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Summer Courses 2021
2021 dkNET Summer of Data Student Program Courses
Program Duration
June 21, 2021 - July 30, 2021
2021 dkNET Summer of Data Student Program Awardee Recipients
Course Syllabus
Welcome to the 2021 dkNET Summer of Data Student Program. The goal of this program is to provide students with an opportunity to utilize the dkNET tools and resources in research projects, to learn the basics of good data management for FAIR (Findable, Accessible, Interoperable, Reusable) data. Students will receive hands-on training on how to use dkNET to find and evaluate research resources, how to use online data and tools to develop hypotheses to enhance their own projects as well as how to learn the best practices in data management for robust and reproducible research.
In the first week of the program, we will have an online bootcamp including an orientation and classes daily at 10:00am - 12:00pm PDT (1:00pm - 3:00pm EDT) from June 21, 2021 to June 25, 2021. At the orientation, we will give a brief introduction of the summer program, the expectations, approaches and the topics to be covered in the program. During the classes, students will learn about dkNET services and tools, including Resource Reports, Discovery Portal, Authentication Reports, Hypothesis Center (Signaling Pathways Project), FAIR data, data management, and other useful tools such as protocols.io. During the bootcamp (June 23 - 25, 2021), students will give an 8-minute presentation to introduce themselves, their research projects, and what dkNET tools/resources they plan to use.
From Week 2 to 6, there will be five weekly discussion sessions. Students will participate in discussion with other students and the dkNET team on their project activities.
A final student project presentation will be held online on July 23, 2021 and July 30, 2021 at 10:00am -12:00pm PDT(1:00 pm - 3:00pm EDT). Students will present their work and provide feedback on their experience, i.e., what did they find useful and not useful? A final standard report (ca. 2 pages in length) and a program survey are also due at the end of the program.
Students are required to attend bootcamp and all discussion sessions. The lectures (June 21: 10am - 11:30am PDT, June 22: 10:00am - 12:00pm PDT; June 23-25: 10:00am - 11:15am PDT) are open to students' Principal Investigators and laboratory members.
Full attendance, project presentation, final report, and survey are required to receive the award check.
Questions about the program should be directed to: Dr. Ko-Wei Lin (koweilin@ucsd.edu)
Dial-in information
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Bootcamp (students are required to attend): please check your email
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Discussion sessions and final project presentations (students are required to attend): please check your email
The main software for joining dkNET live meeting is Zoom. If it is your first time using Zoom, please click the dial-in information for orientation and complete the pre-registration. You will be directed to download the Zoom software, and you only have to download the Zoom software once during the program. However, you need to register each course before you join the webinar.
A computer or laptop with an internet connection, speaker, microphone, and a webcam is required for using Zoom (system requirements for PC, Mac, and Linux)
Before first course
Before our first course (Monday, June 21, 2021), please create the following accounts if you don't have one yet:
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Create a dkNET account (https://dknet.org/join)
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Create an ORCID account (https://orcid.org/register)
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Create a protocols.io account (https://www.protocols.io/create)
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Create a hypothes.is account (https://hypothes.is/signup)
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Accept the following invitations:
a. Slack (https://dknet.slack.com) #summer-program-2021
b. Google shared folder
c. Hypothes.is group - dkNET Summer Program 2021
Course Schedule
| Date/Time | Course | Course Lead | Course Preparation | Course Activity | Resources |
|---|---|---|---|---|---|
| Monday, June 21 ,2021 10am-12pm PDT |
Orientation Introduction to dkNET |
Dr. Maryann Martone Dr. Jeffrey Grethe Dr. Ko-Wei Lin |
Create a dkNET account (https://dknet.org/join) | Networking | https://dknet.org |
| Tuesday, June 22, 2021 10am-12 pm PDT |
Rigor/Reproducibility RRIDs Protocols.io |
Dr. Anita Bandrowski Dr. Lenny Teytelman |
Rigor/Reproducibility and RRIDs: (1) Bring one paper "virtually" to class. The paper should ideally be from your lab or one you are working on. The paper should be original research (a study), not a review or letter and one that includes cell lines, antibodies, or model organisms. Are the resources used properly identified? Attempt to find the RRID for these resources. 2) Create a hypothes.is account (https://hypothes.is/signup) using Google Chrome. Protocols.io: Create your Ptotocols.io account (https://www.protocols.io/create) |
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| Wednesday, June 23, 2021 10am-12pm PDT |
Hypothesis Center - Signaling Pathways Project | Dr. Neil McKenna | Read these papers: 1) https://www.nature.com/articles/s41597-019-0193-4 2) https://www.nature.com/articles/s41597-020-00628-6 3) https://www.jhep-reports.eu/article/S2589-5559(21)00057-4/fulltext |
5 Student Presentations (8 minutes each): Introduce yourself, your research projects, and what dkNET tools/resources you plan to use (2 slides) Presenters: Hannah N. Miles, Filbert Aung, Matthew E. Brown, Justin Choe, Sarah Coleman |
Signaling Pathways Project website: https://www.signalingpathways.org Slides |
| Thursday, June 24, 2021 10am-12pm PDT |
FAIR Data, Data Sharing and Open Science | Dr. Maryann Martone |
Read the FAIR data paper by Wilkinson et al., 2016: https://www.nature.com/articles/sdata201618 Be FAIR to your data: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7320032/ |
5 Student Presentations (8 minutes each): Introduce yourself, your research projects, and what dkNET tools/resources you plan to use (2 slides). Presenters: Mariel Glass, Nathan Ji, Rashid Saadman Karim, Jiayue Liu, Riley Medenwald |
GO FAIR: https://www.go-fair.org/fair-principles/ |
| Friday, June 25, 2021 10am-12pm PDT |
Data management: Best practices for managing data in the laboratory and creating data management plan | Dr. Jeffrey Grethe |
1) Read: Borghi, J., Abrams, S., Lowenberg, D., Simms, S., & Chodacki, J. (2018). Support Your Data: A Research Data Management Guide for Researchers. Research Ideas and Outcomes, 4, e26439. https://doi.org/10.3897/rio.4.e26439 2) Read: Goodman, A., Pepe, A., Blocker, A. W., Borgman, C. L., Cranmer, K., Crosas, M., … Slavkovic, A. (2014). Ten Simple Rules for the Care and Feeding of Scientific Data. PLoS Computational Biology, 10(4), e1003542.https://doi.org/10.1371/journal.pcbi.1003542; SPARC data structure white paper: https://docs.google.com/document/d/1dIzsa-uETIFJyMN2aZKJhHE3HDlyrjAr 3) Review: Frictionless Data - https://frictionlessdata.io/introduction/#why-frictionless |
5 Student Presentations (8 minutes each): Introduce yourself, your research projects, and what dkNET tools/resources you plan to use (2 slides) Presenters: Alexis Adrian, Lilian Mott, Sneha Panda, Alex Parrott, Xi Yu |
|
| Friday, July 2, 2021 10am-12pm PDT |
Discussion Session: Rigor/Reproducibility, RRIDs, Protocols.io | Dr. Anita Bandrowski Dr. Maryann Martone |
Assignment discussion: Students will be asked to annotate a set of papers with Hypothesis and also to create a protocol for their planned research project using Protocols.io. | 1) Check-in project progress 2) Assignment discussion (Rigor/Reproducibility, RRIDs, protocols.io) |
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| Friday, July 9, 2021 10am-12pm PDT |
Discussion Session: SPP |
Dr. Neil McKenna Dr. Maryann Martone or Dr. Jeffrey Grethe |
Assignment discussion: Students will learn how to use the Signaling Pathways Project via the dkNET Hypothesis Center to explore signaling networks underlying various phenotypes. If a student is planning on using the Hypothesis Center/SPP for their summer project, the student can start to explore their question while learning how to use the Hypothesis Center. If the student doesn’t have a relevant project, we will provide a structured exercise. |
1) Check-In project progress 2) Assignment discussion (SPP): 1st half: group discussion; 2nd half: students who use SPP discuss specific questions |
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| Friday, July 16, 2021 10am-12pm PDT |
Discussion Session: FAIR Data and DMP |
Dr. Maryann Martone or Dr. Jeffrey Grethe |
Assignment discussion: 1) Choose database repositories and work through FAIR Check List. 2) Use the selected repository and work through what is needed to publish your data with an associated DMP. 3) Work with some of your data to ensure it is FAIR and Frictionless (https://frictionlessdata.io) |
1) Check-in project progress 2) Assignment discussion (FAIR data; Data Management) |
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| Friday, July 23, 2021 10am-12pm PDT |
Student project presentation |
Dr. Jeffrey Grethe Dr. Maryann Martone Dr. Neil McKenna Dr. Anita Bandrowski Dr. Ko-Wei Lin |
Final presentations (Alexis Adrian, Filbert Aung, Matthew E. Brown, Justin Choe, Sarah Coleman, Mariel Glass, Nathan Ji, Rashid Saadman Karim) |
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| Friday, July 30, 2021 10am-12pm PDT |
Student project presentation and turn in final report and survey |
Dr. Jeffrey Grethe Dr. Maryann Martone Dr. Neil McKenna Dr. Anita Bandrowski Dr. Ko-Wei Lin |
Final presentations (Jiayue Liu, Riley Medenwald, Hannah N. Miles, Lilian Mott, Sneha Panda, Alex Parrott, Xi Yu) |
About
The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant 2U24DK097771-09.
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