022019 Update

UPDATES

A bi-monthly newsletter with updates on data and computing news and events for UW-Madison researchers.

In the Feb. 20, 2019 update:

  • GLBIO 2019
  • Upcoming Campus Events
  • Upcoming Trainings and Workshops
  • Campus Opportunities and Groups
  • External Opportunities

Are you…

  • unsure which campus data and computing resources you need for your research?
  • interested in making connections and starting new collaborations with data scientists and other researchers on campus?
  • looking for training in data and computing skills?

The Data Science Hub can help! Send an email to the Data Science facilitator (facilitator@datascience.wisc.edu) or come by Hub Central in the Discovery Building during office hours (W 9:30-11:30, Th 3:00-5:00pm). Tomorrow’s office hours will feature representatives from across campus! Stop by to ask the experts your research computing and data science questions. Check calendar for latest details and updates.

GLBIO 2019

The International Society for Computational Biology (ISCB) Great Lakes Bioinformatics Conference will be held in Madison on May 19-22.  Sunduz Keles and Mark Craven will be keynote speakers.  There are still opportunities to submit abstracts for oral presentation or posters. For submission information, see https://www.iscb.org/glbio2019-submissions. Abstracts for oral presentations are due March 11.  Poster abstracts are due March 18 or April 15 for late breaking posters.

In addition to the main track, there will be special sessions on precision medicine, RNA biology, microbiome studies, and bioinformatics education that are accepting paper and/or abstract submissions. Please contact conference co-chairs Sushmita Roy or Tony Gitter for more information.

Upcoming Campus Events (Calendar View)

AI@UW: 6:30pm, 1240 Computer Sciences Building
Feb 20, Dr. Matthew Banks, How the Brain Updates its Representations of the World Using Predictive Coding Algorithms. Snacks will be provided!

Statistics Seminar4:00pm, 133 Service Memorial Institute (SMI)
Feb 20, Adapting Maximum Likelihood Theory in Modern Applications, Feng Ruan

Center for Demography of Health and Aging (CDHA) Training Seminar2:00pm-3:15pm, 8417 Sewell Social Science Building
Feb 20, Research Ethics Case Studies, Michal Engelman (sociology)
Feb 27, Regression Diagnostics, Mark Banghart (SSCC)
March 6, Media Relations and Communications Strategies, Veronica Rueckert and Eric Hamilton (university communications)

Systems, Information, Learning, and Optimization (SILO) Seminar12:30pm, Orchard View Room, Discovery Building
Feb 20, Safety and Robustness Guarantees with Learning in the Loop, Nikolai Matni
Feb 27, TBA, Luke Chang
March 6, TBA, Lalit Jain

Sustainable Energy Seminar Series: 4:00pm-5:00pm, Orchard View Room, Discovery Building
Feb 21, Keeping the Lights on: Modeling 100% Renewable Electricity, Michael Ferris

Computer Science Colloquium: 4:00pm-5:00pm, 1240 Computer Sciences
Feb 21, Towards Embodied Visual Intelligence
Feb 28, Rethinking the Role of Optimization in Learning
March 4,  Perceptual Engineering
March 5, Sight and Sound

Applied and Computational Mathematics Seminar (ACMS): 2:25pm, 901 Van Vleck Hall
Feb 22, Uncertainty Characterization in Model-Based Inverse and Imaging Problems, Kui Ren (UT-Austin and Columbia)
March 1, TBA, Guanghong Chen

Machine Learning for Medical Imaging (ML4MI) Initiative Seminar
Feb 28, 4:00pm, 1345 HSLC, Subspecialty-Level Differential Diagnoses by Machine on Clinical Brain MRI, Jim Gee, Penn Medicine

The Wisconsin Association for Computing Machinery – Women in Computing, March 5, 12:15pm-1:15pm, Computer Sciences 2310

Computer Science Seminar
March 6, 11:00am-12:00pm, 1240 Computer Sciences, Hardware is the New Software: Finding Exploitable Bugs in Hardware Designs,  Cynthia Sturton

Biostatistics & Medical Informatics (BMI) Seminar: 12:00pm, Biotechnology Center Auditorium
March 8, Bias and Efficiency of Model-Based Single-Arm Basket Trial Designs,  Mithat Gonen, Memorial Sloan Kettering

Computation and Informatics in Biology and Medicine (CIBM) Seminar4:00pm, 1360 Biotechnology Center
Feb. 26, TBA, Sebastian Raschka (Auditorium)
Mar. 5, TBA,  Catherine Arnott Smith, PhD

Upcoming Trainings and Workshops

CHTC Workflow Tools Workshop

We are excited to announce a Workflow Tools Workshop on Friday, February 22, from 1-4:30pm (full details here) featuring conceptual overviews and some hands-on examples. CHTC staff will introduce the workshop, with training delivered in collaboration with CHTC’s long-time HTC partners from the Cooperative Computing Lab at the University of Notre-Dame, who develop theMakeflow and Work Queue tools for workflow execution. These tools are especially useful for job batches with widely varying memory and disk requirements or varying job durations, and workflows with many separate job steps, among other advantages.

Those interested in attending are asked to REGISTER FOR THE WORKSHOP, so that we can make sure to have enough seats. You are welcome to bring a laptop if you would like to participate in the hands-one examples (will also need an active CHTC account on our HTC System), though doing so is not a requirement. Please send any questions to chtc@cs.wisc.edu.

Library Research Data Management Micro-courses

UW-Madison Libraries have put together micro-courses to help researchers getting started managing their data.  Find them all here on the library mini-course webpage. Courses are available for anyone to take and include:

  • Introduction to Research Data Management – This micro-course covers the reasons to invest time and effort into good data management and then introduces best practices that you can start building into your research process immediately.
  • Responsible Data Planning, Use, and Sharing – This micro-course provides an introduction to the current landscape of policies and regulations regarding data that informs working responsibly with research data, and then discusses developing plans for data management and data sharing.
  • Research Data Management Life Cycle – an interactive tool to explore the stages of the research data management life cycle. Users can explore the 10 stages of the data life cycle and learn about the process of each stage. (Note: this tool is also a part of the Introduction to Research Data Management micro-course mentioned above).

Campus Opportunities and Groups

PyTroll Contributor Week Meeting 

The PyTroll open source python programming group is hosting their week long developer meeting in Madison this spring (May 13th – 17th) at the Pyle Center. Each day attendees work together to fix bugs and add new features to PyTroll tools like SatPy, a library for working with earth-observing satellite data. Those new to PyTroll tools can spend the time adding the tools to their existing workflows. Everyone is welcome. Registration is free but required.

Environmental Data Initiative (EDI) Fellowships

The Environmental Data Initiative (EDI) has ten fellowships available in its ecological data management training program for Summer 2019. The fellowships are intended for undergraduate, graduate and recent postgraduate students. The duration of the fellowship training program is June 10 – August 9, 2019 and requires full-time commitment to the training activities. The fellowship support of $5000 will be administered through the University of Wisconsin-Madison, except for the fellowship with the TERRA_REF project, which will be administered through the University of Arizona. The fellows will receive training in ecological data management and gain hands-on experience through participation in data preparation, archiving and publishing with scientists and information managers at specific host research sites.  Find out more on the program website.

researchERS (Emerging Research Scholars) Program

Free program for UW-Madison undergraduate students featuring a series of evening meetings (food provided) and field trips related to current practices for managing the data used in research projects or lab research in any discipline.  Find more information and the schedule on the program webpage.

Digital Scholarship & Publishing Office Hours

Do you have a publication or copyright question? Do you have questions about a digital humanities tool you’ve seen or about a new project and want to start with good data management? If so, consider dropping by the weekly Digital Scholarship & Publishing Office Hours, Thursdays, 11:30 am – 1:30 pm!  Location alternates between Memorial Library and Steenbock, check the website for the latest information and location. Experts can provide assistance with (but not limited to!) the following:

  • Publishing methods, platforms
  • Copyright, author’s rights, fair use
  • Digital humanities projects
  • Selecting or applying tools, platforms
  • Developing and planning digital projects
  • Data management and sharing

Computational Biology, Ecology, and Evolution (ComBEE)

ComBEE is a group of researchers at UW-Madison interested in computational biology in ecology and evolution. ComBEE offers R, Python, and Julia study groups throughout the semester.  Checkout their website and sign up for their email lists for more information.

Molecular Dynamics Group
Molecular dynamics (MD) simulations can provide a computational microscope for looking at molecular events. However, the art of setting up, running, and interpreting a simulation is challenging. To help, campus MD users and potential users are getting together to share experiences, tools, and codes. Importantly, the group will also discuss best practices, appropriate/inappropriate uses, and how best to use local computer resources. Contact Spencer Ericksen (ssericksen@wisc.edu) if you are interested in joining the group.

Research Systems Administrators Group (RSAG)
This ACI-sponsored group meets on the third Wednesdays of every month and allows systems administrators of research systems to share expertise. Join the email list by sending an email message to join-rsag@lists.wisc.edu for updates and future meetings.

External Opportunities

Microsoft Dissertation Grants

Microsoft recognizes the value of diversity in computing. The Microsoft Research Dissertation Grant aims to increase the pipeline of diverse talent receiving advanced degrees in computing-related fields by providing a research funding opportunity for doctoral students who are underrepresented in the field of computing, which include those who self-identify as a woman, African American, Black, Hispanic, Latinx, American Indian, Alaska Native, Native Hawaiian, Pacific Islander, and/or people with disabilities. The 2019 Microsoft Research Dissertation Grant application period closes on Sunday, March 31, 2019, at 5:00 PM Pacific Time. Additional Details and Submission Instructions can be found on their website.

Data Science and Bayesian Learning

On February 22, the Lubar School of Business will be hosting a series of seminars from 10:30-12:00 in Lubar Hall (S341) related to Data Science and Bayesian Learning. There will be two speakers, Dr. Nicholas Polson and Refik Soyer.

  • Bayesian Decisions via Deep Reinforcement Learning,  Nicholas Polson, Robert Law, Jr. Professor of Econometrics and Statistics, University of Chicago Booth School
  • A Bayesian Competing Risk Model for Assessment of Mortgage Default/Prepayment, Refik Soyer, Mitch Blaser Distinguished Scholar in Business Analytics, George Washington University

2019 Data Science Innovation Lab

The BD2K Training Coordinating Center (BD2K TCC) is organizing a Data Science Innovation Lab to foster the development of new interdisciplinary teams via a facilitated and mentored format to tackle the challenges associated with the analysis, modeling, and visualization of large-scale data sets associated with the biomedicine of rural health and environmental exposures. The BD2K TCC is looking for rural and environmental health scientists, as well as data scientists, interested in forming teams around joint projects and a view toward future NIH grant applications. Deadline to submit applications is Sunday, March 10, 2019. Find out more here.

GOBLET

The Global Organization for Bioinformatics Learning, Education and Training (GOBLET), is a legally registered foundation. Its mission is to cultivate the global bioinformatics trainer community, set standards and provide high-quality resources to support learning, education and training. The GOBLET Training Portal allows you to browse the course pages and training materials, to download content of interest and/or to upload course pages and training materials. If you would like to contribute your training resources, please create an account, or become a member and join GOBLET!

First Midwest Student Conference: Geometry and Topology Meet Data Analysis and Machine Learning

The goal of this new student conference is to gather graduate students to share their research work in applications of Geometry and Topology to Data Analysis and Machine Learning. Held at The Ohio State University (June 1-2, 2019), the aim is to build bridges between academic institutions in the Midwest region, and to enhance discussion and collaboration via poster sessions, short presentations, and discussion panels. A plenary lecture will be delivered by a senior researcher in the field.  Information aboutregistration and abstract/poster submission details will be available soon.  If you have questions, please contact Nicholas Garcia Trillos.

SESYNC

The National Socio-Environmental Synthesis Center (SESYNC) invites applications to a short course on data and coding skills for socio-environmental synthesis. The 6th annual Summer Institute will be held July 23 (optionally 22) through 26 at SESYNC in Annapolis, Maryland. The short course will combine lectures, hands-on computer labs, and project consultation designed to accelerate the adoption of cyber resources for all phases of data-driven research and dissemination.  Apply on the program website by April 19, 2019

Check calendar for latest details and updates for all listed events. If you have a relevant event or group you’d like to see included in next month’s newsletter.  Please send us an email at facilitator@datascience.wisc.edu.