Learnings with HackBio
From novice to better
“ All I knew was that I am fascinated to find the answers regarding how things work in nature. While growing up, I always had a curiosity to know about the science behind everything that happens in life.”
Who am I?
I am Karan Kumar, a Bachelor’s holder in Biotechnology at the National Institute of Technology (NIT) Calicut and currently am pursuing a Ph.D. in Energy at the Indian Institute of Technology (IIT) Guwahati under Prime Minister’s Research Fellowship (PMRF). I am focused, disciplined, and passionate about learning new skills with great versatility; enthusiastic and determined towards goals; altruistic and decisive by nature; comedian at times; and inquisitive about nature.
I research Environmental Engineering and Biotechnology. My interest lies in applications of state-of-the-art techniques from molecular dynamic simulation, systems metabolic engineering, machine learning & artificial intelligence in biological systems.
Life before NIT Calicut
Eight years ago, I was not exactly sure what to do with myself. I had just completed my Secondary School Examination (Class Xth) from a government school in a remote village of Bihar (India). Unlike some of my friends, who had a clear vision about their career, I did not have a clear idea about how to enter into engineering and medical professions.
All I knew was that I was fascinated to find the answers regarding how things work in nature. While growing up, I always had a curiosity to learn the science behind everything that happens in life. The curiosity inside me leads to choosing science as my career.
I pay my sincere gratitude to Mr. Anand Kumar (Super 30, India) for introducing me to IIT-Joint Entrance Examinations. His mentoring and the way of answering the mathematical problems motivated me to choose Engineering.
After my Intermediate Examination in Science in 2014, that same year, I cracked IIT-JEE(Mains) and got enrolled in an institute of national prestige for pursuing a Bachelor of Technology in Biotechnology at the National Institute of Technology (NIT) Calicut, Kerala (India). Apart from the four-year curriculum at NIT-C, I learned many aspects of life, how to deal with real-life problems, developing my personality, and how to make a balance in social and professional life.
Also read “My Journey in science: learning from ups and downs” by Karan Kumar (published in Science and Philosophy)
Hi!! This is Karan Kumar. I’m 24 years old and was born and raised in Bihar, India. In the year 2018, I graduated as a major in Biotechnology at the National Institute of Technology (NIT) Calicut; and joined IIT Guwahati to pursue my doctoral degree in Energy under Prime Minister’s Research Fellowship (PMRF).
E-mail: karan18@iitg.ac.in|karaniitg.pmrf18@gmail.com
|Website |Twitter|RG|YT| GitHub|Google Scholar| LinkedIn|Medium|Insta|
HackBio: my first virtual internship
I successfully applied and been selected for the open virtual internship without much expectation of the program. On August 1, 2020, we held our orientation, where we had a calendar of events shared with us and the internship expectations.
When I saw the calendar, I was a little scared; however, having to experience the dynamics of work in the application of bioinformatics appealed to me. I knew that the challenge would be greater and I was very excited to have this opportunity. The internship had a total of five stages ranging from the stage (0 to 4). Each step brought new challenges. It felt really good when I was able to complete each task of each stage.
When I applied for the internship, I was a complete beginner in the field of Bioinformatics. However, with time being in stage zero, I learned about MATLAB, Python, Git, GitHub, and Bash scripts. At that stage, I worked with Team-Rosalind. We were a team of thirty people. The spirit of teamwork saw a majority of my group members to stage one. Link to our GitHub Repository here, report here, and video demonstration here.
The most rewarding aspect of HackBio internship has been collaborating with people from diverse disciplines and learning from all their collective experiences.
Stage one came with its surprises, where we were required to collaborate in google docs and utilize at least 1 bioinformatics software. My team, Team-Mullis was under the bio-stack, Genomics. We used the edgeR package in R. We did differential gene expression analysis between control and schizophrenia samples using edgeR. I liked the teamwork spirit in this team, thanks to @giwa (our team lead); because of him I learned to write R script with RStudio and used it to explore the GEO expression dataset. Link to our demonstration video here and our google drive here.
The power of collaboration was very evident to actualize the idea.
Stage two, we wrote a proposal under the mentorship of Sarah Carl, who never got tired of reviewing our work. The power of collaboration was very evident to actualize the idea. A proposal that may take four weeks when alone was feasible in less than four days. I contributed to the significance of the research section and thanks to my team members for their contribution to this section of the proposal. The success at this level saw the 29 of us advance to stage three, we only lost one member along the way.
Some useful Links related to HackBio:
Tweet: Final presentation and awards day is here! Join us on 5th September, 2020
Women In STEM series: https://www.youtube.com/playlist?list=PLSp3zewvz-W-3uM_y6KHYaP0UMFepWY9X
Fireside chat series: https://www.youtube.com/playlist?list=PLSp3zewvz-W_Q1oWyPoI3jPEI0l85JX5d
Virtual Tourism on HackBio: https://www.youtube.com/playlist?list=PLSp3zewvz-W8wawREQnbR6eDwho1lzEk9
GitHub and Git: https://www.youtube.com/playlist?list=PLSp3zewvz-W-V8sYkcroZBCL1zC7UIE5J
In stage three, I worked with methodology, result analysis, and reference management team. Hard work was visible here as well, we got on track so fast in downloading data from public databases to analyze in R. This was an excellent opportunity for me to solidify my RNA Seq Analysis skills. Our team got featured as the second-best team of the HackBio program, and we received a token of hard-work for this.
Our team got featured as the second-best team of the HackBio program
We are in stage four (final stage) now. We are into writing a manuscript, which is a great learning opportunity for me. I prepared the graphical abstract for the manuscript. We are looking forward to triumph even as we come to a close of the internship.
Team Genomics-Two: International Collaboration for Transcriptomic Analysis under the HackBio Internship Program
Website: https://genomics-two.carrd.co/#
Skills acquired in this journey
Technical skills:
Python, R, Git GitHub; Genomics and Transcriptomic analysis, Research Proposal writing, Manuscript writing
Soft skills:
Collaboration skills; Journal search skills; Networking skills; Teamwork; Communication skills
Given an opportunity, I would choose HackBio again. I can’t wait to volunteer in forthcoming internships and any other activities organized by HackBio.
