HackBio2020 Internship Experience
Who am I?
I am Winfred Gatua; a Bachelors degree holder in Biomedical science and technology at Laikipia University and a PGD holder in Health Research Methods at Pwani University/KEMRI Wellcome Trust Research Programme and currently am pursuing Masters of Science in Bioinformatics at Pwani University under East Africa Network for Bioinformatics Training (EANBiT) Fellowship.
I am focused, disciplined, and passionate about learning new skills with great versatility.
My first Virtual internship
Having successfully applied and been selected for the Hackbio open virtual internship, I did not know exactly what to expect. 1st of August 2020 we held our orientation where we had a calendar of events shared with us and the expectations of the internship.
When I saw the calendar, I was a little scared since at the same time I was involved in a Bioinformatics virtual training which was equally as demanding as the internship.
However, with resilience, hard work, perseverance, patience, humility, teamwork, and determination I have equally excelled in both programmes.
Stage 0
This opportunity is one of its kind, given task 1 in week 1, I landed myself in team Sanger, it was great working with all my team members. I was very naive. I never wanted to be a leader, but unfortunately, we were only four females in a group of 30 participants. We voted and a majority voted me to be the team lead.
I was shy since all along, I have wanted to be a follower rather than lead, however, thanks to Leadership training held at Pwani University based on the book Developing Global leaders: Insights from African Case Studies by Eva J et al.
These skills were the best at this moment, task 1 was not easy for all of us since a majority had no background in Programming, thanks to Zoom, we held very many meetings to get everyone on board and acquainted with the task and do the task on their own.
Thanks to @Akurut and @Maruf, who were very instrumental as we demonstrated to our members how to write simple scripts in different languages and use of git and GitHub. With the task on board, I was challenged to learn more languages to complement the requirements of the task including javascript and PHP. The spirit of teamwork saw a majority of my group members to stage 1. Link to our GitHub Repository here.
Stage 1
Stage 1 came with its own surprises, where we were required to collaborate in google docs and utilize at least 1 bioinformatics software.
Team Venter, here we are under the bio-stack Genomics. We utilized the following software: MAFFT, IQtree, Jalview, Figtree, Biopython, and above all Conda was very instrumental in all this.
We did a phylogenetic reconstruction of the SARS COV 2 from our countries of our participants' origin. I liked the teamwork spirit in this team, thanks to @Pawan who was my assistant team lead even as we carried out the task. I learned about using the dataset tool in NCBI to download bulk sequences at a go. Link to our GitHub Repository here and our google drive here. As a team we went further from the task given, to perform hands-on variant calling of some E.coli isolates. Here is the link to the recordings of the meeting about the variant calling, a step by step approach to quality SNPs.
Stage 2
Stage 2 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 4 weeks when alone was feasible in less than 4 days.
I was in charge of methodology 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 stage 3, we only lost 1 member along the way.
Stage 3
In stage 3 I was in charge of methods and analysis. The hard work was visible here as well, we really got on track so fast in downloading data from public databases to analyses in R, this was a great opportunity for me to solidify my skills in RNA Seq Analysis. We shared our scripts which made our work very easy in reproducing results.
Stage 4
We are into writing manuscripts which is a great learning opportunity for me to learn. As well as preparations to present our work to the community. Looking forward to triumph even as we come to a close of the internship.
Ask Me Anything (AMA)
Above all, AMA sessions were equally very important, the fireside chats with our mentors were inspiring. Lessons learned: Application of scholarships successfully with ‘Wale Joseph Ogunleye, Sites to learn structural Bioinformatics with Niyi, women in science and choice of career path with Sarah Carl and Galaxy. The transition from academia to industry using already existing technology to address biological questions courtesy of Alice Rathjen, co-founder of DNA Compass.
My research Interests
- Virus evolution and phylodynamics
- Toxin Research
- Human Genetics
- Machine Learning
- Open Science
Skills acquired:
Technical skills
- Programming: Javascript, PHP, Debugging
- Mapping using ArcGIS
- Research Proposal writing
- Manuscript writing
Soft Skills
- Collaboration skills
- Leadership skills
- Journal search skills
- Networking skills
- Team work
Given the opportunity, I would choose HackBio again.
Thanks, ‘Wale Joseph Ogunleye for advocating for women in leadership which saw me in leadership from stage 0 to stage 4. I’m greatly indebted to everyone I interacted with and all my team members in every stage.
I can’t wait to volunteer in forthcoming internships and any activities organized by HackBio.
“We must believe in ourselves or no one else will believe in us; we must match our aspirations with the competence, courage, and determination to succeed.”
- Rosalyn Yalow
Thank you, Science, ✨🌟
Thank you, Hackbio 💪
Let’s connect!
Email address: winfredgatua13@gmail.com
Linkedin address: https://www.linkedin.com/in/winifred-gatua-0b2317101/
Twitter: @gatuaprof
