, while having the ability to reduce the technical jargon and other barriers to understanding and communicating how high-performance computing and data storage aid today’s researchers.

This internship will include creating one or two short videos of selected SDSC researchers, as well as communicating how SDSC resources such as the ‘Comet’ and ‘Gordon’ supercomputers assist researchers in conducting their studies. An overarching goal is to help “take the mystery out of supercomputing” so that a general, less technical audiences understand the benefits that such systems provide. Students will be assisted with the final editing and completion of the videos. See more on this under Item 4, Plan to Integrate Student into Group Activity.

We anticipate that this ‘Science Writing & Video Communications’ track may encourage some students to consider careers in computational sciences, which is one of the more lucrative careers in overall journalism as technical writing remains a sought-after skill.

Project Title: Science Writing & Video Communications: Highlighting SDSC’s Expertis

  1. Research Project Background: The National Science Foundation is urging researchers and science writers alike to write at a more basic level of understanding. This from an email dated January 23, 2015:

National Science Foundation Director France Córdova recently announced important new steps to enhance transparency and accountability at NSF. Under the new directive, principal investigators will work with program officers to draft an award abstract in plain English that describes the project and how it will advance the progress of science, the national defense, or the nation’s health, prosperity and welfare. The move comes amid intense scrutiny from Capitol Hill about the value of research in the social sciences and on climate issues.

  1. Number of Students to be supported: Two
  1. Name of lead mentor: Jan Zverina, Division Director of External Relations, San Diego Supercomputer Center, UC San Diego
  1. Plan to Integrate Student into Group Activity: Jan Zverina will supervise students directly, help them to develop questions to create brief videos of selected SDSC staff, and create a variety of media to articulate the basics of supercomputing expertise in a clear and compelling way to both the general public and their student peers. Students will participate in the poster session at the end of the internship, and are encouraged to be as creative as they want in their presentation. For each project, an initial meeting will be used to outline the basics, with review and editing done both via email and through regularly scheduled in-person meetings. Interns will receive constructive criticism of their work, with constructive suggestions for how it might be improved. Completed articles or videos may appear on the SDSC website or in SDSC’s ‘Innovators’ e-newsletter, with full credit given to students for their work so they may include it in their portfolios. Students may also be invited to report on the SDSC 2016 Big Data Summer Institute in August if they are interested and their schedule allows.
  1. Student Prerequisites: (Required)
    Evidence of ability to write at least at a 10th grade level (A or B grades in 10th grade English)

An A or B grade in at least one science or engineering course at the high school level. The ability to receive constructive criticism of their writing with grace and humor, and to make revisions guided by professional communication staffers. Students will need to be comfortable in interviewing researchers, primarily in person. Mentors will always provide an introduction to the researchers.

  1. Number of hours per week: 10-15 hours.
  1. IT Support: Students will be provided workspace and workstation with internet access and a USB drive. All video equipment will be provided by SDSC Externa Relations, along with a tutorial on how to use it.
  1. Relevant links: All students applying for this internship should familiarize themselves with the following:
  • The San Diego Supercomputer Center website at http://www.sdsc.edu/. Click on ‘Press Releases’ under the ‘News & Events’ tab on the home page to review recent press releases.
  • Review the ‘Researcher Spotlight’ section on the lower part of the SDSC home page.
  • Review the SDSC Annual Report available as a pdf file at http://www.sdsc.edu/pub/index.html. This report provides an overview of the depth and breadth of SDSC’s projects and activities, and the staff members behind them.
  • Review the SDSC Innovators newsletter at http://www.sdsc.edu/news_and_events/newsletter.html

Digital Oceanography Videographer
Dr. Dave Nadeau, Visualization, San Diego Supercomputer Center, UCSD
View Description


The Scripps Institution of Oceanography (SIO) and the San Diego Supercomputer Center (SDSC) are collaborating on new digital techniques to survey large areas of shallow ocean habitats, such as coral reefs. Is the reef healthy? What species are present and how diverse is the reef? How do species vary in size? What types of seafloor do different species prefer? And at what depths and water temperatures?

Prior efforts to answer these questions have used scuba divers making careful measurements by hand of small parts of a reef. But this approach is hard to do over a large area, and small scale data is difficult to use to reliably answer questions about the reefs as a whole and how their health and biodiversity are changing. As coral reefs are increasing threatened by the effects of climate change, we need to know what is happening. We need more data and a faster way to process it.

SIO and SDSC are collaborating on new custom equipment that is towed behind a boat that zig-zags across a large part of a reef. As the boat moves, the equipment photographs the seafloor in high resolution and measures water characteristics such as temperature and saltyness. Later, computers are used to automatically analyze thousands of images and try to identify each coral species present. This is hard, but we hope this new data will help us answer new large-scale questions about coral reefs. We want you to help.

This project is looking for two or more student interns working on two tasks. The other task is described in a separate project description.

Project Description:

You will work together with our communications departments to create a short 3 minute video telling the story of the project and its importance in studying coral reefs. You will use a video camera to interview the scientists involved, and shoot footage of the oceanography lab, equipment, and supercomputers. You will then edit this footage, and existing underwater footage, to create a summary of the project and its results that is suitable for the layperson. At the end of the summer, your video will be presented to the scientists and your fellow students, and then added to the project’s web site and YouTube.

All work will be done at the San Diego Supercomputer Center at UC San Diego. The projects will begin with a tour of SIO where students will meet the scientists involved in this research, see their labs, and learn more about coral reefs and new ways to study them.

Number of Students to be supported: 1

Name of lead person: Dave Nadeau, Visualization Services, San Diego Supercomputer Center, UC San Diego

Student Prerequisite:

To apply for this project, you should have some experience in videography and be prepared to interview scientists and students, plan video shots, and edit video and audio together on a computer. We will provide cameras, lighting, video editing software, and assistance under your direction.

     Number of hours per week: 20 hours per week

     Relevant link: San Diego Supercomputer Center: http://www.sdsc.edu/

Summer Outreach Programs Videographer
Ange Mason, Education Program Manager, San Diego Supercomputer Center, UCSD
View Description

During the past few years, SDSC’s Education and Outreach group has sought to build its social media presence and what we have found is that short videos of our summer workshops and research intern interviews have proven to be very popular.  We place this conten  t and still images on our summer SDSC TV YouTube project and our Facebook pages to showcase our outreach activities year round. Our four Facebook pages are:

The intern will work with the program manager to brainstorm ideas to make our social media content vibrant, fun, appealing and informative with content such as videos, student video spotlights, summer workshop and internship photos, workshop instructor interviews, researcher interviews, and other innovative ideas. Content such as this will comprise a weekly SDSC TV feature, which will be posted each Friday.

This is a super fun (yes, I said super fun) opportunity to work with researchers and students throughout the week, as well as the opportunity to interact with STEM camp instructors and campers. This is a large project with many fun and creative components. Let your talent behind the camera soar!

Students applying on their own will be given the option to work as a team and thus be paired with another applicant, or the option to work alone. Student teams of two may also apply and will be interviewed together. Please indicate the name of your teammate in your application.

Number of Students Requested: 1-2

Name of Lead person: Ange Mason, Education Program Manager, San Diego Supercomputer Center, UCSD

Plan to Integrate Student into Group Activity:
The intern will be a part of the summer student staff working to assist with social media outreach. He or she will attend the group meetings and share in weekly planning and logistical meetings. The student will work closely with the project lead and the other Education team members.

Student Prerequisite:

We are looking for a student who is self-driven and able to work independently and with others. The intern must possess strong interpersonal skills. The intern must posses sstrong organizational skills plus  excellent written and oral skills. The intern must also be comfortable using a camera or video camera and have strong video creation knowledge. For a hint as to what kind of intern we are seeking, please visit YouTube and enter SDSCTV or click on the following link: https://www.youtube.com/results?search_query=SDSCTV.

SDSC will work with you to obtain needed software for this project.

Number of hours per week: 20 hours

Relevant Links:
San Diego Supercomputer Center:nhttp://www.sdsc.edu/

San Diego Supercomputer Center StudentTECH program: http://education.sdsc.edu/studenttech

Sensors, Data Rendering and the Internet of Things: IT Systems Student Assistant
Andrew Ferbert, Server Systems, San Diego Supercomputer Center, UCSD
View Description

The core of science is to create a hypothesis, collect data, and evaluate the outcome. For large scale system deployments like those at SDSC, we have thousands of available data points from built-in sensors. We’d like your help sifting through the available data and presenting to customers and system engineers.

As a team member within SDSC’s division of IT Systems and Services, you would help deploy tools to manage a large sensor network collecting a variety of metrics. A system at SDSC may have 50 temperature sensors, 10 fan tachometers, power meters, CPU utilization collectors, the list goes on. Add to that text based system logs and we have the possibility of gathering thousands of metrics per system per minute. Our division has over 300 servers so we need help.

A few projects that we have thought of:

A 3-D view of the temperature of the SDSC datacenter
Tools to graphically show system utilization
Real-time analysis of incoming log data (70+ million logs per day)
Worldwide “heatmap” of security threats
We also want new ideas from you!

Please consider joining us in finding great ways to use our data.

  1. Number of Students to be supported: 1-2
  2. Name of Lead person: Andrew Ferbert, Server Systems, San Diego Supercomputer Center, UCSD
  3. Plan to Integrate Student into Group Activity

The student will be a part of the IT Systems research team. He or she will attend the group meetings. The student will work closely with the lead person and the other personnel involved.

  1. Number of hours per week: 15-20 hours
  2. Relevant link:
    San Diego Supercomputer Center: http://www.sdsc.edu

SDSC Datacenter Network Performance Monitoring Intern
Tom Hutton, Network Engineer, San Diego Supercomputer Center, UCSD
View Description

This position(s) will be researching the use of and testing the deployment of the PerfSonar Toolkit on small inexpensive microcomputers that could be deployed as a flock of testers within a datacenter.   The individuals working on this position will handle the installation, configuration, testing and then evaluation of a particular hardware platform for datacenter testing purposes.

Planned hardware for testing/deployment will be:
EVS LIVA 32GB running Debian
EVS LIVA 64GB running Debian
ECS Liva-X 32GB running Debian
GigaByte 8G running CentOS
Intel NUC 8G running CentOS
Zotac 8G running CentOS

Number of Students Requested: Two

Name of Lead person: Tom Hutton, Network Architectr, San Diego Supercomputer Center, UCSD

Plan to Integrate Student into Group Activity:

Student will be expected to spend 50% of their time working on this project at SDSC and will be able to spend the other 50% remotely.  Students will have opportunity to directly communicate with the SDSC staff programmers.

Student Prerequisite:

We are looking for students who are self-driven and able to work with minimal supervision.  Student should have familiarity with the LINUX OS and basic operating system installation.

Number of hours per week: 7-20

Relevant Links:
San Diego Supercomputer Center: http://www.sdsc.edu 

Summer Computing and Science Academy Teaching Assistant
Ange Mason, Education Program Manager, San Diego Supercomputer Center, UCSD
View Description

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 environmental science to cinematic arts and Java to physics, C 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.

Don’t worry if you don’t know the software being taught. All you need to do is follow along with the instructor. This is a great opportunity for you to learn many of the new and familiar software packages being used today.

Number of Students Requested: 16

Name of Lead person: Ange Mason, Education Program Manager, San Diego Supercomputer Center, UCSD

Plan to Integrate Student into Group Activity:
The student will be a part of the summer student staff working to assist with our busy schedule of summer workshops. He or she will attend the group meetings and share in weekly planning and logistical meetings. The student will work closely with the project lead and the other Education team members.

Student Prerequisite:
We are looking for a student who is self-driven and able to work with minimal supervision. Student must be customer service oriented and like working with a diverse population of students.
Each week, students will be sent the software links for the following week. Students must become familiar with the software in order to be an effective workshop assistant. This is a position requirement.

Preferred But Not Required
Student TEACHING Assistants should have prior experience working with middle and high school students in a camp or TA environment or have attended previous SDSC workshops.

All student assistants will be required to have a background check through UCSD.

Number of hours per week: 20- 24 hours.  Students are asked to work full days or half days for continuity with the workshop participants.

Relevant Links:
Summer 2015 Programs: http://education.sdsc.edu/studenttech/?page_id=570
San Diego Supercomputer Center: http://www.sdsc.edu/
San Diego Supercomputer Center StudentTECH program: http://education.sdsc.edu/studenttech/

Multiscale Simulations in Chemistry and Biophysics
Dr. Andreas Goetz, San Diego Supercomputer Center, UCSD
View Description

In this REHS project, which will be supervised by Dr. Andreas Goetz at the San Diego Supercomputer Center, the students will make a contribution to our ongoing multiscale simulation software development, optimization, and simulations projects. Work to be performed can cover different aspects, depending on the background and interests of the applicant. This can include performance optimizations and benchmarks of performance critical algorithms on multi and many core (such as GPUs) architectures or numerical simulations of catalytic events in biomolecules or at metal catalyst surfaces with quantum chemistry or biomolecular simulation codes. Depending on the progress of the project and the individual ability of the students, the interns will thus have the possibility to acquire skills in setting up and performing multiscale QM/MM simulations in a Linux based operating system environment, analyzing performance data, and programming in scripting and compiled languages including Bash, Python, Fortran and C, and possibly parallel programming with CUDA and MPI. As an essential part of the internship the students will learn how to document their research, prepare research reports and present their results to their peers– skills that are very important for a successful research and engineering career.

Number of students to be supported:
Up to 2 students, working on complementary aspects such as profiling and optimizations of
different code paths or numerical simulations of different but related catalytic processes.

Person overseeing the student research experience:
Dr. Andreas Goetz

Plan to integrate students into research activities:
Dr. Andreas Goetz who is actively working on the model development, software implementation and simulation projects will closely supervise the students on a daily basis. In addition, the students will have the opportunity to interact with other high school students and undergraduate or graduate interns that will be working on other projects related to molecular simulations.

Student Prerequisites:
Software development/optimization related work requires experience with some compiled languages such as C/C++/Fortran and ideally (though not required) parallelization with
OpenMP, MPI, CUDA, OpenACC. Computational chemistry / biomolecular simulations projectsrequire advanced classes in chemistry or biology. Exposure to scripting languages or familiarity
with Linux and command line environments is expected. Specific knowledge of any of these areas is less critical than exceptional intellectual ability.

Number of work hours per week: 20 to 25

Relevant web links:
AMBER software: www

[/expand].ambermd.org
ADF software: www.scm.com
Dr. Goetz’ web site: www.awgoetz.de[/expand]

Spatial Information Systems Lab Intern
Dr. Ilya Zaslavskey, San Diego Supercomputer Center, UCSD
View Description

This internship will be a part of NSF-funded EarthCube CINERGI (Community Inventory of EarthCube Resources for Geoscience Interoperability) project. EarthCube is a new large-scale NSF project to create a data and knowledge management system for data sharing among geoscientists. We are working with researchers from several geoscience domains to understand what data and models they use, and how they search for appropriate data and evaluate their fitness for use. As part of it, we assemble a collection of metadata documents, validate them, parse their content and try to reconstruct information that is missing. Interns in this project will work with the project’s programming staff to construct, annotate, test, improve and visualize the metadata catalog that will span multiple disciplines in the geosciences.

The tasks will include: working with geoscientists from several domains (in particular, sedimentology, hydrology, paleogeoscience), to assemble descriptions of data they use into searchable catalogs; creating online visualizations of these catalogs; understanding and describing how researches search for data in different fields; assembling and describing geoscience models and processing tools; linking information about datasets with publications, researchers, models, etc

Number of Students to be supported: 1-3

Name of Lead person: Dr. Ilya Zaslavskey, San Diego Supercomputer Center

Plan to Integrate Student into Group Activity
The student will be a part of the research team working on the larger scale project that includes the project described here. He or she will attend the group meetings and communicate with the team members using other methods of communication. The student will work closely with the lead person and the other personnel involved.

Student Prerequisite
We are looking for students who are interested in both environmental science and in computing. Ideal candidates would have some programming and web design skills, ability to read and understand data and model descriptions, and some familiarity with databases.

Number of hours per week: 15-20 hours
Relevant link:
San Diego Supercomputer Center: http://www.sdsc.edu

Elucidation of Common Molecular Mechanisms of Parkinson’s, Alzheimer Diseases, and Diabetes
Dr. Igor Tsigelny, Dept. of Neurosciences, San Diego Supercomputer Center, UCSD
View Description

Aggregation of specific proteins is associated with a number of diseases including Parkinson’s (PD), Alzheimer’s (AD), and other neurodegenerative diseases. Type II diabetes (T2D) is also linked to aggregation of Islet amyloid polypeptides (IAPP) IAPP is found to be significantly accumulated as extracellular amyloid deposits in the pancreas of T2D patients; it is shown that early oligomers are significantly cytotoxic species that lead to beta-cell apoptosis. The mechanisms through which IAPP leads to T2D are unclear. Various lines of evidence appeared to support the contention that IAPP oligomers built in the early stages of aggregation form annular protofibrils and consequently pores in the membranes the same way as amyloid-beta and alpha-synuclein correspondingly create pores in the cell membrane in AD and PD. Increase of calcium influx to the cells can lead to apoptosis in case of all these diseases.

The specific tasks of the project are using computer modeling and simulations to accomplish the following goals: (1) To characterize the interactions between IAPP, amyloid beta, and alpha-synuclein molecules in oligomers, and interactions between molecules and the membranes. (2) To validate a concept of self-assembly of these molecules, using a set of mutants known to enhance or inhibit IAPP aggregation process with identifiable structural properties.

The task will include extensive analysis of research articles in the field, related to modeling and simulations abovementioned proteins and their interactions with the membrane. Computational molecular modeling and molecular dynamics simulations.

  1. Number of Students to be supported: 1
  2. Name of Lead person: Dr. Igor Tsigelny, Dept. of Neurosciences, SDSC
  3. Plan to Integrate Student into Group Activity

The student will be a part of the research team working on the larger scale project that includes the project described here. He or she will attend the group meetings and communicate with the team members using other methods of communication. The student will work closely with the lead person and the other personnel involved.

  1. Student Prerequisite
    We are looking for a student who is interested in both biology and computation.
  1. Number of hours per week: 15-20 hours
  2. Relevant link:
    San Diego Supercomputer Center: http://www.sdsc.edu

Monitoring and Analysis Software Intern
Shava Smallen, Research Programmer, San Diego Supercomputer Center, UCSD
View Description

Inca is an open-source tool that provides user-level monitoring for cyberinfrastructure systems and verification of its software and services.  Inca uses a unique centralized monitoring configuration approach, which is essential for providing consistent monitoring results and a unified and coherent infrastructure for users.   Some key features of Inca are that 1) new types of monitoring data can be plugged into Inca by writing a reporter, an executable program that tests or measures some aspect of a system or installed software, 2) important system and execution metadata is automatically collected by reporter APIs to inform system administrators of exactly how a failure was detected and to see a summary of commands that were run, 3) Inca periodically executes reporters that  test and measure performance components of cyberinfrastructure systems from a regular user account, 4) reporter result histories are archived  to understand reporter execution over time, and 5) Inca provides a wide variety of web status page views from detailed test information to summary and historical reports.

We are interested in students who could help us research available Javascript/JQuery graphing libraries and find new and better ways to visualize our monitoring data.   Previous experience working with Javascript/JQuery desirable but not required.

Number of students to be supported in each activity and in the overall project: 1-3

Name of lead person overseeing the student research experience: Shava Smallen, San iego Supercomputer Center, UCSD

Number of hours the student(s) will be asked to work per week: 10-20 hours

Guidance and Answers at Your Fingertips

Ange Mason of the San Diego Supercomputer Center (amason@ucsd.edu, 858 534-5064) and Lindy Wong (liw030@ucsd.edu) are available to provide guidance and answer any questions you might have. Just ask!