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Summer Courses 2025
2025 dkNET Summer of Data Student Program Courses
Program Duration
June 26, 2025 - August 8, 2025
2025 dkNET Summer of Data Student Program Awardee Recipients
Course Syllabus
Welcome to the 2025 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 principles (Findable, Accessible, Interoperable, Reusable) data, rigor and reproducibility, and data science skills. 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. Students will also do data wrangling, data cleaning, data visualization, and machine learning.
At the beginning of the program, we will have a 6-day online bootcamp including an orientation and classes at 10:00 am - 12:00 pm PDT (1:00 pm - 3:00 pm EDT) on June 26, 27, 30, July 1, 2, and July 9, 2025. 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, principles of FAIR data, data management, other useful tools such as protocols.io, and data science skills. During the bootcamp (on July 2, 2025), students will give a 3-minute flash talk to introduce themselves, their research projects, and what dkNET tools/resources they plan to use for their projects.
From Week 3 to 5, there will be weekly discussion sessions. Students will participate in discussion with other students and the dkNET team on their project activities.
In Week 5, we will have a 3-day data science bootcamp from July 21-23, 2025 (9 am - 1 pm PDT; 12 pm - 4 pm EDT).
A final student project presentation will be held online on August 1, 2025 and August 8, 2025 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 26, 27, 30, July 1 and July 9: 10 am - 12 pm PDT) are open to students' Principal Investigators and laboratory members. The data science bootcamp lecture sessions (July 21–23, 2025) are also open to PIs and lab members; however, please notify us in advance if they plan to attend the data science bootcamp, as computing resources are limited.
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 ([email protected])
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 the first course
Before our first course (Monday, June 26, 2025), 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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Accept the “2025 dkNET Summer of Data Student Program” workspace invitation and create a protocols.io account (https://www.protocols.io/create)
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Accept the following invitations:
a. Slack (https://dknet.slack.com) #summer-program-2025
b. Google shared folder
Course Schedule (https://dknet.org/about/summer_course_2025)
| Date/Time | Course | Course Lead | Course Preparation | Course Activity | Resources |
|---|---|---|---|---|---|
| Thursday, June 26, 2025 10 am-12 pm PDT |
Orientation; Introduction to dkNET |
Dr. Jeffrey Grethe Dr. Ko-Wei Lin |
Create a dkNET account (https://dknet.org/join) | Slack, Protocols.io platform check | https://dknet.org |
| Friday, June 27, 2025 10 am-12 pm PDT |
(1) Protocols.io 10 am - 11 am PT (2) Rigor/Reproducibility and RRIDs 11 am - 12 pm PT |
(1) Dr. Lenny Teytelman (2) Dr. Anita Bandrowski |
Protocols.io Accept the "2025 dkNET Summer of Data Student program" workspace invitation and create your Protocols.io account (https://www.protocols.io/create) If possible, upload a protocol to the “2025 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. Bring a paper you are writing, have written, or one from your lab. You should have read the paper if you didn't write it. |
Protocols.io resources: 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 Rigor/Reproducibility and RRIDs resources: 1) https://rrid.site 2) 2025 NIDDK summer School Rigor and RRIDs |
|
| Monday, June 30, 2025 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, July 1, 2025 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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| Wednesday, July 2, 2025 10 am-12 pm PDT |
(1) Student Flash Talks;
Special Session: (2) The National Institutes of Health(NIH):What is it and how does it work |
(1) Dr. Maryann Martone Dr. Jeffrey Grethe Dr. Ko-Wei Lin (2) Dr. Ronald Margolis |
Prepare a 3-minute flash talk: Student flash talks: Introduce yourself, your research projects, and what dkNET tools/resources you plan to use |
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| Wednesday, July 9, 2025 10 am-12 pm PDT |
Hypothesis Center; Signaling Pathways Project | Dr. Jeffrey Grethe 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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| Friday, July 11, 2025 10 am-12 pm PDT |
Discussion Sessions: (1) Rigor/Reproduclity and RRIDs (2) Protocols.io |
(1) Dr. Anita Bandrowski (2) Dr. Lenny Teytelman |
Rigor/Reproducibility and RRIDs (1) Check-In project progress Assignment discussion (Rigor/Reproduclity and RRIDs) Protocols.io: (1) Assignment discussion (Protocols.io) |
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| Friday, July 18, 2025 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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| Monday, July 21, 2025 9 am-1 pm PDT |
Introduction to data science, data modeling, and data preparation | Dr. Chen Li and Sarah Asad | Getting familiar with concepts related to data science. Students will start a capstone project using provided data. | https://hub.texera.io | |
| Tuesday, July 22, 2025 9 am-1 pm PDT |
Python programming to do data science | Dr. Chen Li and Sarah Asad | Using Python to do data science. Students will continue working the capstone project. | https://hub.texera.io | |
| Tuesday, July 23, 2025 9 am-1 pm PDT |
Introduction to machine learning | Dr. Wei Wang and Alexander Taylor | Getting familiar with concepts related to AI/ML Students will finish the capstone project. | https://hub.texera.io | |
| Friday, July 25, 2025 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, August 1, 2025 10 am-12 pm PDT |
Student project presentation | Dr. Jeffrey Grethe Dr. Maryann Martone Dr. Neil McKenna Dr. Chen Li Dr. Ronald Margolis Dr. Ko-Wei Lin |
Final presentations (Jonathan Chen, Caroline Chizak, Janielle Cuala, Dakota Deiwert, Evelyn Dziekan, Nitanta Garag, Yafei Hu, Amanda Ifft) | Student final presentation I | |
| Friday, August 8, 2025 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. Chen Li Dr. Ronald Margolis Dr. Ko-Wei Lin |
Final presentations (Neil Kumar, Marius Misiunas, Alivia Pavel, Juan J. Rodriguez, Mankirat Singh, Alice Smagorinsky, Papawee Sutthirat, Ronak Wakhlu) | 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 U24DK097771.
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