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Song Gao is Seminar Speaker January 14

Song Gao is Seminar Speaker January 14

Please mark your calendars and plan to attend the first Seminar Series of the year.

Mapping Multiscale Human Mobility Changes and Geospatial Modeling of COVID-19 Spread
presented by

Dr. Song Gao,
Director of Geospatial Data Science Lab, University of Wisconsin-Madison

Thursday, January 14, 2021, 12:30 pm PST via Zoom.
(Email IMCI or IBEST for the Passcode.)

Abstract: To contain the COVID-19 spread, one of the non-pharmaceutical interventions is social distancing. An interactive web-based mapping platform that provides up-to-date mobility information on how people in different counties and states reacted to the social distancing and stay-at-home orders was developed by the GeoDS Lab at UW-Madison. The web portal integrates geographic information systems (GIS) and daily updated human mobility statistical patterns derived from large-scale anonymized and aggregated smartphone location big data in the United States. A mobility-augmented compartmental epidemic model is developed to help monitor COVID-19 spreading dynamics, inform public health policy, and deepen our understanding of human behavior impacts under the unprecedented public health crisis. 

Spring 2021 Carpentries Workshops Announced

Spring 2021 Carpentries Workshops Announced

The Carpentries training program aims to improve data literacy and reproducible science. IMCI sponsors the University of Idaho as a member in the organization.

Postdocs and graduate students will run 3 workshops this spring for upper-level undergraduate students, new graduate students and anyone else interested in good-practices in data management and analysis.

STUDENTS can register for academic credit

Students wishing to take the workshops for credit need to register via the UI course schedule for any combination of BCB 503 01, BCB 503 02, and/or BCB 503 03. Each workshop is 1 credit each.

NON-STUDENTS must also register to attend

If you do not want academic credit, you may attend any workshop for free but must still register. Space is limited.



Unix, Git, and Programming (R/Python) for Novices

Workshop dates: January 19 – February 4; T/Th, 2-5 p.m.

Instructors: Breanna Sipley, Travis Seaborn, Chava Castaneda, Li Huang, Erich Seamon, Angela Crabtree, Akorede Seriki

Description: 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 in Unix, GitHub, R, and Python. Participants will be encouraged to help one another and to apply what they have learned to their own research problems. The course is aimed at graduate students and other researchers but is open to all. You don’t need to have any previous knowledge of the tools that will be presented at the workshop. Participants must have a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. All participants should attend the Unix/Git sections (first week). The R (second week) and Python (third week) sections will each be taught as independent sections.

View Code of Conduct, Detailed Schedule & Set Up Requirements


Data Wrangling and Processing for Genomics

Workshop dates: March 2-11; T/Th, 2-5 p.m.

Instructors: JT Van Leuven, Angela Crabtree, Lukas Grossfurthner, Amanda Stahlke, Travis Seaborn, Breanna Sipley

Description: Data Carpentries aims to teach researchers basic concepts, skills, and tools for working with data so that they can get more done in less time, and with less pain. This hands-on workshop will cover basic concepts and tools, including best practices for organization of bioinformatics projects and data, use of command-line utilities, use of command-line tools (shell and R) to analyze sequence quality and perform variant calling, connecting to and using cloud (AWS) computing, and visualizing genomic data. The course is aimed at graduate students and other researchers but is open to all. While the course is designed for learners that have no prior experience with the tools covered in the workshop, some familiarity with biological concepts (DNA, mutation, population variation) will be useful. Participants must have a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on.

View Code of Conduct, Detailed Schedule & Set Up Requirements


Advanced Geospatial Analysis

Workshop dates: April 20-29; T/Th, 2-5 p.m.

Instructors: Erich Seamon, Li Huang, Travis Seaborn, Lukas Grossfurthner

Description: This hands-on workshop will focus on managing and understanding spatial data formats, understanding coordinate reference systems, and working with raster and vector data in R for analysis and visualization. The course is aimed at graduate students and other researchers but is open to all. Participants will be encouraged to help one another and to apply what they have learned to their own research problems. Introductory knowledge of R is suggested.

View Code of Conduct, Detailed Schedule & Set Up Requirements


Register to Attend a Carpentries Course

The topics of upcoming workshops are always up for discussion and depend on your input. If you have workshops suggestions or requests, please email JT Van Leuven.

If you are a student wishing to take any of these courses for academic credit, please register via the U of I Course Schedule.


SPRING 2021 WORKSHOPS


Unix, Git, and Programming (R/Python) for Novices

Workshop dates: January 19 – February 4; T/Th, 2-5 p.m.

Instructors: Breanna Sipley, Travis Seaborn, Chava Castaneda, Li Huang, Erich Seamon, Angela Crabtree, Akorede Seriki

Description: 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 in Unix, GitHub, R, and Python. Participants will be encouraged to help one another and to apply what they have learned to their own research problems. The course is aimed at graduate students and other researchers but is open to all. You don’t need to have any previous knowledge of the tools that will be presented at the workshop. Participants must have a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on. All participants should attend the Unix/Git sections (first week). The R (second week) and Python (third week) sections will each be taught as independent sections.

NON-STUDENT REGISTRATION: Unix, Git, and Programming (R/Python) for Novices

(If you are a student, please register via the Course Catalog.)


Data Wrangling and Processing for Genomics

Workshop dates: March 2-11; T/Th, 2-5 p.m.

Instructors: JT Van Leuven, Angela Crabtree, Lukas Grossfurthner, Amanda Stahlke, Travis Seaborn, Breanna Sipley

Description: Data Carpentries aims to teach researchers basic concepts, skills, and tools for working with data so that they can get more done in less time, and with less pain. This hands-on workshop will cover basic concepts and tools, including best practices for organization of bioinformatics projects and data, use of command-line utilities, use of command-line tools (shell and R) to analyze sequence quality and perform variant calling, connecting to and using cloud (AWS) computing, and visualizing genomic data. The course is aimed at graduate students and other researchers but is open to all. While the course is designed for learners that have no prior experience with the tools covered in the workshop, some familiarity with biological concepts (DNA, mutation, population variation) will be useful. Participants must have a laptop with a Mac, Linux, or Windows operating system (not a tablet, Chromebook, etc.) that they have administrative privileges on.

NON-STUDENT REGISTRATION: Data Wrangling and Processing for Genomics

(If you are a student, please register via the Course Catalog.)


Advanced Geospatial Analysis

Workshop dates: April 20-29; T/Th, 2-5 p.m.

Instructors: Erich Seamon, Li Huang, Travis Seaborn, Lukas Grossfurthner

Description: This hands-on workshop will focus on managing and understanding spatial data formats, understanding coordinate reference systems, and working with raster and vector data in R for analysis and visualization. The course is aimed at graduate students and other researchers but is open to all. Participants will be encouraged to help one another and to apply what they have learned to their own research problems. Introductory knowledge of R is suggested.

NON-STUDENT REGISTRATION: Advanced Geospatial Analysis

(If you are a student, please register via the Course Catalog.)

Become a Carpentries Instructor

IMCI is continuing its support of our Carpentries workshops so that another cohort of instructors can participate in pedagogy training and become Carpentries instructors. IMCI asks you to teach at least one workshop or co-teach two workshops at U of I after we sponsor your training.

For BCB graduate students, helping with these workshops may satisfy the teaching requirements of your degree (contact Dr. Tank for details).

For postdocs and graduate students wanting teaching experience, we will set up the workshops as official BCB504 courses. 

The instructor training does not teach technical skills but is a way to brush up on teaching methods, best practices for live-coding, and how to facilitate an inclusive learning environment. Of note, Carpentries-trained instructors have the option of being part of a nation-wide pool of instructors available for hire (paid travel) by other institutions.

For more information, contact JT Van Leuven or feel free to email any of the past instructors.


If you are interested in becoming a Carpentries instructor,
please fill out this short form.