markquyn derrun kafflyn
Silvina Spindler
Presented by: John Ringland
Format: Workshop
A hands-on introduction to Python and the Jupyter Notebook for those with experience programming in other languages. The instructor will show a wide variety of applications. Participants must bring a laptop with an up-to-date installation of the Anaconda distribution of Python 3.
Presented by: Dane Taylor
Pre-Keynote Address
Complex networks are a natural representation for datasets describing biological, social and information systems, and it is common practice to gain insights by studying structural patterns in these networks. Two popular examples include centrality analysis (whereby one ranks different parts of the network according to their relative importance) and community detection (whereby one seeks to find clusters). In this talk, I will discuss extensions of these pursuits for multilayer networks that consist of network layers encoding different types of connections, such as categorical social ties (friendships, colleagues, etc.) or a network at different instances in time. I will introduce new methodologies and explore their application to diverse datasets such as the United States Ph.D. exchange in mathematics, co-starring relationships among top-billed actors during the Golden Age of Hollywood, citations between decisions from the United States Supreme Court, and data-fusion for the Human Microbiome Project. I will also highlight how mathematical theory development can improve our understanding of these endeavors, which helps close the gap between the popular heuristics in place and the development of theory-supported methods derived from first principles in mathematics and statistics.
Presented by: Lang Li
Keynote Address
Pharmacoinformatics drives a new era of translational biomedical research. It translates drug effects from epidemiological discoveries in the health record data to their pharmacology mechanisms through pre-clinical experiments and vice versa. Our pioneer pharmacoinformatics research successfully tested and validated that simvastatin and loratadine interaction had increased myopathy risk in both Indiana Network of Patient Care (INPC) database and Federal Adverse Events Reporting System (FAERS). We further demonstrated that their pharmacodynamics interaction mechanism in the rat myocytes. Recently, we successfully validated the epidemiological evidence for an increased risk of myopathy via the three-drug interaction among omeprazole, fluconazole, and clonidine. We then corroborated the pharmacokinetics model by showing that the tri-drug interaction is due to the increased omeprazole drug exposure through inhibiting its CYP3A and CYP2C19 metabolism pathways by fluconazole and clonidine. Using these examples, we will demonstrate that the innovative pharmacoinformatics research is built upon the synergies among informatics, pharmaco-epidemiology, statistics, computer science, pharmacometrics, and system pharmacology. Dr Li will also highlight some new pharmacoinformatics research areas, and their translational impacts.
Presented by: Joana Gaia
Format: Workshop
As data collection has increased exponentially, so has the need for people skilled at using and interacting with data. Some of the skills needed to interact with data include being able to communicate with database systems. Database systems use their own language to communicate: SQL. This course is designed to give an overview of the fundamentals of SQL and working with data. This course starts with the basics and assumes no prior knowledge or skills in SQL. In addition to setting this foundation, this workshop will also discuss methods to create tables, move data into them, filter that data or combine it with even more data.
Presented by: Roger Ghanem
Keynote Address - refreshments served
Increasingly, critical decisions are demanded for situations where likelihoods are not sufficiently constrained by models. This could be caused by the lack of suitable mathematical models or the inability to compute the behavior of these models, or observe the associated physical phenomena, under a sufficient number of operating conditions. In many of these situations, the criticality of the decisions is manifested by the need to make inferences on high consequence events, which are typically rare. The setting is thus one of characterizing extreme events when useful models are lacking, computational models are expensive, or empirical evidence is sparse. We have found adaptation and learning to provide transformative capabilities in all of these settings. A key observation is that models and parameters are typically associated with comprehensive constraints that impose conservation laws over space and time, whose solution yields spatio-temporal fields, and that require comprehensive calibration with exhaustive data. Decisions typically depend on quantities of interest (QoI) that are agnostic to this complexity and that are constructed through an aggregation process over space, time, or behaviors. A regularization is thus imposed by allowing the QoIs to drive the complexity of the problem. But then one has to learn the QoIs. This talk will describe recent procedures for probabilistic learning of QoIs on diffusion manifolds. TRhe method is demonstrated to problems in science and engineering where models are either too expensive to compute or too inconclusive to provide acceptable interpolation to data. Probabilistic inferences are then possible as required by risk assessment and probabilistic-based design.
Presented by: Shawn Matott
Format: Workshop
CCR OnDemand is a convenient web portal for accessing all aspects of UB's high performance computing resources. The easy-to-use interface allows users to upload and download files, create, edit, submit, and monitor jobs, run GUI applications, and connect via SSH. And this can all be done via a web broswer, with no client software to install and configure. The presentation will demonstrate some of the unique features of CCR OnDemand and compare it with alternative approaches that can require installing and using a variety of disparate programs like Putty, FileZilla, XMing, VNC, etc. Participants who wish to follow along with the workshop demos should bring a laptop and register for a CCR user account - see ccr.buffalo.edu/support/ccr-help/accounts.html
Presented by: Oliver Kreylos
Format: Workshop
Immersive visualization using virtual reality (VR) display technology offers tremendous benefits for the visual analysis of complex three-dimensional data like those commonly obtained from geophysical and geological observations and models. Unlike "traditional" visualization, which has to project 3D data onto a 2D screen for display, VR can side-step this projection and display 3D data directly, in a pseudo-holographic (head-tracked stereoscopic) form, and does therefore not suffer the distortions of relative positions, sizes, distances, and angles that are inherent in 2D projection. As a result, researchers can apply their spatial reasoning skills to virtual data in the same way they can to real objects or environments.
This workshop will present VR methods for data analysis that have been developed at the UC Davis W.M. Keck Center for Active Visualization in the Earth Sciences (KeckCAVES), and will focus on low-cost commodity VR display systems such as the HTC Vive VR headset.
Presented by: Paul Bauman and Matt Knepley
Format: Workshop
Computational science is now dependent on a shared software infrastructure which enables the use of cutting edge hardware, optimal algorithms, and sophisticated data analysis and visualization strategies. In this tutorial, we will enable students to use the Git system for version control (including a useful policy layer), configuration and build tools, and the LaTeX documentation system
Presented by: Bina Ramamurthy
Format: Workshop
We will work on problem solving and programming on the Ethereum blockchain. This tutorial will focus on (i) Smart contract development using Solidity language and on Remix Integrated Development Environment (IDE) and (ii) Decentralized Application (Dapp) development using Truffle IDE. You will work on a virtual machine image preloaded with the required software. Remix is a web IDE.
Presented by: Margarete Jadamec
Format: Presentation
In the Earth Sciences, the modeling of tectonic plate boundaries has traditionally been approached through parameter sweeps on generalized problems or global representations at coarse resolution. Advances in high performance computing and access to large data volumes define a new computational landscape, within which the next generation of fluid dynamics simulations of solid state deformation in the Earth can be both formulated and run. Here I present the first three-dimensional configuration of the Alaska tectonic plate boundary, the site of the tallest mountain in North America (Denali), the second largest recorded earthquake (Great Alaska Earthquake), and anomalous volcanic edifices (the Wrangell volcanics). The data-assimilated three-dimensional configuration is used in large-scale numerical simulations of non-linear viscous flow of the Alaska plate boundary, comprised of over 400 million unknowns and over 20,000 CPU hours per simulation. By constructing the detailed model of this kind, we provide the first comprehensive model for the mechanisms generating Denali, the Great Alaska Earthquake, and the Wrangell volcanics, explained in a self-consistent model. As we move into the frontier of Exascale computing, 3D immersive visualization plays an increasingly important role. Examples of the critical role 3D immersive virtual reality can play in leveraging high-performance computing for scientific discovery are also shown.
Presented by: Robert Harrison
Keynote Address - refreshments served
As we progress towards and beyond exa-scale computation, disruptive changes are causing many people to question whether our current approaches to developing software for science and engineering are sustainable. In particular, can we deliver to the world the full benefits expected from high-performance simulation? Or is innovative science being stifled by the increasing complexities of all aspects of our problem space (rapidly changing hardware, software, multidisciplinary physics, etc.)?