The CGC Community
CGC as a Teaching and Training platform
The National Institutes of Health (NIH) has made several foundational investments in funding basic and translational research which generates massive amounts of data as well as data analysis ecosystems or platforms to empower the scientific community to analyze these large datasets. Over the years, the Seven Bridges Cancer Genomics Cloud platform has not only enabled researchers to perform collaborative research, but it has been used as an effective teaching platform for training the next generation of national research workforce. Several universities and research institutes are effectively utilizing the CGC for their teaching and training programs.
SYSTEMATIC APPROACH TO TEACHING
Search through harmonized public data or upload your own.
Add students and collaborators to the class project and change permissions accordingly.
Monitor progress of the class workflows in real time, take notes, and share results.
Benefits to using the CGC:
Simple visual representation of the steps in the workflow
Easy for participants to grasp basic concepts, before using command line
Easy to run pipeline, mostly point and click
Easy for instructor to monitor in class work and homework
One billing group allows for easy monitoring of resources
Collaborative environment with Seven Bridges provides support to the class
Participants are encouraged to attend Seven Bridges Office Hours
SUCCESS STORIES
TEACHING USING THE CGC - GEORGETOWN UNIVERSITY
We interviewed our long term collaborators Dr. Yuriy Gusev and Ms. Krithika Bhuvaneshwar from Georgetown University who have been using the CGC platform for the past 3 years to train the next generation of data scientists in their Masters in Health Informatics and Data Science Program. Here are a few excerpts from their interview:
“To make it easier for students, we decided to use Seven Bridges’ collection of tools, because they are presented in a very user-friendly, graphical interface where students have this low barrier to understand and start using the pipelines which otherwise would require a lot of additional training.” Dr. Gusev
“I think the Seven Bridges has a nice framework for teaching, because the way we set up the infrastructure is: we have one project which we create for each of our students, and then we copy the pipeline and we teach them how to copy the data as well.” Ms. Bhuvaneshwar
2. TEACHING USING THE CGC - UCSD
Professor Jeremy Chien from UC Davis used CGC to teach a streamlined, hands-on course in cancer genomics to undergraduates. The platform eliminated the lengthy setup and steep learning curve usually associated with bioinformatics, allowing students to dive directly into real-world data analysis. The results? Engaged students who gained valuable skills and appreciated the hands-on approach.
To educators considering using the CGC, Dr. Chien says: “Just do it!” In our post-course interview with him, he emphasized the ease of use, availability of public data, and strong support from the CGC team. The CGC is an excellent platform that makes bioinformatics accessible and engaging, maximizing the educational impact in a short period. For those interested in leveraging CGC’s educational capabilities, support is just an email away.
3. TEACHING USING THE CGC - PURDUE UNIVERSITY
We partnered with Min Zhang at Purdue University to deliver a four-part series on RNAseq as part of their STAT-581 course. Each class consisted of a lecture on an RNAseq topic and hands-on training on implementing an analysis on the CGC. We used data in the Sequence Read Archive, providing a real world example for the students to follow. All students were able to accomplish the training in each class. Here is some of the written feedback we received:
“I wasn't aware of that many public datasets before so knowing that I can access all of them from CGC instead of downloading them myself definitely saves effort. And the pipeline makes it easier to complete multiple steps of analysis in several clicks. It is efficient and easy for researchers with no computing background to perform the analysis.”
“Before [the CGC] lecture series, Bulk RNA-Seq felt like it was a lot more complicated and it would have taken me a lot longer to understand this. But this lecture series helped in simplifying it.”
All lectures were recorded and are freely available on the Purdue Website, as linked below.