# Bioinformatics Interns Blogs

## Transitioning from Bioinformatics intern to an EANBiT MSc. Fellow

**Transitioning from Bioinformatics intern to an EANBiT MSc. Fellow**

Amidst the highly competitive Bioinformatics internship opportunity at ICIPE, we managed to secure positions to enable us to explore the Bioinformatics niche. The four months journey provided not only an introduction to key concepts in bioinformatics such as Programming languages, NGS and Basic Phylogenetics but also an opportunity for the cultivation of professionally relevant soft skills. We got the opportunity to apply the skills through collaboratively working on different mini-projects.

“Coding has always fascinated me. Being from an Applied Bioengineering (genomics-based)
background, I was actively looking for a bridge between the two. The internship provided an opportunity to learn and polish my programming skills under the guidance and see its application in multi-omics data processing using real-life problems. Moreover, it cultivated a self-learning discipline that has played a key role in continuously solidifying and expanding my Bioinformatics knowledge. The skills and experience gained during the internship gave me a competitive advantage when applying for Bioinformatics opportunities hence paving the way to getting the EANBiT master’s fellowship. The internship increased my resilience and self-discipline which still plays a key role in my MSc Bioinformatics journey.”


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“ The internship training demystified my career path in bioinformatics. The introduction to Python programming skills, Linux, R, and Data analysis skills, and collaborative mini-project on RNASeq motivated me to enroll in short courses in Bioinformatics such as the NGS training by H3BioNet after the internship. Additionally, I got to interact with experts in the field through the Bioinformatics Hub of Kenya. My quest to acquire more skills kept me on my toes as I sought to advance my skills to a Master's level. Following highly competitive interviews, I emerged as one of the beneficiaries of the EANBiT fellowship. I am grateful for the support towards achieving my career goal. I look forward to sharing my experiences with the upcoming Bioinformaticians.”

“The internship opportunity laid a foundation for my current career in Bioinformatics. It was designed to equip me with Bioinformatics skills. I got to learn programming languages such as Python and R, Introduction to Biological databases. It helped me improve my communication skills through journal presentations and project progress meetings. I was privileged to collaborate on a mini-project, where I got to put the gained skills into practice through real-time analysis of data. The four months of exposure and mentorship turned me into a Bioinformatics enthusiast and stirred my interest even more to become an authority in the field of Bioinformatics. This led to my application and acceptance as an EANBiT masters fellow.”

“With substantial skills in programming, the Internship served as a platform for me to reconcile my knowledge in Molecular Biology and Computing skills. The introductory training on the concepts of bioinformatics was key in putting my career vision into a clear perspective. It was from the internship program that I established that my interests were more aligned to building software involved in bioinformatics research. From the internship, I learned one key lesson, no single person ever has all the answers to a problem and it’s only by working together and appreciating the different perspectives and ideologies others bring to the table that we get to put the whole big picture together. Currently, I am pursuing my MSc in Bioinformatics, with the hope of eventually fulfilling my long-term vision of becoming a Bioinformatics engineer, a career path and vision I only got to establish during my time as an intern.”

**Wilson Mudaki** MSc Bioinformatics EANBiT Fellow

We are thankful for the immense support we received at ICIPE and we shall keep on sharing what we have learned.

## Nelly Wambui

My name is Nelly Wambui. A friend of mine encouraged me to apply for the internship as it was quite helpful to her growth as an upcoming scientist. The moment I became a bioinformatics intern I felt like a fish in new waters, capable to swim, but we do feel a bit lost in new places, right? The mentors gave us so much guidance and in the end I not only grew in my bioinformatics skills but also in finding a clear career path. The internship was engaging through the various mini-projects and trainings that helped us know what bioinformatics really entails.

In the four months I interned at ICIPE, I gained bioinformatics, planning, presentation and communication skills. The bioinformatics skills made me confident in making applications for bioinformatics job opportunities and scholarships. The planning skills helped me know the importance of having a good schedule for my work to ensure I complete my tasks in good time and in a well done manner. The presentation and communication skills I got from each code review and journal club meeting built my courage in speaking in front of people and I learnt how to make my presentations clear and to the point.

I developed more love for bioinformatics as part of the internship and was therefore sure I would love to do a Masters in Bioinformatics. I have been well mentored by our internship supervisors, even after the four months. Whenever I required a mock interview for a job opportunity they have been available to guide me and I am grateful for having them. It was a wholesome experience that did more than encourage me to be a better person in science. Apart from that, it opened me up to a world of endless opportunities in coding to earn.

I am grateful to have been part of the cohort 4 interns. I do hope that more and more people get to pass through the great team of bioinformaticians at ICIPE and afterwards find themselves in great bioinformatics and genomic science roles in the scientific community.

## Luka Lmelias
My name is Luka Lmelias, I am now studying MSc Bioinformatics on full scholarship at Wageningen University in The Netherlands. I was offered this opportunity after completing a Bioinformatics internship at ICIPE. This Internship was probably the most important transition point in my career, it was the launching pad for my journey in bioinformatics. First, this was where I got introduced to real bioinformatics research. This was very important in opening my research eyes to see how bioinformatics can be applied to improve human well being in terms of agriculture and health care.

Before then, I was passionate about bioinformatics, but I did not have a clear picture of what it was, or how exactly it is being applied to solve real world problems, I didn't even have the picture of how powerful it is in advancing our understanding of biology. Towards the end of the internship, I applied for admission into MSc Bioinformatics at Wageningen University, and after a few months I was accepted and even more exciting, they invited me to apply for a full scholarship that they were offering to 10 African students (African Scholarship Programme). It was a very competitive program where the applicants were to

demonstrate how their respective fields of study are important or will be game changing to the situation in their home countries and how they will contribute in achieving at least three United Nations Sustainable Developments Goals (UN-SDGs). Exposure to bioinformatics at ICIPE was very vital in the application process because it meant I had a much clear picture of bioinformatics and so I could write concise and clear research goals, eventually I was successful.

Second, we received good hands-on training especially in programming in python, R, and basic understanding of Linux OS. This proved to be handy for me now that I am deep into bioinformatics, most of the courses here assume good programming knowledge, the education system is quite different here, learning is like a marathon, and given I am from a biological background, it is quite a task to keep up with a masters in basically computer science. If I did not receive some introductory training into some of the foundational concepts in programming, I doubt I could have kept up the rate of learning here. I am forever grateful to Dr Caleb and Festus for the time and energy they spent in training us.

We were the first cohort of the bioinformatics internship at ICIPE and two out of five won prestigious full scholarships abroad even before completing the internships. This is but a highlight of how impactful an opportunity of four months can be to the careers of young scientists like me. Thank you ICIPE, thank you NIH Fogarty and every one involved in creating such an opportunity."

## **MY BIOINFORMATICS INTERNSHIP EXPERIENCE**

If I were to choose a word to describe my bioinformatics internship at International Centre for Insect Physiology and Ecology, that word would be eye-opening!

I joined the mentorship and incubation program on 3rd June 2021 with the hope of getting to learn more about bioinformatics that was just slightly introduced to me in my undergraduate. I

never fancied wet lab as I regarded it as boring and so immediately after graduating, I knew it was time to find a new path that is exciting and fulfilling for me. I sought guidance from Dr. Caleb, a Bioinformatician at icipe. I got to learn about the amazing opportunity to be mentored and learn more about bioinformatics, and successfully applied for the Bioinformatics Incubation and Mentorship Program.

My bioinformatics journey began with an onboarding activity where we were introduced to the program, how it will run and some rules to abide by. We were then asked to put pen on paper concerning the short-term and the long-term goals together with a road map to achieving them. Writing down my goals ensured that I never lost sight of the bigger picture and helped me get my vision clearer.

The first week, I got to learn about collaborative tools like slack for communications and Git and GitHub for version control. The second week, I got introduced to Bioinformatics where I learned Next-generation sequencing, biological databases, genomics, phylogenetics, Open Science, and project management. Then came the week to learn Python, Bash, and R programming languages which I had never encountered before. I was a bit scared of programming because of the notion that it was hard. At first, I was only concerned with getting the code running and then slowly into knowing what the code does to my data.

There was no better way to conquer my fear of programming than through learning by problem- solving. I got to reproduce a research paper on RNA-Seq analysis with my partner Dorcus Namikelwa. This experience enabled me to hone my problem-solving skills together with collaborative skills. As I completed my first bioinformatics project, I felt a sense of accomplishment, self-confidence, and deep satisfaction. It was then that I realized, bioinformatics is the career for me. With the newfound enthusiasm for bioinformatics, I was eager to do much more for the mini-project.

The beauty of the internship was the collaborative spirit and the positive environment created by the great team at icipe. As I did my mini-project on the identification of Fungal Species from Bee pollen metagenomics data, I would occasionally encounter code errors and would seek help from the EANBit fellows who were always ready to help us. Learning in an environment with no judgment and great support from my supervisors Festus Nyasimi and Dr.Caleb together with the EANBit fellows, enabled me to grow my bioinformatics skills together with self-confidence.

I am grateful to my supervisors, the EANBiT fellows for mentoring me and enabling me to discover my niche, which is bioinformatics. I now continue with my pursuit of gaining mastery in Bioinformatics and to eventually be able to solve the disease burden in Africa. Cheers!

## Simeon Hebrew
My name is Simeon Hebrew and I am currently in my first year of my Masters program in Life Sciences and Health (Genetics, Genomics, Epigenetics and Evolution track) at Université Paris-Saclay in France.

During my final year of undergraduate studies, I was excited to learn about the existence of an intersection between computational methods and biological data; so much in fact that I ended up taking an *in silico* approach to my final year project.

In effort to fulfill this emerging curiosity, I pursued a self-teaching schedule majorly on the foundational concepts of programming in languages which are renowned in the bioinformatics community such as perl and python. This coincided with my timely acceptance into the EANBiT Bioinformatics incubation program based at the International Centre of Insect Physiology and Ecology (ICIPE) which presented the perfect opportunity for me to solidify the self-taught introductory elements as well as learn and apply new knowledge on bioinformatics under the guidance of experienced instructors. To achieve this, I developed a roadmap which enabled me to prioritize my areas of learning in tandem with the proposed internship timeline . These were divided into learning collaborative and version control tools, understanding programming frameworks such as Bash and python, analyzing genomic data using dedicated tools and finally applying the mentioned aspects in an assigned mini-project. This was supplemented by key modules such as navigating high performance computing environments, workflow management platforms such as Galaxy and Nextflow, journal club presentations that allowed us to practise scientific delivery of published research and the concept of open science. As steep as the learning curve was in the time allocated, the journey was priceless. The challenges encountered offered an ideal opportunity to harness problem-solving skills both individually and collectively with my colleagues.

The perfect measure of skill-retention was the mini-project that we (Rose and I) were tasked with that aimed to examine the role of sylvatic transmission of African Animal Trypanosomiasis in livestock by quantifying wildlife-to-livestock transmission in Shimba Hills National Park by genotyping individual parasites using Whole Genome Sequencing (WGS) data analysis. Collaborative working was one of the primary skills that I enhanced during this period. It was essential to completely understand the scope of the project, split tasks, set short-term goals and work towards the realization of these goals. This was complemented by a reinforcement in skills such as how to benchmark bioinformatics tools for analysis , developing reproducible workflows using Nextflow, data visualization using R and scientific reporting. During this time, I had the chance to offer assistance to bioinformatics novels that had enrolled into the Introduction to Bioinformatics course organized by H3ABionet and this served as a helpful platform to share the knowledge I had acquired.

This internship proved to greatly influence my academic and career progression as I inclined towards looking for postgraduate opportunities that were centered on genomics and bioinformatics.Fortunately enough, I was accepted into the earlier mentioned Masters program and so far, I have thoroughly applied the skills I obtained during my internship to actively participate in bioinformatics lectures and practical sessions. I have also used tools such as R to analyze data in wet-lab settings hence proving the universality of the language. This experience not only helped me get accepted to a Masters program, but also gave me confidence to take up bioinformatics-oriented projects such as my current Masters internship which is based on using ATAC-Seq to characterize the regulatory epigenetic landscape of *Platynereis dumerilii* during its posterior regeneration.

I am looking forward to seeing what lies ahead as I continue improving my computational skills and understanding how to continuously apply them in the context of biological data analysis.

## Bryan Abuchery

My journey as a Bioinformatics Intern Student and Job Perspectives.

My interest in Bioinformatics began when I was an intern at the Basic Sciences Laboratory in Kisumu’s Kenya-USA joint Walter Reed Project housed by KEMRI. There, I had some exposure to sequencing (specifically, Illumina Sequencing), whence I became so fascinated with the idea of sequencing data analysis. Immediately after this internship, I applied for EANBit Masters Program 2020 scholarship program at Pwani University, which I did not get. I was perhaps not baked enough yet. However, I was able to get into ICIPE’s Bioinformatics Internship program where I was introduced into bioinformatics, serving as a catalyst for my bioinformatics enthusiasm. There, I received training on what is, and how to handle data analysis. It was while I was there that I got another opportunity to pursue a Masters in Genetics scholarship offered by the São Paulo State University in Brazil.

The training that I received at ICIPE played a big role in helping me prepare for my exams and interviews for my masters degree. With the basic skills and knowledge that I received there, I finally understood that it was not enough to just produce data. Generated data had to be collected, analyzed and presented in ways that justified doing researches or experiments in the first place. Currently I have been able to apply some of the basic skills learnt to do some data analysis such as exploration of phylogenies of some of the important genes being studied (Python and Bash), manipulation of different organism treatment data using R software and code archiving and/or sharing on GitHub. While I have not been able to focus exclusively on Bioinformatics as a study course yet, I feel that these skills have just opened me up to huge potentials in terms of future possibilities and job perspectives.

In future, I intend to fully pursue Bioinformatics in its purity and keep growing my data analysis and presentation skills. I have been and always will be enthralled with genetic data and how these can be used to add onto current knowledge which would greatly help in finding some of the solutions of problems that have plagued us. In my mind, I feel that the training program received at ICIPE has opened up my mind to see data collection (wet lab) and bioinformatics (dry lab) as parts of a whole and therefore greatly expanded my options for a career path as a scientist. The demand for professionals in bioinformaticians is on the rise, even with the rise of data being generated as we get to understand more the world around us. Already I am eying excellent bioinformatics institutions such as the Max Planck Institute in Germany to help me prepare for the future. Who knows, with bioinformatics, the possibilities are limitless!

## Rose
The Bioinformatics Incubation and Mentorship Program under Eastern African Network for Bioinformatics Training (EANBIT) granted me a prestigious bioinformatics internship and mentorship program at *icipe* under the Molecular Biology and Bioinformatics Unit (MBBU).

I learnt the importance of open science in the bioinformatics field. I had the chance to learn how to use collaborative tools in research including Github and Slack for communication and project management. These tools played an important role in the success of my internship through enabling efficient collaboration and communication with fellow bioinformaticians in the projects that I participated in. To date I still use Slack and GitHub in collaboration and communication in other virtual bioinformatics projects including the BOSS mini projects organized by Bioinformatics Hub of Kenya Initiative (BHKi).

On joining the program, my expectations of the bioinformatics internship were to understand, analyze and come up with relevant biological inferences to genomic data. My expectations were met as part of the program was an intense training facilitated by competent and highly motivated bioinformaticians. I learnt programming languages including bash, python and R from the basics to using the programming languages in parsing genomic data. I also enjoyed the opportunities on virtual workshops and seminars from H3Abionet and Galaxy that supplemented training offered by my trainers; Festus Nyasimi, Geoffrey Kimani, Andrew Espira and supervisor, Dr.Caleb Kibet. One of the best virtual courses that I attended was GTN Smörgåsbord: A Global Galaxy Course which covered the general introduction to the Galaxy platform, NGS analysis (DNA-seq and RNA-seq), and proteomics. I have been participating in other courses and workshops up to now. Currently, I am enrolled in a virtual online short-course organized by H3Abionet on Genomics Medicine.

The bioinformatics team at *icipe* is not only limited to trainers and supervisors who guided me, but also a group of EANBIT’s Master’s students in Bioinformatics. My interaction with the highly motivated MSc. students further enhanced my understanding of some concepts in bioinformatics and even guided me in troubleshooting tricks whenever I encountered some challenges.

The best part of the internship program was the problem-solving skills that I gained by engaging in the 16SrRNA analysis for H3ABionet accreditation and the development of a variant calling- pipeline for microbes using GATK. I also delighted in participating in the journal club sessions

that were held biweekly on Thursday. These sessions were key to me as I gained insights and knowledge on different topics. I was quite fascinated by the presentation on Molecular digital data storage using DNA. Other than journal club sessions, was the Monday update meeting which aided me in utilizing a schedule plan and being goal-oriented.

This internship experience laid a strong foundation for me in bioinformatics and genomics and helped me in transitioning and securing other opportunities in my career. As I write this, I am an Assistant Research Officer at KEMRI-Wellcome Trust Research Program, working with Professor Philip Bejon’s lab, leveraging control human infectious studies in studying the efficacy and safety of Malaria and Shigella vaccines. Additionally, I am also enrolled in an African Genomic Medicine Training (AGMT) 2022 course organized by H3Abionet. I am deeply grateful to the EANBIT program, and *icipe* for the incredible internship opportunity.