What to expect from the HackBio genomics internship

The HackBio Genomics internship is here again and it is another opportunity for researchers worldwide to connect for the purpose of learning and career development.

A little bit of history: The first edition of the internship happened between August and September, 2020 (about 4 years ago). It was a fast paced, accelerated and project based learning experience. With about 700 students (and 69 finalists; < 10%), we hosted the first edition of the internship successfully with lots of gifts and memories. Since then we have hosted the internship 2 more times with over 5000 students, 20+ projects/publications and lots of success stories.

Historically, the internship is divided into 5 stages (0,1,2,3 & 4), with each stage representing a really hard task to be solved in one week. Also, the internship is known to be unforgiving; failure to meet up with the deadline and requirements for teamwork means you are out.

This time, we are rethinking this steps have included major fixes to help people who need more time to learn, connect with their teams and solve the tasks. Major Fixes include:

• 5 stages is now reduced to 4 stages
• 5 weeks is now increased to 8 weeks. Meaning, 2 weeks for each stage.
• Fortnight meeting with mentors to explain task and assign appropriate learning resources.
• We retain elimination and deadlines at each round to maintain dedication.
• People who are resourceful/helpful also gain extra points for their efforts.
• Cool gifts by the end of the internship to amazing people and teams.
• If you gather up to 50 resourcefulness points, special perks await you

Recommended Learning Resource: HackBio’s genomics course.

We will also suggest some youtube videos for you to use along the way if you are unable to purchase the course.

Stage One (2 weeks): This time, we are ignoring the stage zero, because we want participants to ease into the program, integrate with your team take their time to learn and build their confidence. I have personally received reports that people who could not scale through stage zero have developed some level of hate for bioinformatics which is not our goal.

In this phase, you will learn how to program in BASh. There are two tasks in this stage:

• You will complete simulate a day in the life of a molecular biologists using BASh
• You will create a conda environment loaded with at least 5 bioinformatics tools

Stage Two (2 weeks): Here, you will build a fully functional NGS data analysis pipeline that can handle any given NGS dataset and spit out the mutations in the dataset. This is the foundation of genomics. It has a little bit of software and data engineering components but we provide enough resources to help you solve them. You will write everything in BASh. You will use this pipeline at later stages in the internship, so make sure it works well on any dataset or device/system.

Everything in this stage will be fully tested for speed, accuracy and reproducibility. We prioritize more on reproducibility and accuracy over speed. Also, at the end of this stage, someone in your team should be selected randomly to present your pipeline and how it works.

Stage Three (2 weeks): This is the first CV worthy project you will do. We should also inform you that you will have to split your team into 2; the technical people that will work on the coding side of the projects; and the communications part that will work on writing a technical report as well as a short video describing what you did in simple language.

Stage Four (2 weeks): This is another CV worthy project that will help you utilize your genomic skills to solve important questions on several applications of genomics. We will provide datasets for 1 cancer subtype, plant disease, neurodegenerative disorder and lifestyle related disorder. At this stage, if you also have a project idea, it is also welcome and you can convince your teammates to join you in solving it together.

What you stand to gain:

• Learn and develop new expertise in bioinformatics and genomics
• Accomplish you learning and upskilling goals
• Win amazing prizes
• Lifelong Network and bragging rights
• Learn about other people, cities and culture
• Preparation ground for graduate school
• Build invaluable project and research experience in bioinformatics
• Develop interesting bioinformatics tools and pipelines to solve top research questions

We look forward to having you around for the internship. Be ready to learn, network and willing to share your knowledge with others as well.

HackBio Team