Just do it!
The Most Prolific 5 Weeks Internship with HackBio
A journey of growth
Who am I?
I am a medical graduate from Bangladesh, currently pursuing my Doctor of Medicine (MD) in Virology at Bangabandhu Sheikh Mujib Medical University. I am passionate about impactful research and constantly on the hunt to acquire new skills.
What drives me
I am driven by an insatiable thirst to explore new things and my quest to solve existing problems using an interdisciplinary approach. I have a passion to integrate multiple disciplines to tackle an existing problem and bring a new perspective to the table. What I realized is that the problems we are tackling now are beyond the borders of a specific discipline. So, approaching these problems with an interdisciplinary approach yields better results.
With the advent of NGS platforms, the data being generated is beyond manual curation. So, an understanding of the bioinformatics approach is a must to glean insights/knowledge from complex data.
I remember one saying by The New York Times best selling author Shiv Khera, “We are drowning in information but starving for knowledge”.
My scientific interest
- Genomics
- Transcriptomics
- Proteomics
- Vaccinomics
- Immunoinformatics
- Cheminformatics
- Single-cell RNA sequencing (scRNASeq)
- Artificial intelligence (Machine learning, Deep learning)
- Computer-aided drug design
Experience with HackBio
The most rewarding aspect of the HackBio internship has been the ability to collaborate with people from diverse disciplines, cultures, and learning from all their collective experiences. The 5 weeks online internship was divided into 5 stages with each stage associated with its distinct task. Failing to perform an assigned task led to elimination at the end of each week/stage.
Stage 0
For stage zero, we were (team-sanger) tasked with writing a bash script that will able to create a comma-separated value (CSV) file from at least 7 different bash executable programming languages with the details of each participant, that was supposed to be deposited in a GitHub repository. I wrote my script in 5 languages (Python, R, Perl, PHP, Ruby) and learned the basics of each language. The team was lead by my colleague Winfredgatua. I was tasked with the role of the team-assistant to coordinate our task with 15 members of diverse backgrounds both in education and culture.
For example, my Perl code looked like this. The rest of my personal codes are available in this GitHub repository.
#!/usr/local/bin/perl
$name = 'Maruf Ahmed Bhuiyan';
$email = 'dr.marufahmed89@gmail.com';
$language = 'Perl';
$biostack = 'Genomics';
$slack = '@Maruf';
print "$name, $email, $language, $biostack, $slack";Our team GitHub repository could be found here.
Stage 1
In stage 1, we were to create a team and come up with our own idea to explore any query that involved a bioinformatics approach. I founded team-venter, named after the famous scientist Craig Venter, along with Pawan Verma. We were lead by Winfredgatua for this job and assisted by Pawan Verma. We developed a phylogenetic tree from the countries our team members were hailing from. The script we developed would select 10 complete genomes of SARS-CoV-2 randomly, for each country, from the NCBI database, and create a phylogenetic tree using MAFFT and IQ-TREE, based on the retrieved genomes. More information can be found here.
Stage 2
For stage 2, we (Team genomics-two) were to come with an independent research proposal that will materialize in the following stages. We came up with the research proposal to do transcriptomic analysis on publicly available RNA-seq data on nasopharyngeal and peripheral blood mononuclear cells samples in COVID-19 subjects compared to healthy controls. We were constantly guided throughout this process by our mentor Sarah Carl.
Stage 3 & 4
The entire team of 23 members of diverse backgrounds sprung into action to materialize the proposal into an impactful scientific article. The team was divided into sub-teams to take action on each specific task. With the relentless work of the entire team, the tender bud of proposal slowly but surely turned into a full-blown scientific article. I took part in the analysis of the datasets using the DESeq tool in R and generated the principal component analysis (PCA) plots while constantly providing feedback and writing with the methodology and other manuscript sections. I also developed the website to showcase our work with the rest of the world.
At the end of the internship, our team was chosen as the best team amongst the five teams that participated in the internship. I express my sincere love and gratitude to each member of the team, specially Winfredgatua, Caroline, Karan Kumar.
Skills acquired at HackBio
My experience with HackBio led me to take online courses to gather more knowledge. You can see some of the courses I took here.
The HackBio experience has enriched me in many ways that are beyond measure. It provided me confidence, enthusiasm, new vigor, and love for bioinformatics. Here are just a few highlights of some of the tangible skills that I acquired during the internship.
Technical Skills
- Bash, Command Line Interface (CLI)
- HTML, Markup language
- Git Versioning
- Proposal Writing
Soft Skills
- Collaboration skills
- Leadership skills
- Communication skills
Thank you Science, thank you HackBio! 🔥
Hobbies
I have an intense love and passion for Photography. When I am not preoccupied with research, I love traveling and photographing the world through my lens. Sometimes I love to cook.
You can check out some of my photographs here.
Contact
Email: dr.marufahmed89@gmail.com
