041719 Update


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

In the April 17, 2019 update:

  • Go Exponential 2019
  • Upcoming Campus Events
  • Upcoming Training 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 3:00-5:00 P.M.). This Thursday’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.

Go Exponential 2019: 10x Single Cell Technology Day at UW-Madison.

Whether you want to overcome the limitations of current short-read technology, dissect cell-type differences, or investigate the adaptive immune system, the Chromium System 10x Genomics is the answer. Study phased structural variants with the long-range information obtained through the power of Linked Reads, characterize and profile from hundreds to tens of thousand of single cells, or build new genome assemblies. Learn how to enhance your biological discoveries with our genomics and high-throughput single cell transcriptomics products and explore our newest single cell technologies.

Featured Speakers:

  • Keith Cockrum, Technical Sales Specialist, 10x Genomics- “Single Cell Solutions for Genomics, Transcriptomics, and Epigenomics”
  • Krishanu Saha, PhD, Assistant Professor, Department of Biomedical Engineering & Wisconsin Institute for Discovery, UW-Madison- “Probing travnscriptional responses to genome editing at the single cell level”
  • Dagna Sheerar, SCYM(ASCP), UWCCC Flow Cytometry Lab Manager, UW-Madison- “Flow Cytometry in the Single Cell Genomics Pipeline”
  • Claire White, Sequencing Sales Specialist, Illumina – “NovaSeq 6000: Overview and Introduction to Pilot Program”

This free event takes place on Thursday, April 18 from 10:00am-12:00pm in UWBC Auditorium. Register here.

Upcoming Campus Events (Calendar View)

Center for Demography of Health and Aging (CDHA) Training Seminar, 2:00pm-3:15pm, 8417 Sewell Social Science Building
April 17, 
Introducing the UW Survey Center, Nora Cate Schaeffer
April 24, Embodying Landscapes of Violence: Impacts of Conflict- and Displacement-related Stressors on Women’s Health at the Thai-Burma Border, Stephanie Koning
May 1, Information Design and Presentation Best Practices, James R. Carey (Davis)

Systems, Information, Learning, and Optimization (SILO) Seminar, 12:30pm-1:30pm, Orchard View Room, Discovery Building
April 17, Data-Driven Discovery and Control of Complex Systems: Uncovering Interpretable and Generalizable Nonlinear Models, Steven L. Brunton (University of Washington)
April 24, TBA, Guillermo Saipro
May 1, TBA, Güzin Bayraksan

Statistics Seminar, 4:00 P.M. 140 Bardeen
April 17, Modified Multidimensional Scaling, Qiang Sun
April 24, Object Oriented Data Analysis with Applications to Neuroimaging Studies, Dehan Kong

Applied and Computational Mathematics Seminar (ACMS), 2:25pm-3:25 PM, 901 Van Vleck
April 19, Strategies for Extreme Event Quantification in Intermittent Dynamical Systems, Mustafa Mohamad (NYU/ Courant)
April 26, The Random Batch Method and Its Application to Sampling, Lei Li (Shanghai Jiao Tong University)
May 3, 2-D Strokes Immersed Boundary Problem and its Regularizations: Well-posedness, Singular Limit, and Error Estimates. Jiajun Tong (UCLA)


Biostatistics & Medical Informatics (BMI) Seminar:  Biotechnology Center Auditorium
April 19, 12:00pm-1:00pm,​ A Two-Part Model for Individualized Treatment Rule Estimation with Semi-Continuous Outcomes, Guanhua Chen
April 26, 10:15pm-11:15pm, Practical and Challenging Issues in Regulatory Science, Shein-Chung Chow (Duke)

Computation and Informatics in Biology and Medicine (CIBM) Seminar: 4:00 PM-5:00 PM, 1360 Biotechnology Center 
April 23, TBA, David R. Bell
April 30, TBA, Deborah Chasman

AI@UW: 6:30pm, 1240 Computer Sciences Building
April 24, Do People Teach Others As If They Are Reinforcement Learners, Joe Austerweil

Machine Learning for Medical Imaging (ML4MI) Initiative Seminar
April 24, 4:00pm, F2/401 Juhl Conference Room, CSC, Computer Vision and Data Science Transforming (Develop) Mental Health and Deep Brain Stimulation, Guillermo Saipro (Duke Professor of Electrical and Computer Engineering)

The Wisconsin Association for Computing Machinery – Women in Computing, 5:30pm-7:30pm, Memorial Union Terrace
April 25, WACM’s End of the Year Ice Cream Social, Please RSVP.

Computer Science Colloquium: 4:00pm-5:10pm, 1240 Computer Sciences
April 29, Made to Order: Verifying Correctness and Security of Hardware through Event Orderings


Upcoming Training and Workshops

Next Generation Data Analysis Workshop 
The Bioinformatics Resource Core (BRC) at the UW Biotechnology Center (UWBC) is offering Next-Generation Sequencing (NGS) Data Analysis skills with open-source software on a  Linux platform. Workshops are heavily hands-on. Seats are limited (Max: 8-12 participants depending on workshop).

  • mRNA-SeqMonday, 4/22/19 (1360 Biotech Center)

Keys to a Successful Data Management Plan
As more funders require data management plans on grant applications, writing and following an effective DMP is critical to research success. Clare Michaud and Morgan Witte will introduce the components of a strong DMP – with an emphasis on the guidelines for the NSF’s research directorates – and demonstrate how to use DMPTool online to create data management plans that meet institutional and funder requirements.  April 24, 12:00-1:00 P.M. Memorial Library Room 126

Campus Opportunities and Groups

UW-Madison LEaP Institute
The I-LEaP (Instructor-Learning Environment and Pedagogics) Institute is an introduction to teaching and learning ideas and techniques designed for faculty and instructors. TA-LEaP is designed for teaching assistants and all graduate students interested in learning about teaching techniques. LEaP participants engage in a 2-day workshop designed to introduce them to the basic of teaching and learning using a curriculum developed and taught by the UW-Madison Teaching Academy.

TA-LEaP Institute (for graduate student teaching assistants): August 20-21, 9:00am-3:30pm, 2317 Engineering Hall.
I-LEaP Institute (for academic staff, instructional staff, faculty): August 22-23, 9:00am-3:30pm, 2317 Engineering Hall.

Predoctoral Training Program in Bio-Data Science (BDS)
Research to improve the analysis of big biomedical data is active at the interface of computer sciences, statistics, and various biomedical disciplines, including genomics, molecular biology, neuroscience, cancer research, and population health.  The mission of the Bio-Data Science (BDS) training program is to provide predoctoral research training at this interface, preparing graduate students for key roles in academia, industry, or government. If you are interested in participating, send your personal statement, current CV, and the names of two faculty who can testify to your work here at UW-Madison to Beth Bierman.

Teaching & Research Application Development (TRAD)
The Teaching & Research Application Development (TRAD) service partners with instructors, researchers and campus staff to conceptualize, design and implement innovative custom software solutions and library applications. We specialize in supporting campus teaching, learning and research ideas.

The Midwest Machine Learning Symposium
The Midwest ML Symposium aims to convene regional machine learning researchers for stimulating discussions and debates, to foster cross-institutional collaboration, and to showcase the collective talent of ML researchers at all career stages. It will be held at the Memorial Union on June 6-7, 2019. You can register here.

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.

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 A.M.– 1:30 P.M.  Location alternates between Memorial Library and Steenbock, check the website for the latest information and location.

Computational Plant Sciences (ComPS) Group
A common problem both bench and field plant scientists face is that advance in high-throughput measurement platforms have outpaced our ability to readily analyze the datasets produced. To help solve this problem, the researchers in Plant Sciences formed a community of practice, a peer-to-peer mentoring network that will work across lab, departmental, and college boundaries to help plant scientists build computational and data science skillsets. They hold monthly meetings the first Tuesday of every month at noon.

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

Post-Doctorate Scientist Position at UNL
Dr. Helikar in the Computational and Systems Biology Group at the University of Nebraska-Lincoln has an opening for a Post-Doctoral Scientist with expertise in Computational Biology and/ or molecular modeling and/or immunology expertise to help build the first ‘Virtual Human Immune system’ model ever. The indication is that this will be a ground breaking innovation that has the trajectory to be brought to market and be very successful. This project is funded and currently being researched at one of the BIG10 universities in the United States and is open to sponsoring a Visa if necessary. More details and market intel by a professional consultant whom will make sure all your questions are answered. All interested applicants should contact Johnathan L. King.

6th Annual Business Intelligence & Analytics Symposium
Join AE Business Solutions & 250+ Wisconsin based IT professionals at the 6th Annual Business intelligence & Analytical Symposium at the Harley-Davidson Museum & Conference Center in Milwaukee, WI on April 18th, 2019. Registration and breakfast begins at 8:15 AM.

Course at Computational Genomics Summer Institute at UCLA
The Computational Genomics Summer Institute brings together mathematical and computational scientists, sequencing technology developers in both industry and academia, and the biologists who use the instruments for particular research applications. The CGSI program is a great learning opportunity for students and postdocs (and faculty). If you are interested, please check out. The deadline for registering is coming up soon (May 1st).

Data Science Fellowship Calls For Application
The Data Incubator is a Cornell-funded data science training organization. We run a free advanced 8-week fellowship (think data science bootcamp) for PhDs looking to enter industry. A variety of innovative companies partner with The Data Incubator for their hiring and training needs, including LinkedIn, Genentech, Capital One, Pfizer, and many others. The program is free for admitted Fellows – see the FAQ below for more information. Fellows have the option to participate in the program either in person in New York, San Francisco Bay Area, Boston New, Washington DC, or online. Deadline: April 22, 2019.

Data Driven Wisconsin 2019 Call For Proposals
We  are pleased to announce the fourth annual Data-Driven Wisconsin conference (formerly Big Data Wisconsin conference), to be held in Milwaukee on Wednesday, July 31. We are seeking speakers to give talks on all aspects of data science, big data technology, and their applications in business, science, government and health. 

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 about registration and abstract/poster submission details will be available soon.  If you have questions, please contact Nicholas Garcia Trillos.

The National Socio-Environmental Synthesis Center SESYNC
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

The North American Data Documentation Initiative Conference (NADDI)
NADDI is an opportunity for those using metadata standards and those interested in learning more to come together and learn from each other. Modeled on the successful European DDI Conference, NADDI 2019 will be a two day conference (April 25-26) with invited and contributed presentations, and should be of interest to both researchers and data professionals in the official statistics, social sciences and other disciplines. A full day of training sessions will precede the conference (April 24th).

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 newsletter@datascience.wisc.edu.