050119 Update


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

In the May 1, 2019 update:

  • Badger Talks Hub
  • 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.

Badger Talks Hub

Formerly the UW Madison’s Speakers Bureau, the Badger Talks Hub has a roster of over 250 UW-Madison faculty, academic staff and graduate students who volunteer their time and talent by sharing the latest discoveries, ongoing research and areas of expertise through talks and workshops. Here is a list of current topics which are linked to respective speakers. Many new topic areas are being added and if you would like to see more talks specifically related to Data Science please consider reaching out to the Badger Talks Hub. They are currently enrolling new speakers and invite you to join this highly regarded team. You may self-nominate, or nominate a colleague here. Speakers volunteer their time, and the Hub covers mileage, per diem, and hotel (if applicable), based on reimbursement rates set by the University.

Upcoming Campus Events (Calendar View)

Center for Demography of Health and Aging (CDHA) Training Seminar, 2:00pm-3:15pm, 8417 Sewell Social Science Building
May 1, Information Design and Presentation Best Practices, James R. Carey (Davis)

Computation and Informatics in Biology and Medicine (CIBM) Seminar: 4:00 PM-5:00 PM, 1360 Biotechnology Center 
May 1, Data-Driven Protein Engineering, Philip Romero

Systems, Information, Learning, and Optimization (SILO) Seminar, 12:30pm-1:30pm, Orchard View Room, Discovery Building
May 1, Multistage Distributionally Robust Optimization with Total Variation Distance: Modeling and Effective Scenarios, Güzin Bayraksan
May 8Billion-degree of freedom Computational Dynamics: from granular flows to 3D printing and on to river fording simulation, Dan Negrut
May 15, TBA, Lalitha Sankar

Statistics Seminar, 4:00 P.M. 140 Bardeen
May 1, Unsupervised Geometric Learning: Theory and Applications, James Murphy

Applied and Computational Mathematics Seminar (ACMS), 2:25pm-3:25 PM, 901 Van Vleck
May 32-D Strokes Immersed Boundary Problem and its Regularizations: Well-posedness, Singular Limit, and Error Estimates. Jiajun Tong (UCLA)

Morgridge Institute Metabolics Colloquium – Computational Biology Seminar, 3:30pm-4:30pm, Discovery Building, HF DeLuca Forum – Room 1255
May 14, TBA, Ernest Frankel (MIT)

The Wisconsin Association for Computing Machinery – Women in Computing, May 7, 12:00pm-1:00pm, Computer Sciences 2310

Upcoming Training and Workshops

Microbiome Analysis Using QIIME2
This workshop will cover amplicon-based microbiome analysis using the QIIME2. This all-day workshop will consist of lectures and hands on training to analyze from raw dataset through publication-quality statistics and visualizations. This workshop will be held on 5/8/19 at the Biotch center room 1360. Participants are expected to have base knowledge of the Linux environment and a basic understanding of statistical methods Registration link: Microbiome analysis using QIIME2

Health Science Data Carpentry, 8:30am – 4:30pm, June 11-12, 2019
This hands-on workshop teaches basic concepts, skills and tools for working more effectively with health science related data. The workshop is for any researcher who has data they want to analyze, and no prior computational experience is required. Event hosted by the Data Science Hub. Registration opens: May 2nd @ 5pm

Software Carpentry Workshop, 8:30am – 4:30pm, June 13-14, 2019
Software Carpentry aims to help researchers get their work done in less time and with less pain by teaching them basic research computing skills. This hands-on workshop will cover basic concepts and tools, including program design, version control, data management, and task automation. Participants will be encouraged to help one another and to apply what they have learned to their own research problems. Event hosted by the Data Science Hub. Registration opens: May 2nd @ 5pm

Geospatial Data Carpentry8:30am – 4:30pm, July 11-12, 2019
This hands-on workshop teaches basic concepts, skills and tools for working more effectively with geospatial data. The workshop is for any researcher who has data they want to analyze, and no prior computational experience is required. Event hosted by the Data Science Hub. Registration opens: TBA

Campus Opportunities and Groups

Research Assistant Positions
The Tang Lab is recruiting a Graduate Research Assistant starting Fall 2019. The successful applicant will work primarily on developing statistical methods for analyzing microbiome data. The position is one-year and potentially renewable. Applicants should have quantitative background with strong statistical and computational skills. They should know at least one programming language (e.g., C/C++, Perl, Python) and at least one statistical software (e.g., SAS, R, MatLab). If you are interested in applying the position, please email your CV to Zhengzheng (Jane) Tang.

There are two positions for graduate research assistantship under the direction of Professors Menggang Yu and Guanhua Chen with close collaboration with Health Innovation Program at UW-Madison. The successful applicants will work primarily on developing statistical and machine learning methods in the area of big health care data, causal inference, and precision medicine. The main projects are related, but not limited to, personalized treatment recommendation using high dimensional electronic health records and health insurance claims. The applicants will have opportunities to get training in statistical methodology development, software implementation, and direct collaboration with health care professionals. Suitable applicants should be second or third year PhD students in Statistics, or Biostatistics, who are self-motivated and interested in solving real biostatistics problems. Interested applicants should send CV and the transcript(s) to both Professor Menggang Yu and Professor Guanhua Chen.

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.

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.

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.edufor updates and future meetings.

External Opportunities

Community Call – Security for R
Applying security best practices is essential not only for developers or sensitive data storage but also for the everyday R user installing R packages, contributing to open source, working with APIs or remote servers. However, keeping up-to-date with security best practices and applying them meticulously requires significant effort and is difficult without expert knowledge. On this call you’ll hear about how the ropsec package can help you and you’ll learn the inner secrets of maintaining confidentiality, integrity, and availability throughout all your data science workflows. Join the call on Tuesday, May 7th, 11:00am AM PDT. Additional details and resources can be found here.

Midwest Mobility from Poverty Network
The Midwest Mobility from Poverty Network will host its Network Convening Meeting on May 8, 2019 in Ann Arbor MI. This initial meeting will explore how to use rapid response data and analysis in partnership with communities and governments to inform efforts on mobility and decreasing poverty. Learn more and register here.

Midwest Big Data Summer School
Registration is still open for the 2019 Midwest Big Data Summer School for early career researchers and practitioners, held at Iowa State University in Ames. Late registration ends May 20. Invited speakers include industry leaders from Google, FiveThirtyEight.com, Microsoft Research, Corteva, and Microsoft Chicago (May 20-23, Iowa State University). Learn more and register here.

Shared BigData Gateway for Research Libraries
The NSF Big Data Hubs: Data Sharing and Cyberinfrastructure Working Group is hosting a webinar on May 3, 2019 at 2:00 pm CT. Dr. Valentin Pentchev from Indiana University’s Network Science Institute (IUNI) will provide a talk entitled, Shared BigData Gateway for Research Libraries. You can
Zoom the livestream here.

Postdoctoral Fellowships at University of Washington, Seattle
Three postdoctoral fellowships (see below) are available in the lab of William Stafford Noble in the Department of Genome Sciences at the University of Washington, Seattle. Applications will be accepted until the positions are filled. Please submit a CV, research statement and names of at least three references to william-noble@uw.edu.

  1. Genomics and proteomics of the malaria parasite. This project’s main goal is to characterize the molecular determinants that control chromatin organization and gene regulation in this pathogen. The research continues a longstanding collaboration between the Le Roch and Noble labs.
  2. 3D genome architecture changes in HIV and methamphetamine use. This project will use genomic technologies to elucidate the role of 3D chromatin architecture in maintaining HIV reservoirs and examine how methamphetamine use impacts the reservoir. This is a collaboration with the lab of Jim Mullins (Microbiology).
  3. Bioinformatics and cardiac biology. Together with the lab of Chuck Murry (Pathology), this high priority project involves the characterization of the role of genome architecture dynamics during the differentiation of cardiovascular cells from human pluripotent stem cells.

Plant Breeding Data Scientist 
Corteva Agriscience™ has a rich history of scientific discovery that has enabled countless innovations. They are looking for more people to collaborate to create a market-shaping, agriculture company with leading positions in seed technologies, crop protection and digital agriculture. They need Data Scientists to collaborate with visionary plant breeders, biostatisticians, genomicists, and crop scientists to build digitally enabled science and business capabilities. Additional details and application information can be found here.

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.

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.