Volume 1, Issue 1, January 24, 2014
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Newsletter: Institute for Digital Research and Education
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Research Spotlight I News & Publications I Talks I Workshops & EventsGrant Opportunities
Spotlight on Research: The Role of the Hoffman2 Cluster in Bioinformatics Research
First opened to users in January 2008, the Hoffman2 Shared Research Cluster is an IDRE project that serves thousands of members of the UCLA research community, allowing researchers to run multi-level simulations, do complex data analysis and perform large-scale computations.

Eleazar Eskin, a professor in the departments of computer science and human genetics at UCLA, is one of the Hoffman2 Cluster’s biggest users and strongest advocates.  Eskin shares how the Hoffman2 Cluster has been an invaluable resource in his bioinformatics and computational genetics research.

Photo: Eleazar Eskin

Eskin explains that most of his research focuses on “the analysis of human genetic variation data, which is understanding the relationship between genetic variation and traits.” By analyzing human genetic variation data, researchers can begin to “understand why certain people are at a higher risk for a particular disease and others are not,” Eskin stated.   In large studies known as genome-wide association studies, researchers “study hundreds of thousands of individuals who have a certain disease and compare them to individuals who don’t have that disease. Then [researchers] look for genetic variation between the groups,” said Eskin. His group then “develops statistical algorithms and methods for how to analyze [the] kind of data” produced by these large studies.

Eskin was quick to identify the Hoffman2 Cluster as the most beneficial resource available to him at UCLA because so much of his research is dependent upon it. “The Hoffman2 Cluster really plays two major roles … One aspect is that we use the Hoffman2Cluster for research in general. The second aspect is that it enables collaboration between different research groups,” stated Eskin.

To read the full interview, click here.
News | Publications
IDRE and Department of Physics and Astronomy Receive Physics at the Information Frontier Grant
The Department of Physics and Astronomy and the Institute for Digital Research and Education (IDRE) have been awarded a three year grant from the National Science Foundation under their Physics at the Information Frontier Program.
IDRE Partners with Physics and Electrical Engineering to Receive $4,000,000 NSF Grant
The Institute for Digital Research and Education, together with the Departments of Physics and Astronomy and Electrical Engineering, was awarded a five year $4,000,000 grant from the National Science Foundation to create the Particle-in-Cell and Kinetic Simulation Software Center (PICKSC) at UCLA.
UCLA to offer Summer Institute on Digital Humanities and Art History
UCLA's Digital Humanities program has received a grant from the Getty Foundation to offer an institute on digital humanities and art history in the summer of 2014. "Beyond the Digitized Slide Library" will provide digital humanities training, instruction, and context for twelve art historians over the course of eight days on UCLA's campus. Participants will learn about debates and key concepts in the digital humanities, gain hands-on experience with tools and techniques for art historical research, and explore possibilities for the conjunction of these two fields.
HPC and Statistical Computing Class Materials
Did you miss one of our workshops in high performance computing or statistical computing? Check out the lecture slides to get the information you missed:

Using Hoffman2 Cluster
Intro to Parallel Computing and OpenMP
Introduction to MPI
Running Parallel Jobs Efficiently
IDRE related Lectures, Seminars & Colloquia
Applied Math Colloquium: Winter 2014
Extracting hidden structure from data: Robust Subspace Clustering and Phase Retrieval. Speaker is Mahdi Soltanolkotabi (Stanford University). January 29 from 4:00 pm to 5:00 pm in Math Sciences 6229.
Biomathematics Seminars
Monday Bioinformatics seminar series. 4:00 to 5:00 pm in Boyer 159/173.
Computer Science Seminars
Jon Postel Distinguished Lecture: The Functionality of Data - Understanding Geometric Data. Speaker is Leonidas Guibas (Stanford University). January 30 from 4:15 pm to 5:45 pm. To learn more, click here.
Open Stack-Havana Release
Seminar on private cloud-compute resource deployment in Infrastructure as a Service model using Open Stack-Havana release. The Virtual Computing Laboratory of IDRE invites you to a presentation of private cloud-compute deployment in Infrastructure as a Service (IaaS) model using Open Stack-Havana release open source software package. In this presentation we will discuss the OpenStack IaaS architecture as well as the actual deployment of Havana release on CentOS 6.5 and Ubuntu 12.04 operating systems. January 29 from 10:00 am - 12:00 pm in the Visualization Portal (5628 Math Sciences). Speaker is Prakashan Korambath.
IDRE related Workshops & Events
GIS Trainings and Workshops
IDRE's GIS team offers hands-on training and workshops on a variety of geo-spatial topics. Currently these workshops are offered on a per request basis. Click the link to find out what topics are offered and request a workshop tailored to your needs.
Past Statistical Consulting Classes Available Online
Past statistical consulting workshops and classes, covering topics such as Stata, SAS, SPSS, R, Multilevel Modeling, Survey Data Analysis, Power Analysis and SUDAAN, are available online.
Department of Health Policy and Management
Excel Skills for the Intermediate User
Come learn how to use Excel for analyzing and interpreting data! Presented by Adrian Manalang, the director of finance and administration at the UCLA Center for Health Policy Research. February 7 from 2:00 pm to 4:00 pm.
Experiential Learning Conference
Theme: Interdisciplinary Collaborations and Creative Connections. The conference will bring together those who would like to develop creative ideas related to interdisciplinary collaborations and the expansion of high impact education practices. January 31 at the Cross-Cultural Center, UC San Diego.
UCLA  IPAM Workshop: Translating Cancer Data and Models to Clinical Practice
This workshop will emphasize an integrated approach to understanding cancer initiation, progression, metastasis, and treatment. Participants will include clinicians and experimentalists whose approach and research may complement and motivate new mathematical and physical modeling, as well as empirical or clinical investigations. Our ultimate goals will be to examine and discuss approaches for improving clinical “standards of care” and to foster new investigative directions in applied cancer research that involve the right level of detail in emerging mathematical and physical approaches. February 10-14 in 460 Portola Plaza. 

Blackboard Collaborate Presentation
This event will cover what is new in Collaborate 12, converting MP3 and MP4 recordings, how to use Blackboard on your mobile phone, and will end with a Q&A session. January 28 from 10:00 am to 12:00 pm in Math Sciences 5628. To RSVP, click here.
ITSec Talk: Puppet, Next-Generation Server Automation Tool
Demonstration of management tools, discussion of implementation steps, along with practical tips (Disabling unnecessary services, removing unneeded packages, restricting access to sensitive files, removing insecure/default configurations, modifying firewall, implementing two form factor authentication and more…) will be the topic of this Puppet presentation. January 29 from 2:00 pm to 3:30 pm in the Visualization Portal (5628 Math Sciences). To RSVP, click here.

Accessing and Analyzing CHIS Data
This workshop will provide an overview of the California Health Interview Survey (CHIS), information on how to access CHIS data and example analyses using CHIS data. Other topics will include pooling multiple years of CHIS data, data linkage and GIS, and imputation of missing values. February 28 from 10:00 am to 12:00 pm in the Visualization Portal (5628 Math Sciences). To RSVP, click here.
Grant & Funding Opportunities

NSF | NIH | DOE | Federal | Nonfederal

Upcoming NSF Opportunities:

Innovative Technology Experiences for Students and Teachers 
The ITEST program seeks to build understandings of best practice factors, contexts and processes contributing to K-12 students' motivation and participation in the science, technology, engineering, and mathematics (STEM) core domains along with other STEM cognate domains (e.g., information and communications technology (ICT), computing, computer sciences, data analytics, among others) that inform education programs and workforce domains. The ITEST program funds foundational and applied research projects addressing the development, implementation, and dissemination of innovative strategies, tools, and models for engaging students to be aware of STEM and cognate careers, and to pursue formal school-based and informal out-of-school educational experiences to prepare for such careers.
Deadline February 11, 2014
Budget: $300,000 - $2.15 million
Computing Education for the 21st Century
The Computing Education for the 21st Century (CE21) program aims to build a robust computing research community, a computationally competent 21st century workforce, and a computationally empowered citizenry. In this undertaking, there are three interrelated challenges: the significant underproduction of degrees needed for the computing and computing-related workforce, the longstanding underrepresentation of many segments of our population, and the lack of a presence of computing in K-12.
Deadline: March 12, 2014
Budget: $200,000 - $10 million
Annual Call: Second Wednesday in March, annually.
Dynamical Systems
This program supports innovative research on the theories of dynamical systems, including new analytical and computational tools, as well as the novel application of dynamical systems to engineered systems. The program is especially interested in transformative research in the area of complex systems, uncertain or stochastic nonlinear dynamical systems, model order reduction of nonlinear or infinite dimensional dynamical systems, discrete nonlinear dynamical systems, and modeling, simulation, analysis and design of multi-scale multi-physics dynamical systems.
Deadline: February 15, 2014; October 1, 2014.
Budget: Not listed
Annual Call: January 15 - February 15; September 1 - October 1
EarthCube is a community-driven activity sponsored through a partnership between the NSF Directorate of Geosciences and Office of Cyberinfrastructure to transform the conduct of geosciences research and education. EarthCube aims to create a well-connected and facile environment to share data and knowledge in an open, transparent, and inclusive manner, thus accelerating the ability of the geosciences community to understand and predict the Earth system.
Deadline: March 12, 2014
Budget: Total program funding is $5 million
Exploiting Parallelism and Scalability
The Exploiting Parallelism and Scalability (XPS) program aims to support groundbreaking research leading to a new era of parallel computing. Achieving the needed breakthroughs will require a collaborative effort among researchers representing all areas-- from services and applications down to the micro-architecture-- and will be built on new concepts, theories, and foundational principles. New approaches to achieve scalable performance and usability need new abstract models and algorithms, new programming models and languages, new hardware architectures, compilers, operating systems and run-time systems, and must exploit domain and application-specific knowledge. Research is also needed on energy efficiency, communication efficiency, and on enabling the division of effort between edge devices and clouds.
Deadline: March 24, 2014.
Budget: $1 million
Innovative Technology Experiences for Students and Teachers
The ITEST program through research and model-building activities seeks to build understandings of best practice factors, contexts and processes contributing to K-12 students' motivation and participation in the science, technology, engineering, and mathematics (STEM) core domains along with other STEM cognate domains (e.g., information and communications technology (ICT), computing, computer sciences, data analytics, among others) that inform education programs and workforce domains.
Deadline: February 11, 2014.
Budget: $300,000 - $2.15 million
Operations Research
The OR program supports fundamental research leading to the creation of innovative mathematical models, analysis, and algorithms for optimal or near optimal decision-making, applicable to the design and operation of manufacturing, service, and other complex systems. In addition to the traditional areas of Operations Research which includes discrete and continuous optimization as well as stochastic modeling and analysis, new research thrusts include simulation optimization and self-optimizing systems that can observe, learn, and adapt to changing environments.
Deadline: February 15, 2014
Budget: Not listed
Annual Call: January 15 - Febrary 15 Annually; September 1 - October 1 Annually
Science, Technology and Society
STS considers proposals for scientific research into the interface between science (including engineering) or technology, and society. STS researchers use diverse methods including social science, historical, and philosophical methods. Successful proposals will be transferrable (i.e., generate results that provide insights for other scientific contexts that are suitably similar). They will produce outcomes that address pertinent problems and issues at the interface of science, technology and society, such as those having to do with practices and assumptions, ethics, values, governance, and policy.
Deadline: February 3, 2014
Funding amount: $3,000 - $180,000
Annual Call: February 1, Annually thereafter; August 1, Annually thereafter
Science of Organizations
The Science of Organizations (SoO) program funds basic research that yields a scientific evidence base for improving the design and emergence, development and deployment, and management and ultimate effectiveness of organizations of all kinds.
Deadline February 2, 2014
Budget: Total program funding is $3.27 million

Upcoming NIH Opportunities:

Modeling the Scientific Workforce
This FOA solicits cooperative agreement applications that propose to develop computational models for better understanding of the dynamics of the scientific workforce in the United States. These models may be used to inform program development and management, identify questions that need additional research, and guide the collection and analysis of the data to answer these questions.
Deadline: February 4, 2014
Budget: $250,000

Upcoming DOE Opportunities:

Scientific Data Management, Analysis and Visualization at Extreme Scale
This FOA solicits cooperative agreement applications that propose to develop computational models for better understanding of the dynamics of the scientific workforce in the United States. These models may be used to inform program development and management, identify questions that need additional research, and guide the collection and analysis of the data to answer these questions.
Deadline: April 2, 2014
Budget: $4 million per year

Other Federal Opportunities:

Biotechnology Risk Assessments Grants Program
The purpose of the BRAG program is to support the generation of new information that will assist Federal regulatory agencies in making science-based decisions about the effects of introducing into the environment genetically engineered organisms (GE), including plants, microorganisms (including fungi, bacteria, and viruses), arthropods, fish, birds, mammals and other animals excluding humans. Investigations of effects on both managed and natural environments are relevant. The BRAG program accomplishes its purpose by providing Federal regulatory agencies with scientific information relevant to regulatory issues. rapid advances in scientific areas of interest to the DoD.
Deadline: March 19, 2013. 
Budget: $25,000 - $1 million
Digital Humanities Implementation Grant
This program is designed to fund the implementation of innovative digital-humanities projects that have successfully completed a start-up phase and demonstrated their value to the field. Such projects might enhance our understanding of central problems in the humanities, raise new questions in the humanities, or develop new digital applications and approaches for use in the humanities.
Deadline: February 19, 2014
Budget: $100,000 - $325,000
Exploratory Research for Extreme-Scale Science
The Advanced Scientific Computing Research (ASCR) program of the Office of Science (SC), U.S. Department of Energy (DOE), hereby invites exploratory basic research proposals with the potential to deliver significantly advanced or improved science capabilities in light of emerging and disruptive technology changes. Desired outcomes include advances that will make massively parallel, heterogeneous computer architectures more efficient and practical to use in carrying out scientific research activities. A complementary ASCR objective is to build up the computational research infrastructure for enabling data-intensive science advances.
Deadline: February 28, 2014 
Budget: Not listed
Information innovation Office-Wide BAA
The Defense Advanced Research Projects Agency (DARPA) is soliciting innovative research proposals of interest to the Information Innovation Office (I2O). Proposed research should investigate innovative approaches that enable revolutionary advances in science, devices, or systems. Specifically excluded is research that primarily results in evolutionary improvements to the existing state of the art. I2O seeks unconventional approaches that are outside the mainstream, undertaking directions that challenge assumptions and have the potential to radically change established practice. See Full Announcement, DARPA-BAA-13-32 (I2O Office Wide) pdf for further details.
Deadline: June 25, 2014 
Budget: Not listed
National Security Science and Engineering Faculty Fellowship
The National Security Science and Engineering Faculty Fellowship (NSSEFF) program is sponsored by the Basic Research Office, Office of Assistant Secretary of Defense for Research and Engineering (ASD (R&E)). NSSEFF supports innovative basic research within academia, as well as education initiatives that seek to create and develop the next generation of scientists and engineers for the defense and national security workforce.
Deadline: March 12, 2014
Budget: Not listed

Non-Federal Opportunities:

ACS - Doctoral New Investigator Grants
Provides start-up funding for scientists and engineers in the U.S. who are within the first 3 years of their first academic appointment. DNI grants are to be used to illustrate proof of principle or concept, to test a hypothesis or demonstrate the feasibility of an approach.
Deadline: March 14, 2014
Budget: $110,000 over two years
UCLA CTSI - Funding Opportunities
In order to strengthen current research aims, UCLA Clinical and Translational Science Institute offers opportunities through assistance with grants and career openings to doctors and researchers who align themselves with the goals and methodologies of translational research. Several opportunities are currently available.
UC Research Opportunity Fund
The Office of Research and Graduate studies (ORGS) has limited funds available for the one-time support of projects. Funds are to pilot new projects that can demonstrate a strong systemwide benefit to UC research and enhance UC’s ability to compete for funding, advance research discoveries, inform public policy or otherwise impact the lives of Californians.
Winter Deadline: January 30,2014.
Budget: Typical requests should be no more than $20,000.
UCLA Office of Information Technology
Institute for Digital Research and Education
310-825-6635 I
5308 Math Sciences
Box 951557, Mail Code 155705
Los Angeles, CA 90095-1557

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