OSDC PIRE Year 2 Researchers (2012)
Fellows
Meet this year’s PIRE fellows. These researchers are working to make scientific compute clouds better.
David Hanley
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Researcher at the University of Chicago
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Field: Scalable Computing
As a graduate student in the late 90’s, David Hanley worked on several projects, including PTool, which won several awards and was used by Fermilab to manage data in the search for the top quark. With his focus in high performance computing, David worked in private industry developing applications for MRI scanners, Bioinformatics pipelines, and video encoding and streaming. Returning to academia, David has worked on UDT, a high-performance data transport protocol, UDR, a file synchronization system based on UDT, Sidgrid, a social sciences data management cloud, Bionimbus, a bioinformatics cloud-driven CMS, processing code for SDSS, the Sloan Digital Sky Survey, and DSTP for Dataspace. His primary research interests are scalable computing, high-performance functional programming.
Matthew Greenway
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Researcher at the University of Chicago
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Field: Computer Science
I work in Robert Grossman’s Laboratory for Advanced at Computing at the University of Chicago. I have been working on projects that support the OSDC’s cloud infrastructure. One of these projects is a web front end to the OSDC clouds named Tukey after the statistician John Tukey. I have also worked on a filesystem client for WebDAV for serving genomic and other data to the cloud: https://github.com/mtgreenway/fusedav. Lately I have been working on adding SSL/TLS encryption to UDR, our rsync over UDT project, available at https://github.com/LabAdvComp/UDR.
Allison Heath, PhD
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Research Scientist at the University of Chicago
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Field: Computer and Information Science, Systems Biology, Cloud Computing, Data-intensive Science
I am a research scientist with Dr. Robert Grossman in the Institute for Genomics and Systems Biology at the University of Chicago. I completed my PhD in Computer Science at Rice University with Dr. Lydia Kavraki, where I developed algorithms for computational problems in structural and systems biology. My current research interests are in cloud computing systems and algorithms tailored for data intensive science. My projects revolve around the design and implementation of computational methods for analyzing large genomic datasets. I also work on creating utilities for managing large data sets in cloud computing environments.
Rafael Suarez
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Undergraduate student at the University of Chicago
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Field: Computation, Physics
Rafael is currently completing a degree in Physics at the University of Chicago. He is interested in large scale computation and modeling and is considering pursuing computational physics and urban studies at the graduate level. Rafael works with the Open Science Data Cloud on the automated deployment of new clouds and data set acquisition. To those ends, he has several years of experience with Linux administration, infrastructure management, and big data.
Ray Powell
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Researcher at the University of Chicago
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Field: Computer Engineering, Systems Administration
Ray graduated with a Masters in Computer Engineering from Illinois Institute of Technology and is now involved in different project with implementation of QA Analysis, Virtualization, Linux Distributed Systems, and Network Infrastructure Deployment as Senior Linux System Administrator. Currently, Ray is working on OSDC ongoing research with several petabytes of public scientific data storage spread across distributed OSDC clusters at the Laboratory for Advanced Computing at the University of Chicago. He is also working on analysis and distribution of Earth satellite images from OSDC Project Matsu and NASA.
Aashish Jha
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PhD student at the University of Chicago
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Field: Evolutionary biology
I am a PhD Student in Kevin White’s lab at The University of Chicago Institute for Genomics and Systems Biology and a Pre-doctoral fellow at The University of Chicago Center for Systems Biology of Oxygen Sensing. My research focuses on using experimental evolution of Drosophila melanogaster followed by next generation sequencing to understand the role of natural selection in evolution of complex traits such as adaptation to hypoxia (low oxygen). I am an OSDC Bionimbus cloud beta user and have been contributing to its evolution since 2010. I use Bionimbus cloud computing to run computational pipelines (in Perl) and statistical methods to analyze next-generation-sequencing data (in R). Using Bionimbus I am currently working on several collaborative projects such as (a) Identification of genetic architecture of adaptation to hypoxia (in collaboration with Gabriel Haddad, University of California San Diego), (b) Understand the role of microRNA (mir9a) in evolution of scutellar bristles (in collaboration with Richard Carthew, Northwestern University, Chicago), (c) Characterize genetic variation in governing egg size (in collaboration with Martin Kreitman, The University of Chicago), (d) Describe genetic variation in European populations of Drosophila melanogaster.
Christine Harvey
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Graduate student
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Field: Computational Science
As a graduate student in Computational Science, Christine’s education has focused on using high performance computing among other technologies to analyze various problems in mathematics and science. Her first internship was with the Army Research Laboratory at the Aberdeen Proving Ground, where she used Monte Carlo simulations to model the dispersion of the M1028 Canister Round. Her second internship was with the Maryland Department of the Environment, where she created an application in Java for a team of meteorologists to search a database and return the requested information from all over the country for the meteorologists to review the data. She is currently beginning her thesis research on Probability and Random Processes, specifically modeling Markov Chains. While researching in Edinburgh, Christine is interested in studying mathematical models/simulations and topics related to computational science. She is most interested in hazard prediction in brittle rock failure experiments and exploring the OSDC as an infrastructure for massive seismic trace correlation tasks.
Kyle Jorgensen
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Undergraduate student at the University of California Santa Barbara
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Field: Computer Science
Kyle views computer science as problem solving and every project as a puzzle in which a computer is used as means to solve that puzzle. Last summer he participated in an internship where he gained experience in web development using the Grails framework, working on server-side and client-side code. This experience gave him a great insight into what it is like to develop software for large-scale applications. He is interested in problems dealing with large amounts of data. Kyle’s research advisor is Professor John Gilbert. Research at the Combinatorial Scientific Computing Laboratory includes combinatorial scientific computing, high-performance graph algorithms, tools and software for computational science and engineering, numerical linear algebra, and distributed sensing and control.
Felipe Navarro
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Researcher at Florida International University
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Field: Computer Engineering
Felipe has developed applications using a wide variety of languages such as Java, C/C++, C#, Intel and MIPS assembly, and IBM’s Z/OS Mainframe. He also has experience developing web-based database applications using PostgreSQL, Microsoft SQL Server, HTML and CSS. His main area of expertise is hardware design and implementation, which he has continued through his graduate and post-graduate studies and extends all the way to the gate level of design. His most recent projects include power aware computing in many-core and cloud based-systems using the experimental Intel Single-Chip Cloud Computer, as well as the implementation of a cloud system as a cloud computing and network engineer for FIU CIARA. In the summer of 2012 he will be implementing another cloud system in Sao Paulo Brazil as the second of many cloud systems to be implemented in various locations around the world and integrated to function as a single system.
Mario Consuegra
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Researcher at Florida International University
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Field: Computer Science
Mario Consuegra received his B.S. in Computer Science from Florida International University in 2010 and is a research assistant at FIU. He is currently doing research on power-efficient computing. He explores techniques from the areas of approximation algorithms, randomized algorithms, online algorithms, probabilistic and amortized analysis, complexity theory, and other mathematical techniques. He is interested on working on practical problems related to task scheduling and resource allocation for cloud computing systems from both a theoretical framework and a practical perspective. Mario is also interested in distributed systems and understanding how to combine cloud architectures with scientific computing in large scale databases. He would like to develop big-data tools for application to pattern discovery in protein structures and more, developing stable algorithms that take account of structural knowledge about data, when distributing them on ingest into an OSDC cluster, or when marshaling them prior to dispatch.
Misael (Mitch) Fernandez
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Undergraduate student at Florida International University
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Field: Biology and Chemistry
Mitch plans to pursue graduate studies in genomics, bioinformatics or a related bio-medical science. His main interest is in modeling biological systems and finding computational approaches to understanding human diseases. He has a B.A. from the University of Florida in Russian Language and Literature and is currently in his senior year of pursuing a second bachelor’s degree at FIU, double majoring in Biological Sciences and Chemistry with a minor in Computer Science. Professionally, he has worked as an intelligence analyst and was also a Microsoft Certified Systems Engineer and has experience working as a network administrator.
Mitch works in the Bioinformatics Research Group (BIORG) headed by Dr. Giri Narasimhan in the College of Engineering and Computing. His principle project involves a metagenomic analysis of the human lung microbiome. He has also been working for Dr. Xiaotang Wang in the Chemistry Department of the College of Arts and Sciences on a project involving single-site mutagenesis of a fungal enzyme, chloroperoxidase (CPO). Mitch is currently investigating three-dimensional patterns in protein structures and would like to work on integrating scientific databases with the OSDC architecture using the resulting data.
Rodolfo Tobon
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Researcher at Florida International University
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Field: Civil Engineering
Rodolfo is a post-graduate researcher that just received a Bachelors of Science in Civil Engineering from Florida International University. He would like to pursue a Masters in structural engineering and a Masters in business. He has taken classes such as reinforced concrete and steel, where he and his group designed and calculated beam deflection and moments of many types of structures. He learned the importance of scheduling and reading plans from previous classes taken, as well as project planning and construction management. During his time at FIU, he was able to participate in the American Society of Civil Engineering (ASCE) national competition, mainly designing a concrete canoe and steel bridge. Rodolfo is excited for this research opportunity; he will be learning how to connect and set up computer server racks and monitor the progress of big data transfers between FIU, the university of Chicago, and Brazil.