A bi-monthly newsletter with updates on data and computing news and events for UW-Madison researchers.
In the March 20, 2019 update:
- Open Science Grid User School 2019
- Upcoming Campus Events
- Upcoming Trainings and Workshops
- Campus Opportunities and Groups
- External Opportunities
- 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 (firstname.lastname@example.org) 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.
If you could access hundreds or even thousands of computers for your scholarly work or the work you support, what could you do? How could it transform research? What discoveries might be made? Find out in the Open Science Grid (OSG) User School 2019, which takes place July 15-19 at the beautiful University of Wisconsin in Madison. Participants will learn to use high throughput computing (HTC) to harness vast amounts of computing power for research, applicable to nearly any field of study (e.g., physics, chemistry, engineering, life sciences, earth sciences, agricultural and animal sciences, economics, social sciences, medicine, and more).
Ideal candidates are graduate students doing research and staff (e.g., facilitators, admins) supporting research that involves or could involve large-scale computing – work that cannot be done on one laptop or a handful of computers. Basic travel, hotel, and food costs are covered for applicants who are selected to attend.
Application Period (OPEN NOW): 11 March – 12 April 2019
Upcoming Campus Events (Calendar View)
Biochemistry Colloquium, 3:30pm-4:30pm, 1211 HFD Biochemical Sciences Building
March 25, Global Coordination of Transcription and Translation in E. Coli, Terry Hwa (UCSD)
Computer Science Colloquium: 4:00pm-5:00pm, 1240 Computer Sciences
March 25, Language as a Scaffold for Grounded Intelligence
March 26, Empiricism-Informed Secure System Design: From Improving Passwords to Helping Domestic Violence Victims
March 28, Computational Wireless Sensing at Scale
April 1, Made to Order: Verifying Correctness and Security of Hardware Through Event Orderings
April 2, Towards Realizing the Internet-of-Things Vision: In-Body, Homes, Cities and Farms
April 4, Visualization for People+Systems
Biostatistics & Medical Informatics (BMI) Seminar: 12:00pm
March 26, Manifold Learning Uncovers Hidden Structure in Complex Cellular State Space, David van Dijk (Waisman Center, Room 216)
March 29, TBA, Lu Mao (Biotech Auditorium)
Computation and Informatics in Biology and Medicine (CIBM) Seminar: 4:00pm, 1360 Biotechnology Center
March 26, TBA, Andrew Hasley
April 2, TBA, Mostafa Zamanian, (Auditorium)
Center for Demography of Health and Aging (CDHA) Training Seminar: 2:00pm-3:15pm, 8417 Sewell Social Science Building
March 27, PAA practice talks
- Multigenerational Class Gradients in Housing Tenure Trajectories during Young Adulthood, Qian He
- Segregation and Violence Reconsidered: Do Whites Benefit from Residential Segregation?, Julia Thomas
- Changes in Social Networks after Retirement: Comparison of the USA and European Countries, Won-tak Joo
- Intersectionality and Intentionality: The Effects of Tolerance for Risk of Unintended Pregnancy, Side Effects, and Identity on Contraceptive Practices over Time, Kelsey Quinn Wright
Systems, Information, Learning, and Optimization (SILO) Seminar: 12:30pm, Orchard View Room, Discovery Building
March 27, Learning From Sub-Optimal Data, Bradly Stadie
April 3, TBA, Santiago Segarra (Rice University)
Machine Learning for Medical Imaging (ML4MI) Initiative Seminar
March 28, 1:00pm, 1240 CS, TBA, Miki Lustig, (Berkeley Electrical Engineering and Computer Science)
Statistics Seminar: 4:00pm, 133 Service Memorial Institute (SMI)
March 28, Three Principles of Data Science: Predictability, Computability, and Stability (PCS), Bin Yu
Applied and Computational Mathematics Seminar (ACMS): 2:25pm, 901 Van Vleck Hall
March 29, The Mathematics of Burger Flipping, Jean-Luc Thiffeault
The Wisconsin Association for Computing Machinery – Women in Computing, April 2, 12:15pm-1:15pm, Computer Sciences 2310
Upcoming Trainings and Workshops
Next Generation Data Analysis Workshops
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).
- Linux Essentials (1): Monday, 4/08/19 (1360 Biotech Center)
- Intro to NGS Data Analysis: Monday, 4/15/19 (1360 Biotech Center)
- mRNA-Seq: Monday, 4/22/19 (1360 Biotech Center)
Identity and Access Management for Research
Identity federation enables cross-institutional access to research facilities, data and resources both within the US and across the world. Tom Jordan and Jon Miner will provide some background on how identity federation can be used to make resources available to other institutions, and to allow UW-Madison researchers access to facilities within the national and international community.
March 27, 12:00-1:00 pm, Memorial Library 126.
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 pm, Memorial Library Room 126
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
The 42nd Annual Midwest Biopharmaceutical Statistics Workshop (MBSW) will be held from May 20-22, 2019 at Renaissance Indianapolis North Hotel, Carmel, Indiana. The MBSW’s purpose is to foster discussion on Statistical methodology in the Pharmaceutical industry. The detailed information and submission of poster proposals is available (online registration). Students who are interested in MBSW 2019 seeking financial support must fill out student financial application form to apply for a limited number of student travel grants as per instructions available at MBSW 2019 website. Abstract submission for posters is required and must be submitted online via this link by April 12, 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. Poster abstracts are due 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.
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.
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.
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.
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.
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. The next meeting will be on April 2.
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 (email@example.com) 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 firstname.lastname@example.org for updates and future meetings.
This conference seeks to highlight the multi-disciplinary challenges of Data Science, a growing field that uses data and computing to improve everyday life. Keynote speakers are (in alphabetical order) Anna Gilbert (U Michigan), Michael Jordan (UC Berkeley), Tamara Kolda (Sandia National Labs), Vahab Mirrokni (Google Research), Christos Papadimitriou (Columbia), and Rachel Ward (UT Austin). The conference will take place at Purdue University (West Lafayette, IN) on April 12-13, 2019 and full conference schedule and registration details are available here.
The Data Observation Network for Earth (DataONE) is a virtual organization dedicated to providing open, persistent, robust, and secure access to biodiversity and environmental data, supported by the U.S. National Science Foundation. DataONE is pleased to announce the availability of summer research internships for undergraduates, graduate students and recent postgraduates. Interns undertake a 9-week program of work centered around one of the projects listed below. Each intern will be paired with one primary mentor and, in some cases, secondary and tertiary mentors. Interns need not necessarily be at the same location or institution as their mentor(s). The deadline for receipt of applications is at midnight (Mountain time) on March 22.
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.
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 about registration and abstract/poster submission details will be available soon. If you have questions, please contactNicholas Garcia Trillos.
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 email@example.com.