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Summer Courses 2023
2023 dkNET Summer of Data Student Program Courses
Program Duration
June 12, 2023 - July 21, 2023
2023 dkNET Summer of Data Student Program Awardee Recipients
Course Syllabus
Welcome to the 2023 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 and second week of the program, we will have a 7-day online bootcamp including an orientation and classes daily at 10:00 am - 12:00 pm PDT (1:00 pm - 3:00 pm EDT) from June 12 to June 16, June 20, and June 23, 2023. 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 (on June 20, 2023), students will give a 3-minute flash talk to introduce themselves, their research projects, and what dkNET tools/resources they plan to use.
From Week 3 to 4, there will be 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 14, 2023 and July 21, 2023 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 12: 10 am - 12 pm PDT, June 13: 10:30 am - 12:00 pm PDT; June 14-16: 10:00 am - 12 pm PDT, June 23, 10 am - 11 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.
Each week, optional one-hour office hours will be held to address any questions you may have. The current scheduled dates are Thursdays (June 29, July 6, July 13) from 11 am - 12 pm PDT (2 pm - 3 pm EDT) and Monday, July 17 from 1 pm - 2 pm PDT ( 4 pm - 5 pm EDT). The final dates will be confirmed later, taking into account the availability of the instructors.
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 12, 2023), 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 “2023 dkNET Summer of Data Student Program” workspace invitation
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Accept the following invitations:
a. Slack (https://dknet.slack.com) #summer-program-2023
b. Google shared folder
Course Schedule (https://dknet.org/about/summer_course_2023)
| Date/Time | Course | Course Lead | Course Preparation | Course Activity | Resources |
|---|---|---|---|---|---|
| Monday, June 12 ,2023 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) | Slack, Protocols.io, Networking platform check | https://dknet.org |
| Tuesday, June 13, 2023 10 am-12 pm PDT |
Special Session: The National Institutes of Health(NIH):What is it and how does it work; Protocols.io |
Dr. Ronald Margolis Dr. Gabriel Gasque |
Protocols.io: Create your Ptotocols.io account (https://www.protocols.io/create) If possible, upload a protocol to the “2023 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.
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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 |
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| Wednesday, June 14, 2023 10 am-12 pm PDT |
Hypothesis Center; Signaling Pathways Project | Dr. Ko-Wei Lin 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.jidonline.org/article/S0022-202X(23)01941-3/fulltext 4) https://www.jhep-reports.eu/article/S2589-5559(21)00057-4/fulltext |
1) dkNET Hypothesis Center: https://dknet.org/hypothesis-center 2) Signaling Pathways Project website: https://www.signalingpathways.org |
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| Thursday, June 15, 2023 10 am-12 pm PDT |
Data management: Best practices for managing data in the laboratory and creating a 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 |
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| Friday, June 16, 2023 10 am-12 pm PDT |
FAIR Data, Data Sharing and Open Science | Dr. Maryann Martone | 1) Read the FAIR data paper by Wilkinson et al., 2016: https://www.nature.com/articles/sdata201618 2) New NIH data sharing policy: https://grants.nih.gov/grants/guide/notice-files/NOT-OD-21-013.html |
dkNET exercise discussion | GO FAIR: https://www.go-fair.org/fair-principles/ |
| Tuesday, June 20, 2023 10 am-12 pm PDT |
Student Flash Talks; Networking |
Dr. Maryann Martone Dr. Jeffrey Grethe Dr. Ko-Wei Lin |
prepare a 3-minute flash talk to introduce themselves, their research projects, and what dkNET tools/resources they plan to use. | 1) Student flash talks 2) Networking |
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| Friday, June 23, 2022 10 am-12 pm PDT |
Rigor/Reproducibility and RRIDs | Dr. Anita Bandrowski | 1) Bring a paper you are writing, have written or one from their lab. You should have read the paper if you didn't write it. 2) Assignment discussion: Students will create a detailed scientific protocol for their planned research project using some of the specialized features available in Protocols.io. |
Assignment discussion (protocols.io) | |
| Friday, June 30, 2023 10 am-12 pm PDT |
Discussion Session: Hypothesis Center and SPP |
Dr. Jeffrey Grethe Dr. Neil McKenna |
Assignment discussion: 1) Visit the hypothesis center and complete two tutorials: a)Be prepared to provide feedback on the tutorials and Hypothesis Center. b)Students will be given some practice exercises for Hypothesis Center 2) 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 (Hypothesis Center and SPP) |
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| Friday, July 7, 2023 10 am-12 pm PDT |
Discussion Session: FAIR Data and DMSP |
Dr. Maryann Martone Dr. Jeffrey Grethe |
Assignment discussion: 1) Based on your research project and the data it is using, use dkNET tools to help you select appropriate repository(s) and work through what is needed to manage and share your data in compliance with NIH’s new DMSP requirements. Work with some of your data to ensure it is FAIR and Frictionless (https://frictionlessdata.io) - document what would be needed as part of your data collection and management practices. |
1) Check-in project progress 2) Assignment discussion (FAIR data; Data Management) |
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| Friday, July 14, 2023 10 am-12 pm PDT |
Student project presentation |
Dr. Jeffrey Grethe Dr. Maryann Martone Dr. Neil McKenna Dr. Ronald Margolis Dr. Ko-Wei Lin |
Final presentations (Mahad Ahmed, Manvir Bamrah, Benjamin Ding, Brandon Garcia, Phoebe Keiser, Ajinkya Limkar, Paula M. Mañán Mejías, Theodore Nelson) | Student final presentation I | |
| Friday, July 21, 2023 10 am-12 pm PDT |
Student project presentation and turn in final report and survey |
Dr. Jeffrey Grethe Dr. Maryann Martone Dr. Neil McKenna Dr. Ronald Margolis Dr. Ko-Wei Lin |
Final presentations (Amanda Pan, Sanjay Ravindran, Cassandra Secunda, Sara Stuedemann, Emma Warrner, Lindsey Yoo, Laura Zhang) | Student final presentation II |
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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