Internet2 Bio IT 2016 v2

Briefing to The Quilt Visit to Calit2’s Qualcomm Institute University of California, San Diego February 10, 2016

Keynote Presentation NSF Workshop on Applications and Services in 2021 Washington, DC January 28, 2016

The Pacific Research Platform will create a regional "Big Data Freeway System" along the West Coast to support science. It will connect major research institutions with high-speed optical networks, allowing them to share vast amounts of data and computational resources. This will enable new forms of collaborative, data-intensive research for fields like particle physics, astronomy, biomedicine, and earth sciences. The first phase aims to establish a basic networked infrastructure, with later phases advancing capabilities to 100Gbps and beyond with security and distributed technologies.

Opening Keynote Lecture 15th Annual ON*VECTOR International Photonics Workshop Calit2’s Qualcomm Institute University of California, San Diego February 29, 2016

Invited presentation by Calit2 Director Larry Smarr to the UC IT Leadership Council in Oakland, Calif., on May 19, 2014.

The document summarizes Dr. Larry Smarr's presentation on building the Pacific Research Platform (PRP) to enable big data science across research universities on the West Coast. The PRP provides 100-1000 times more bandwidth than today's internet to support research fields from particle physics to climate change. In under 2 years, the prototype PRP has connected researchers and datasets across California through optical networks and is now expanding nationally and globally. The next steps involve adding machine learning capabilities to the PRP through GPU clusters to enable new discoveries from massive datasets.

The Pacific Research Platform (PRP) is a high-bandwidth global private "cloud" connected to commercial clouds that provides researchers with distributed computing resources. It links Science DMZs at universities across California and beyond using a high-performance network. The PRP utilizes Data Transfer Nodes called FIONAs to transfer data at near full network speeds. It has adopted Kubernetes to orchestrate software containers across its resources. The PRP provides petabytes of distributed storage and hundreds of GPUs for machine learning. It allows researchers to perform data-intensive science across multiple universities much faster than possible individually.

Cyberenvironments integrate shared and custom cyberinfrastructure resources into a process-oriented framework to support scientific communities and allow researchers to focus on their work rather than managing infrastructure. They enable more complex multi-disciplinary challenges to be tackled through enhanced knowledge production and application. Key challenges include coordinating distributed resources and users without centralization and evolving systems rapidly to keep pace with advancing science.

The document provides an overview of the development of the NIH Data Commons. It discusses factors driving the need for a data commons, including large amounts of data being generated and increased support for data sharing. It outlines the goals of making data findable, accessible, interoperable and reusable. Several pilots are exploring the feasibility of the commons framework, including placing large datasets in the cloud and developing indexing methods. Considerations in fully realizing the commons are also discussed, such as standards, discoverability, policies and incentives.

This document discusses the development of the NIH Data Commons, which aims to create a shared framework and infrastructure for biomedical data. It notes the increasing amounts of data being generated and the need for data sharing and interoperability. The Data Commons framework treats data, tools, and publications as digital objects that are findable, accessible, interoperable and reusable. Current pilots include deploying reference datasets in the cloud, indexing data and tools, and a credits system for cloud resources. Challenges discussed include metrics, costs, standards, incentives and sustainability. The framework's relevance for supporting open data in Australia is also addressed.

The document discusses the benefits of exercise for mental health. Regular physical activity can help reduce anxiety and depression and improve mood and cognitive functioning. Exercise boosts blood flow, releases endorphins, and promotes changes in the brain which help regulate emotions and stress levels.

The Pacific Research Platform (PRP) connects research institutions across the western United States with high-speed networks to enable data-intensive science collaborations. Key points: - The PRP connects 15 campuses across California and links to the Great Plains Network, allowing researchers to access remote supercomputers, share large datasets, and collaborate on projects like analyzing data from the Large Hadron Collider. - The PRP utilizes Science DMZ architectures with dedicated data transfer nodes called FIONAs to achieve high-speed transfer of large files. Kubernetes is used to manage distributed storage and computing resources. - Early applications include distributed climate modeling, wildfire science, plankton imaging, and cancer genomics. The PR

The document discusses the vision and progress of the Pacific Research Platform (PRP) in creating a "big data freeway" across the West Coast to enable data-intensive science. It outlines how the PRP builds on previous NSF and DOE networking investments to provide dedicated high-performance computing resources, like GPU clusters and Jupyter hubs, connected by high-speed networks at multiple universities. Several science driver teams are highlighted, including particle physics, astronomy, microbiology, earth sciences, and visualization, that will leverage PRP resources for large-scale collaborative data analysis projects.

Cybersecurity Engagement in a Research Environment Workshop Rady School of Management, UC San Diego December 5, 2019

This document provides an overview of the development of national research platforms (NRPs) from 1985 to the present, with a focus on the Pacific Research Platform (PRP). It describes the evolution of the PRP from early NSF-funded supercomputing centers to today's distributed cyberinfrastructure utilizing optical networking, containers, Kubernetes, and distributed storage. The PRP now connects over 15 universities across the US and internationally to enable data-intensive science and machine learning applications across multiple domains. Going forward, the document discusses plans to further integrate regional networks and partner with new NSF-funded initiatives to develop the next generation of NRPs through 2025.

Science Gateways Community Institute presentation on a panel at the Earth Science Information Partners summer 2018 meeting.

In this deck from PASC18, David Bader from Georgia Tech presents: Massive-Scale Analytics Applied to Real-World Problems. "Emerging real-world graph problems include: detecting and preventing disease in human populations; revealing community structure in large social networks; and improving the resilience of the electric power grid. Unlike traditional applications in computational science and engineering, solving these social problems at scale often raises new challenges because of the sparsity and lack of locality in the data, the need for research on scalable algorithms and development of frameworks for solving these real-world problems on high performance computers, and for improved models that capture the noise and bias inherent in the torrential data streams. In this talk, Bader will discuss the opportunities and challenges in massive data-intensive computing for applications in social sciences, physical sciences, and engineering." Watch the video: https://wp.me/p3RLHQ-iPk Learn more: https://pasc18.pasc-conference.org/ Sign up for our insideHPC Newsletter: http://insidehpc.com/newsletter

Talk at DOE CIO's Big Data Tech Summit -- latest take on why and wherefore of software as a service (SaaS) for science, and the Globus Online work we are doing, with various DOE examples.

The Clinical Decision Support Consortium aims to advance clinical decision support through several research projects. The Consortium will assess, define, demonstrate, and evaluate best practices for clinical decision support across multiple healthcare settings and electronic health record platforms. Several research teams will focus on knowledge management, clinical guideline translation, decision support content development and delivery, and evaluating demonstrations of decision support. The goal is to improve healthcare quality by facilitating widespread use of evidence-based clinical decision support.

This document summarizes a presentation about providing next-generation sequencing analysis capabilities using Globus Genomics. It outlines challenges with current manual approaches to sequencing data analysis, including difficulties moving large datasets between locations and maintaining complex analysis scripts. The presentation introduces Globus Genomics, which uses Globus data transfer services integrated with Galaxy to provide a workflow-based system for sequencing analysis without requiring local installation or configuration. Key benefits include on-demand access to scalable cloud resources, ability to easily modify and reuse analysis workflows, and integration with data sources. The system aims to accelerate genomic research by automating and simplifying analysis.

1) Globus Genomics addresses challenges in sequencing analysis by providing a platform that integrates data transfer via Globus Online, workflow management in Galaxy, and scalable compute resources in AWS. 2) An example collaboration with the Dobyns Lab saw over a 10x speedup in exome data analysis by replacing a manual process with Globus Genomics. 3) Globus Genomics leverages XSEDE services like Globus Transfer and Nexus while integrating additional resources like sequencing centers and cloud computing, in order to reduce the costs and complexities of genomic research for communities not traditionally using advanced cyberinfrastructure.

This poster is prepared for the upcoming BD2K All hands meeting. We present the BDDS Knowledge Discovery platform as applied to understanding the role of amyloid burden in Alzheimers and Parkisons.

Globus Genomics provides tools and services to help researchers manage and analyze large genomic datasets. It uses Globus data management tools to securely transfer data between institutions. Researchers can then run analysis workflows on cloud compute resources through Galaxy interfaces. This enables researchers to assemble diverse datasets, apply multiple computational models, and publish results for others to discover, validate, and reuse. Examples show researchers using Globus Genomics to process petabytes of sequencing data and perform genome-wide analysis across many institutions. The goal is to accelerate scientific discovery by making it easier for researchers to find "needles in haystacks" through data-intensive computational approaches.

Presentation offered at http://www.smartiotlondon.com/2016-seminar-programme/big-data-and-genomics-the-future-of-genetic-engineering Bioinformatics: the marriage of biology and Big Data, and how this will change the way we perform genetic engineering. This presentation explain our company (Alkol Biotech) compares DNA strands, focusing on its development of the “EunergyCane” sugarcane crop: Europe’s only sugarcane variety. It explain the tools the company uses such as Big Data, Machine Learning, and Fast Sequencing. Learning Outcomes: 1 – Learn on the new field of “Bioinformatics”, which is the marriage of IT and biology 2 – Learn how Big Data is changing the game on genetic engineering 3 – Learn what are the tools used and expected results

This is the presentation given to the HL7 Clinical Interoperability Council on Clinical Decision Suppoprt (referenced in the post below), April, 2009.

The document summarizes the ADAS&ME project which aims to develop advanced driver assistance systems that can automatically transfer control between the vehicle and driver based on the driver's state and environmental context. The project has a budget of 9.5 million euros over 42 months and involves companies and research institutions developing technologies like high-definition maps, vehicle connectivity, and systems for monitoring driver state and handling non-reactive drivers. Several use cases are outlined focusing on commercial vehicles and motorcycles, with scenarios presented for smooth transitions between automated and manual driving and handling emergencies if the driver does not respond.

The document discusses effective ways to use Ansible including setting up passwordless SSH authentication, limiting playbooks to single machines, managing private keys, using roles for scalability, and tuning Ansible for performance. The objective is to deploy Kubernetes from scratch with one command using best practices for Ansible configuration, authentication, and organization.

This document summarizes a presentation about Globus Genomics, a service that provides genomic data analysis tools and workflows through a web interface. It allows users to securely transfer data, run standardized analysis pipelines, access computational resources on demand through Amazon Web Services, and collaborate on shared data and workflows. The service aims to make genomic analysis more accessible, reproducible, and sustainable through various pricing models and support for individual labs and bioinformatics cores.

This document summarizes Senator Barack Obama's health policy plan, which focuses on achieving universal health care coverage, health care reform, and strengthening public health. It outlines some of the key problems in the current US healthcare system from the perspectives of providers, purchasers, and consumers. Obama's plan would invest in health information technology and reform reimbursement to align with quality. The plan is estimated to cost $50-65 billion annually but could save $120-200 billion through reduced administrative costs, improved disease management, and health IT savings. If implemented, it could lower family insurance costs by $2,500 and cover 10 million more people.

This document provides an overview of Apache Sqoop and discusses the transition from Sqoop 1 to Sqoop 2. Sqoop is a tool for transferring data between relational databases and Hadoop. Sqoop 1 was connector-based and had challenges around usability and security. Sqoop 2 addresses these with a new architecture separating connections from jobs, centralized metadata management, and role-based security for database access. Sqoop 2 is the primary focus of ongoing development to improve ease of use, extensibility, and security of data transfers with Hadoop.

Ramesh Raskar MIT Media Lab Ramesh Raskar is an Associate Professor at MIT Media Lab. Ramesh Raskar joined the Media Lab from Mitsubishi Electric Research Laboratories in 2008 as head of the Lab’s Camera Culture research group. His research interests span the fields of computational photography, inverse problems in imaging and human-computer interaction. Recent projects and inventions include transient imaging to look around a corner, a next generation CAT-Scan machine, imperceptible markers for motion capture (Prakash), long distance barcodes (Bokode), touch+hover 3D interaction displays (BiDi screen), low-cost eye care devices (Netra,Catra), new theoretical models to augment light fields (ALF) to represent wave phenomena and algebraic rank constraints for 3D displays(HR3D). In 2004, Raskar received the TR100 Award from Technology Review, which recognizes top young innovators under the age of 35, and in 2003, the Global Indus Technovator Award, instituted at MIT to recognize the top 20 Indian technology innovators worldwide. In 2009, he was awarded a Sloan Research Fellowship. In 2010, he received the Darpa Young Faculty award. Other awards include Marr Prize honorable mention 2009, LAUNCH Health Innovation Award, presented by NASA, USAID, US State Dept and NIKE, 2010, Vodafone Wireless Innovation Project Award (first place), 2011. He holds over 50 US patents and has received four Mitsubishi Electric Invention Awards. He is currently co-authoring a book on Computational Photography.

This document provides an overview of the Leap Motion controller and its capabilities for tracking hand gestures and finger positions. It explains how to set up a basic Leap Motion application using a 2D canvas, initialize the Leap controller, and include an animation loop to continuously draw hand tracking data. Examples are given for visualizing the Leap geometric system, common gestures like swipes and taps, and hand parameters using online code snippets and demos.

This document discusses various types of 3D displays. It begins with an overview of depth cues that can be presented to the human visual system, both monocular cues like size and occlusion, as well as binocular cues like retinal disparity and convergence. The document then presents a taxonomy of 3D display technologies, categorizing them as either glasses-bound or unencumbered designs. Specific display types are described in more detail, including head-mounted displays, spatial and temporal multiplexing, parallax barriers, integral imaging, and volumetric and holographic displays. Multi-view rendering techniques for generating stereoscopic images are also covered, such as using OpenGL for anaglyph generation and off-axis perspective projection.

'Media' is a plural for medium. The medium for impact of digital technologies at MIT Media Lab can be photons, electrons, neurons, atoms, cells, musical notes and more. Over the last 40 years, computing has moved from processor, network, social and more sensory. MIT Media Lab works at the intersection of computing and such media for human-centric technologies.

This document provides an overview of the pipeline for multiview computer vision. It describes taking multiple photographs, detecting and matching features between images, estimating homographies to relate the images, generating blended intermediate frames, and creating a video from the sequence of frames. It also provides details on steps like feature detection and description, matching features, estimating homographies, image blending, and writing video files.

Glass contains a 1 GHz processor, 16GB storage, 512MB RAM, GPS, Bluetooth, WiFi, 5MP camera, bone conduction speaker, gyroscope, accelerometer, and 640x360 display. It detects blinks and winks using a proximity sensor and IR emitter/receiver near the right eye. Developers can build apps using the Mirror API or by sideloading Android APKs that utilize Glass-specific APIs. The documentation provides examples of building simple apps.

What is SIGGRAPH NEXT? By Juliet Fiss What will be the next big thing at SIGGRAPH, and how can the SIGGRAPH community contribute in an impactful way to fields outside of traditional computer graphics? SIGGRAPH NEXT at SIGGRAPH 2015 explored these questions. In this new addition to the SIGGRAPH program, an eclectic set of speakers gave TED-style talks and posed grand challenges to the SIGGRAPH community. In this blog post, Professor Ramesh Raskar of the MIT Media Lab introduces SIGGRAPH NEXT and outlines his vision for it. What will be the next big thing at SIGGRAPH? The SIGGRAPH community has a set of hammers that it uses to solve problems: geometry processing, rendering, animation, and imaging. What will be the next hammer, the next major field of study, appear at SIGGRAPH? Let’s examine where our research ideas come from. Often, advances in machine learning, optimization, signal processing, and optics forge our hammers. Our selection of hammer also depends on the nails we see. The most common application areas of computer graphics currently include computer-aided design, movies, games, and photography. We often ask: “Does this work contribute to SIGGRAPH techniques?” We should also ask, “Does this work contribute SIGGRAPH techniques to _____?” When we answer the challenges posed by these traditional application areas of computer graphics, we are “drinking our own champagne.” We have made amazing progress in these application areas, and we should celebrate! SIGGRAPH NEXT is about finding new varieties of champagne; for that, we need new varieties of grapes. We should invite others from nontraditional and emerging application areas to enjoy our champagne with us, and they will become part of our community. First, we can expand our work in existing areas like mobile, user interaction, virtual reality, fabrication, and new types of cameras. We can also expand into emerging areas such as healthcare, energy, education, entrepreneurship, materials, tissue fabrication, and social media. What’s next? Professor Raskar highlights three top areas where we can make an impact. One big take-home message is that many of these applications involve biology: bio is the new digital, and it will affect us ubiquitously.

Panel Presentation CENIC Annual Conference University of California, Irvine - Irvine, CA March 9, 2015

Keynote Presentation, CineGrid International Workshop 2015, Calit2’s Qualcomm Institute, University of California, San Diego December 11, 2015

BeSTGRID aims to enhance research capability in New Zealand by providing skills and infrastructure to help researchers engage with new eResearch services and kick start centralized infrastructure. Since 2006, BeSTGRID has delivered services and tools to support research collaboration on shared datasets and computational resources. BeSTGRID coordinates access to compute and data resources, provides discipline-specific services and applications, and builds a sustainable community to develop middleware, applications, and services.

The document summarizes the Safe Share project, which aims to enable the secure exchange of health data between research sites for medical research. It establishes a higher assurance network using encrypted overlays between network nodes. It also explores implementing an authentication, authorization and accounting infrastructure to allow researchers to access data and systems using their home institution credentials. Several pilot programs are underway to test the network and authentication capabilities. The overall goal is to accelerate medical research while maintaining strict security and privacy of sensitive health data.

Panel Presentation Larry Smarr and Grant Scott MOREnet 2022 Annual Conference October 19, 2022