The year continues to fly past and we are approaching the end of a rather turbulent 2020 on the “Coronacoaster”. I have not seen the H3ABioNet central team since mid March, apart from the odd glimpse when someone is brave enough to turn on their video in one of our endless Zoom meetings. I am very productive working from home (with my dog on my lap) but do miss our interactions and ad hoc discussions. Nevertheless we have all adapted and the show has gone on.
At Central we have worked hard to release the H3Africa Data and Biospecimen catalogue, where users can now search for and request access to data in the EGA and samples in the biorepositories. We have also submitted additional datasets to the EGA. Some of our team were involved in the recent GA4GH virtual plenary as members of the organization committee, other committees or working groups, or giving short talks. Otherwise it is business as usual, juggling many tasks, especially for those currently running the Intermediate Bioinformatics Course.
This newsletter provides several reflections from members of H3ABioNet on their activities within work packages, as node ambassadors, as a PI, and a journey through our Introduction to Bioinformatics course. We also have some useful information on Bioconductor and introducing the REDCap offerings in H3ABioNet. One of the announcements describes the publication in Nature of the H3Africa effort on analysis of whole genome sequences from Africa. This was a long, collaborative process and a demonstration of how the capacity the consortium has built has enabled the analysis and interpretation of human genomes on the continent. Enjoy the read.
Being a PhD Student and Career Aspirations, How it Feels like to Publish and Achieve while the World is on Fire
By: David Twesigomwe
It is a huge understatement to say that the world is on fire in 2020 as challenge after challenge continues to arise. The COVID-19 pandemic is perhaps the most notable scourge as it has led to numerous hospitalisations, loss of life, and lockdowns globally. Silver linings are few and far between given the sudden change to life as we know it.
For me, being a PhD student feels so surreal after a successful upgrade from MSc (Med) Human Genetics at the University of the Witwatersrand in March 2020. My MSc work involved bioinformatics analysis of the pharmacogenomic variation in the CYP2D6 gene in African populations. The first publication from this work is a comparison of star allele calling tools (https://doi.org/10.1038/s41525-020-0135-2). The PhD part of the research entails the development of a novel star allele calling algorithm for cytochrome P450 genes as well as the validation of novel African-specific CYP2D6, CYP2A6 and CYP2B6 alleles via long-read resequencing. Probably the most notable highlight in this challenging time has been access to more opportunities to present my research at virtual conferences which I may not have been able to attend in-person. These small victories have boosted my motivation throughout lockdown especially after having to endure delays to our lab work.
My main career aspiration is to contribute to the implementation of precision medicine approaches in Africa preferably as part of the African Pharmacogenomics Consortium, which was launched to promote capacity development and to address challenges such as poor drug efficacy and safety. In one way or another, the dire search for an effective and safe COVID-19 vaccine and/or cure is underlining the importance of precision medicine even further. I dream of a time when sizeable African-specific pharmacogenetic data is readily available to contribute to the success of such causes and more. Additionally, I would like to continue being involved in the activities of the H3ABioNet or similar bioinformatics networks to follow as I have found great joy in serving as the H3ABioNet Wits node ambassador.
There is definitely a long way to go during my PhD research and the challenges in 2020 are not doing us any favours. Nonetheless, I attribute my progress so far to the guidance and support of my supervisors (Prof Scott Hazelhurst and Prof Zane Lombard) and everyone that’s part of the H3A/GSK ADME collaboration.
All You Need to Know About Getting Started with Bioconductor
By: Yagoub Ali Ibrahim Adam
Bioconductor is an open-source and open-development software project for computational biology and bioinformatics. Bioconductor is based on the R programming environment for statistical computing and graphical display. The Bioconductor project started in 2001; however, its first version (Bioconductor 1.0) was released in May 2002. Bioconductor aims to provide well-documented tools for genomics data analysis. In the beginning, Bioconductor has lined up its effort on developing tools for analyzing and visualizing microarrays data (Chip technologies); however, these days, Bioconductor provides a wide range of R packages for various Bioinformatics research areas. Bioconductor provides statistical data analysis tools to analyze different life science experiments, including microarray, next-generation sequence, Chromatin precipitation, GWAS data, proteomic data, and other data. Besides providing computational methods for genomics data analysis and visualization, Bioconductor also provides R packages for biological metadata integrations and provides biological data annotations resources.
The Bioconductor packages are grouped into the following categories: (i) Analysis software packages, (ii) Annotation packages, (iii) Experiment data packages, and (iv) Workflow packages. For instance, the recent Bioinconductor version (Bioconductor 3.11) released in April 2020 consists of 1903 software packages, 391 experiment data packages, 961 annotation packages, and 27 workflows. Bioconductor provides the BiocManager package as a robust tool for installing and updating Bioconductor packages. For most Bioconductor users, there is no need to have advanced programming skills; however, a good knowledge of the R programming environment is necessary. Besides providing R packages for genomic data analysis, Bioconductor offers many educational resources to train bioinformaticians in computational and statistical methods to study genomic data. The Bioconductor training materials can be found by clicking here.
To promote its mission, Bioconductor has various advisory boards that provide project oversight. These advisory boards are the scientific advisory boards, the technical advisory boards, and the community advisory boards.
In summary, Bioconductor is an open-source project associated with the R programming language and statistical environment. Its mission is to promote the statistical analysis of high-throughput biological data. Bioconductor provides high-quality bioinformatics workflow, documented packages, and it helps foster reproducible research and enhances scientific communication and collaboration. Also, Bioconductor provides the resources for developing and deploying extensible, scalable, and interoperable bioinformatics software. Moreover, Bioconductor facilities for the researchers using biological data annotations from different resources.
Journey through IBT, from Start to Phylogenetics
Creative piece by: Adebowale A. Alade (MNIM)
IBT 2020 participant
I didn't know where I was going but I knew I needed to move from where I was, I needed to move forward, I needed something more challenging, I needed to grow, I needed to try to quench my insatiable hunger for knowledge. I was told about a park that could take me from where I was to where I needed to be. I went there, since it was true, would I have hesitated? I hopped on the bus, met a lot and different kinds of people, a few were like me too.
Prrrr-jam! The bus door was shut, we were ready to move. We moved. I was going into the unknown but mentally prepared. As an intelligent person, I noted every route we passed just in case things go south. I put every signpost we passed by to paper. Weird me right?
The journey into the unknown started with an introduction to 'Biological Databases and Resources' then to 'Literature Searching', I even came across an interesting signage 'DNAseqAnalysis', I didn't really get the message but we moved. Now we were in the 'LINUX' city. Trust me, the language in this city was entirely different from any I've ever heard. We stopped in this city to answer the stomach call. I ate before I left home, so I only came out of the bus to stretch my legs. I met some citizens of the city and it only took me a few minutes to understand and speak the language of the city. Interesting? I told you I'm intelligent 😊
To cut the long journey short, we entered a very beautiful and interesting city, to me, the 'SEQALIGNMENT'. D**N! 'MSA' is interesting. Wish you were with me. Then we moved up north, to the most beautiful city in that state, 'JALVIEW'. A city with an amazing art and act of the journey, you need to see that city please. Moreover, We made it to 'GENOME BROWSERS' city where we see 'variant' individuals. We even made it to 'NGS and COMPARATIVE GENOMICS' cities too.
Finally to the last city, this city left me with many unknowns. I came into the unknown journey initially because I believed I would get answers, but table turns, now I'm leaving with many unknowns. The city of 'MOLECULAR EVOLUTION and PHYLOGENETICS' taught me a lot. I realized that it was good to leave with unknowns. This would make me explore more to know more. The more we know, the more we realize the unknowns. I'm happy I'm leaving with unknowns, I'll get the answers to them soon to face another set of unknowns. The solution to a problem is another problem after all.
This is my journey being a participant at the #IBT2020 iteration. I'm so grateful to the tutors and coordinators, I love them all, they are all amazing people. My big thanks to H3ABioNet for her mission and vision for Africa. Keep soaring and exploring without limitations. Thanks for the privilege.
Alade, Adebowale A.
Tell us a bit about yourself:
I am Shakuntala Baichoo from the University of Mauritius (UoM). I joined the university in 1996, as a lecturer in the field of Computer Science, I am a computer scientist by training and I have an undergraduate degree in computer engineering, an MSc in distributed systems and a PhD in Computer Science. I finished my PhD in 2006 and after that, I changed my research orientation from computer science to bioinformatics. I work as an associate professor at the University of Mauritius, in the Department of Digital Technologies which is in the Faculty of Information, Communication and Digital Technologies (FoICDT). I teach modules like programming, data structures, computing for life sciences and distributed systems.
Tell us a bit about your institution:
The University of Mauritius is the main university on the Island. FoICDT was formerly the Dept of Computer Science and Engineering, as part of the Faculty of Engineering when I joined; it was created about 3 years ago. The University also has other faculties such as the Faculty of Science, Social Sciences & Humanities, Law & Management, Engineering and Agriculture. Our main business consists of teaching, but we are also encouraged to do research at the university. In 2014, I along with other colleagues, organized a computational metagenomics workshop, as an H3ABioNet event, with collaborators from Greece, Cyprus, South Africa and Sweden.
How did you get into bioinformatics?
After I finished my PhD in 2006 I wanted to change my orientation. Coincidentally in 2009, an external examiner, Prof. Niranjan from the UK, introduced the field of bioinformatics to a few of us. Thereafter we had a meeting with him and Prof. Yasmina Jaufeerally-Fakim and that was how we started. In 2010, Yasmina organized a workshop on bioinformatics under the SANBio initiative which I followed. In 2012, H3ABioNet had started with Yasmina as our site PI and accordingly in 2014, I was in attendance for the first H3ABioNet AGM meeting in Casablanca, Morocco, with Yasmina and this happened to be my first experience with many H3ABioNet members. I would say H3ABioNet has been one of the main reasons I got into bioinformatics.
What are your research interests?
Currently, I’m working in the field of computational genomics, more specifically in the area of cancer genomics; this is because I have also recently joined another international project called the MADCaP (Men of African Descent and Carcinoma of the Prostate). Moreover I am very interested in that field, because Mauritius has quite a high incidence of some cancer types. Additionally, cancer is a heterogeneous disease and a lot can still be done in the field of oncology, by mining publicly available genomics and clinical data. Besides, I am also very interested in applications of machine learning to genomics data and deployment of computerized workflows for genomics data analyses.
What does your typical workday look like?
My main job at the University consists of teaching as well as supervising student projects, as I am an academic. As an associate professor, I am also involved in several committees at the University, so I have to attend meetings. When I’m not teaching, I do my research activities related to the H3ABioNet, my internally funded project and MADCaP. I am also part of the health informatics group at the University, so I spend some time with projects in that area.
What do you enjoy most about your job?
Being in academia, we are also allowed to do research, and we are given the time and opportunity to do so, which is the most interesting thing about academia. Also, our institution provides opportunities to everyone to do research, and our management and colleagues are very supportive.
What do you enjoy least about your job?
Not much though, except when I see some students putting in little effort when they could have put in their best, I feel bad about it.
How has being a part of the H3ABioNet community impacted your research group?
It has shaped my research; H3ABioNet has provided me with the environment and the platform to learn and I have grown with H3ABioNet . I have learnt from everyone in the group. Likewise, I have met a lot of nice, positive and encouraging people in H3ABioNet.
What advice would you give a young person that is interested in pursuing a career in bioinformatics?
Everything is now going digital, and we receive calls for a lot of meetings on webinars that are being organized these days. I would advise younger members in H3ABioNet to attend these webinars because that is where people get to know about the latest in the field and the cutting edge of what is happening; this can help them decide which areas they would want to grow in their career. Furthermore, if someone is from the field of biology, s/he can take a few computational courses, while those from computing backgrounds should learn a bit about biology, as this will help them bridge the gap to get into the field of bioinformatics. Most importantly, they should keep learning.
I have enjoyed being part of H3ABioNet and everyone who is part of the H3ABioNet community should take advantage of the opportunities they are being presented with. This platform has been very good at learning and networking with people.