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Summer Courses 2022
2022 dkNET Summer of Data Student Program Courses
Program Duration
June 13, 2022 - July 22, 2022
2022 dkNET Summer of Data Student Program Awardee Recipients
Course Syllabus
Welcome to the 2022 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 10:00 am - 12:00 pm PDT (1:00pm - 3:00pm EDT) from June 13, 2022 to June 17, 2022. 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 15 - 17, 2022), students will give a 5-minute flash talk 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 15, 2022 and July 22, 2022 at 10:00 am -12:00 pm 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 13: 10 am - 11:30 am PDT, June 14: 10:00 am - 12:00 pm PDT; June 15-17: 10:00 am - 11:15 am 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 the dkNET live meetings 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 for 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 13, 2022), 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) and accept the “2022 dkNET Summer of Data Student Program” workspace invitation
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Accept the following invitations:
a. Slack (https://dknet.slack.com) #summer-program-2022
b. Google shared folder
Course Schedule
| Date/Time | Course | Course Lead | Course Preparation | Course Activity | Resources |
|---|---|---|---|---|---|
| Monday, June 13 ,2022 10 am-12 pm 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 14, 2022 10 am-12 pm PDT | Rigor/Reproducibility RRIDs Protocols.io | Dr. Maryann Martone Dr. Gabriel Gasque | Protocols.io: Create your Ptotocols.io account (https://www.protocols.io/create) If possible, upload a protocol to the “2022 dkNET Summer of Data Student Program” workspace to be used as an example during class. This protocol can be in any format: PDF, word document. This is not compulsory, but it would be nice to have a real example to work on. You should only upload the protocol if you feel comfortable sharing it with the class. | 1) https://www.aje.com/en/arc/how-to-write-an-easily-reproducible-protocol/ 2) https://www.protocols.io/view/how-to-make-your-protocol-more-reproducible-discov-8epv52qdv1bz/v4 | |
| Wednesday, June 15, 2022 10 am-12 pm PDT | Hypothesis Center; Signaling Pathways Project | Dr. Neil McKenna Dr. Jeffrey Grethe | 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 flash talk (5 minutes each): Introduce yourself, your research projects, and what dkNET tools/resources you plan to use (2 slides) Presenters: Shreya Bellampalli, Talia Cheifetz, Tsz Kiu Chui, Alexandra Hoff, Sephora Jean | 1) Signaling Pathways Project website: https://www.signalingpathways.org 2) dkNET Hypothesis Center: https://dknet.org/hypothesis-center |
| Thursday, June 16, 2022 10 am-12 pm 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 New NIH data sharing policy: https://grants.nih.gov/grants/guide/notice-files/NOT-OD-21-013.html | 6 Student flash talks (5 minutes each): Introduce yourself, your research projects, and what dkNET tools/resources you plan to use (2 slides). Presenters: Sara Koh, Ryan Liu, Thanh Nguyen, Sreevidya Rao, Mason Schmidt, Mary Stangis | GO FAIR: https://www.go-fair.org/fair-principles/ |
| Friday, June 17, 2022 10 am-12 pm 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 flash talks (5 minutes each): Introduce yourself, your research projects, and what dkNET tools/resources you plan to use (2 slides) Presenters: Muen Wang, Jen Xu, Mari Yamamoto, Katie Yanez, Zoe Yu | |
| Friday, Juun 24, 2022 10 am-12 pm PDT | Discussion Session: Rigor/Reproducibility, RRIDs, Protocols.io | Dr. Maryann Martone Dr. Anita Bandrowski | Assignment discussion: Students will be asked to create a detailed scientific protocol for their planned research project using some of the specialized features available in Protocols.io. | 1) Check-in project progress 2) Assignment discussion (Rigor/Reproducibility, RRIDs, protocols.io) | |
| Friday, July 1, 2022 10 am-12 pm PDT | Discussion Session: Hypothesis Center and SPP | Dr. Neil McKenna 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 and Hypothesis Center) | |
| Friday, July 8, 2022 10 am-12 pm PDT | Discussion Session: FAIR Data and DMP | Dr. Maryann Martone Dr. Jeffrey Grethe | Assignment discussion: 1) Assignment may be changed. Choose database repositories and work through FAIR Check List. 2) Based on FAIR Data session - 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) | |
| Friday, July 15, 2022 10 am-12 pm PDT | Student project presentation | Dr. Jeffrey Grethe Dr. Neil McKenna Dr. Ko-Wei Lin | Final presentations (Shreya Bellampalli, Talia Cheifetz, Tsz Kiu Chui, Alexandra Hoff, Sephora Jean, Sara Koh, Ryan Liu, Thanh Nguyen) | ||
| Friday, July 22, 2022 10 am-12 pm PDT (Special Session: 12 pm - 12: 30 pm: Meet Dr. Ronald Margolis) | Student project presentation and turn in final report and survey | Dr. Jeffrey Grethe Dr. Maryann Martone Dr. Neil McKenna Dr. Ko-Wei Lin | Final presentations (Sreevidya Rao, Mason Schmidt, Mary Stangis, Muen Wang, Jen Xu, Mari Yamamoto, Katie Yanez, Zoe 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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