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H3ABioNet Newsletter Issue 35: November 2020

FOREWORD

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.

Nicky Mulder

H3ABioNet PI

Reflections on My Role as a SOWP Member and Minute Taker over the Year - Highlights and Lowlights, Lessons Learnt

By: Zainab Kashim

I am Zainab Kashim, the secretariat for the sustainability and outreach work package and also the Node ambassador for National Biotechnology Development Agency (NABDA node) Nigeria. I have a Master’s degree in Microbiology and Environmental Science and also work as Senior Scientific Officer at NABDA Abuja, Nigeria. I became the secretariat in early 2018 when volunteers were needed at the beginning of the year. The position was made open by the Chair- Jonathan Kayondo and the then Co-chair- Amel Ghouila, they always asked for volunteers at the end of meetings to occupy the role of the secretariat, but there was no response for quite a while. And then I took it upon myself that I was going to offer to assist, even though I was not quite sure if I would be able to deliver as expected. Upon assuming the task I tried my best, I actually learnt on the job, by sending out reminders of meetings to the members of the work package, taking minutes during meetings, sharing minutes to members after the meetings and any other job assigned to me by the Chair, Co-chair and system administrator.

The meetings usually took place on Adobe connect before it was later migrated to the zoom platform. An interesting thing about members is that they try their best to attend a scheduled meeting which is commendable, or rather take excuses for their unavailability via email or active collab.

My challenges were those times when I struggled with accents of some members and when I was also not familiar with some of the work package projects. Therefore, I usually wrote the bits I could get and shared with Jonathan and Amel who then went through the document and made necessary corrections to make it look perfect, before disseminating it to other members of the work package. Later with the help of Sumir Panji and Paballo Chauke, I could get access to meeting recordings which made it easier for me, by replaying it and drafting the main points discussed.

From March 2018 to date, a minimum of about twenty meetings have been held except for months where we had to postpone meetings due to other H3AbioNet activities or when we figured that attendance might be low due to excuses tendered before the scheduled meeting.

I have learnt a lot upon taking up this responsibility which includes increasing the potential of my interaction with people across the globe and also it has sharpened my social, communication and writing skills. It has been a smooth journey so far with the help of a great team, including the present co-chair Caleb Kibet. I will always appreciate the opportunity given to me to work as the secretariat of the work package.

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.

Talking REDCap

By: Katherine Johnston

For those consortium members who have an interest in phenotypic data this is going to be a space for you to learn more about why we recommend REDCap and how to use it effectively for clinical research data collection and storage. We will also throw in some administrator use cases for REDCap which are helpful to the H3ABioNet Central Node.

Whether you’re a total newbie, regular user or REDCap administrator we plan to offer tips and information in this space on a regular basis.

Some helpful links and information to get started:

  • Every month we run a REDCap Africa call, at 2pm (CAT), on the last Wednesday of every month. REDCap Africa is a group of users and administrators across the African continent who work together to build a supportive and helpful REDCap community on the continent. The calls usually have a topic for training that we focus on sharing and we always welcome topics to cover by request or people who want to share their own projects and use cases. You can join the REDCap Africa mailing by clicking here.
  • H3ABioNet has it’s on REDCap instance (administered by Katherine Johnston and Mamana Mbiyavanga) and anyone in the consortium who wishes to implement a project can approach the UCT CBIO node for access via this link.

What is REDCap?

REDCap is a secure online platform used to build databases with the ability to capture data with online surveys and electronic data capture directly to multiple projects. The official REDCap website can be found at: https://www.project-redcap.org/

How does it apply to our consortium?

A number of H3Africa projects are using it to collect their clinical / phenotype data; in H3ABioNet we use it for building practical data collection instruments for phenotype standards (e.g. Standard CRF) and also a number of administrative tasks and workflows (e.g. online training registration forms; internship applications and training evaluations; even our Friday lunch meetings. We also use it to host harmonised phenotype data repositories for H3Africa projects such as the CHAIR resource.

How can I learn more?

REDCap itself provides extensive training videos and learning materials developed by the many institutions using REDCap worldwide abound online. We will be sharing more tips, use cases and tricks in REDCap in future. For now those interested, and lacking training can start with the available REDCap online videos.

Tip of the month - eConsent:

REDCap allows electronic capture of Informed Consent that can be 21 CFR Part 11 compliant depending on the method and training process implemented. The following link provides a great set of instructional videos describing how to set up various levels of eConsent: click here.

Did you know...

all the H3ABioNet members’ website Biography Profiles and their consortium memberships are tracked and captured by H3ABioNet Central Node through online surveys built in REDCap?

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.

Yours sincerely

Alade, Adebowale A.

Meet the PI: Shakuntala Baichoo

By: Deborah Fasesan

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.

Final words:

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.
  • The H3Africa collaboration to analyze and interpret whole genome sequences from Africa has finally culminated in a Nature paper published this week: https://www.nature.com/articles/s41586-020-2859-7, involving contributions from several H3ABioNet members.
  • The H3ABioNet flagship Introduction to Bioinformatics (IBT) course wrapped up in August 2020. Even though the course went fully online we still had 44 classrooms and over 1200 participants join us this year. More than 500 people were awarded the course letter of completion. We thank all the classroom staff, TAs and course coordinators for their efforts in ensuring the course’s success!
  • The H3ABioNet 16S rRNA Microbiome Intermediate Bioinformatics Training Course (Int-BT) shifted to a fully online model this year as well, with just over 150 participants and more than 10 classrooms. It was extremely challenging but the course has just wrapped up and over 130 participants took the course right to the end. A special thank you to all staff and trainers for their concerted efforts throughout the course this year!
  • The 2020 Call for Nominations for the African Academy of Sciences Fellowship is open. For more info, click here. Application deadline – 7 Dec 2020.
  • Did you miss the 16th H3Africa Consortium Meeting? It is available on demand via the Labroots platform here: https://www.labroots.com/ms/virtual-event/16th-h3africa-consortium-meeting.
  • A total of nine institutes of the National Institutes of Health invite applications for their small research grant programme (parent R03 clinical trial not allowed) AIDS-related funding opportunity. This supports small AIDS-related research projects that can be carried out in a short period of time with limited resources. Projects may include pilot and feasibility studies, secondary analysis of existing data, small, self-contained research projects, development of research methodology and development of new research technology. Clinical trials are not allowed. For more info, click here. Application deadline – 8 May 2023.
  • Update – Research And Development Goals for COVID-19 In Africa.
  • Free Online Software/Data Carpentry Workshop – Applications accepted now! 7 - 8 November 2020 (Two full weekend days). Apply here. Course URL here.
  • Relevant funding opportunities available on “Research Professional” for genomics specialisations: can be found by clicking here.
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Verena Ras
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