Checking in with the Bioinformatics teams

First of all, goodbye to students who are leaving!

It was a pleasure having you with us! Hope you had a great experience. We will notify you when your certificates are ready.

Thank you to those who sent me personal notes. Unfortunately I do not have the time to respond as of now. I do appreciate your note and will reply as soon as the July session gets rolling!

If you are applying for a new pathway in the July session, please follow the posts in

Tip - Use the office hours that are early on in the week to ramp up on the new pathway. Office hours will start getting more crowded later on in the week.

Speaking of office hours, special thanks to Alec, Alicia, Anca, Anya, Kristen, Medhini, Priscilla, Yoga for hosting Bioinformatics office hours for new students! You are making it possible for us to meet our mission of expanding STEM opportunities!

For those who are remaining on for the next 3 weeks, your leads are continuing. Annie has to leave after Week 7 but has offered to help out as much as possible. Thanks Annie!

Initially, we had though of letting students work on pipeline customization after we finish with the STEM-Away pipeline that all of you have been working on. Personally, I think it is time to step back from coding and revisit the big picture with the bottom-up knowledge that you have acquired. Revisit it with help from your leads, Ali, and other mentors.

My proposal is to have students pick up a paper and make a presentation that documents the pipeline, highlight the portions of the pipeline that you are now familiar with, highlight the parts that are new, recommend projects for the winter session! If we pick your recommendation, you are automatically in :slight_smile:

I am open to suggestions. If the majority prefer to continue coding, I will listen.

Finally, for the students who are interested in the next session. I will share more details shortly. But in brief, the changes are:

  • There will be technical changes to the STEM-Away pipeline. The two datasets will be combined to introduce a batch effect. This will ensure a significant amount of new technical learning. Mentors will work on introducing additional changes as well.

  • And an idea proposed by your mentor Jia that I think will really improve the overall execution in terms of engagement and catering to a range of experience levels.

The concept of functional roles will be introduced. For example: the data curator is responsible for data input, metadata processing and data visualization. Analyst is responsible for pre-processing and statistical analysis. Biologist is responsible for pathway analysis and interpretation of results.

Participants can choose roles to work on based on their interests and skills. We will still go through the full pipeline. But instead of a mandatory deliverable for each stage, participants will have a mandatory deliverable based on the role (or roles) picked. They will do a deep dive into the part they are looking into. And explore that role to a great depth.

We will work out the scheduling such that every role can get started without having to wait for the final deliverable from the previous role. All deliverable will be combined at the end to get the final pipeline.

1 Like