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H3ABioNet Newsletter Issue 33: May 2020

FOREWORD

At the beginning of 2020, who would have thought we would be in the situation we are in, living through movie scenes out of “Contagion” and “Outbreak”? I have to admit, even when the news broke of an outbreak in China, I could not possibly imagine we would be sitting in a lockdown that has gone on for so long. It is surreal to go out and see everyone, including children, in masks. I am a very active person and this restriction on movement is rapidly driving me insane. Nevertheless, we have to adapt. Working from home is not so bad if one didn’t have to homeschool at the same time. However, I do find I am spending most of my day on online calls, sometimes up to 7 hours or more, particularly the last few weeks as all the meetings and conferences I was due to attend took place virtually. You can find out more about how others are coping in the first article of this newsletter.

At least as bioinformaticians our work can continue from anywhere with an Internet connection, so we have managed at H3ABioNet central, to keep the work going. We have cancelled face to face courses and meetings but Verena and Paballo are bravely taking on the adapted fully online IBT course with over 1000 participants! For our other courses and the AGM we will wait and see how the travel situation evolves. The newsletter describes an example of how one of our nodes is supporting the COVID-19 activities in their country, describes an interview with PI of the Sudan node, Faisal Fadlemola, and provides some tips from our grantmaster Victor Jongeneel on writing grants. I hope you enjoy the reading.

I wish everyone strength in these difficult times and hope you and your loved ones stay safe. I look forward to one day seeing many of you again in person.

Nicky Mulder

H3ABioNet PI

Working in COVID-times: How have the H3ABioNet staff adapted

By: Verena Ras

The sudden lockdowns across the African continent meant that many H3ABioNet staff were forced to work from home. This came with a variety of challenges ranging from home-schooling kids, to no real office equipment. Our staff became creative and somehow continued to remain as productive as ever. Unfortunately many events, especially training events, had to be canceled but our multiple-delivery-model approach employed in our flagship Introduction to Bioinformatics Training Course (IBT) meant at least some of our training could go on (though with some adaptations). Read more about working from home from the H3ABioNet and H3Africa communities below.

Taking IBT online

Although H3ABioNet training activities were severely impacted by the lockdowns and meant that many of our scheduled training events had to be cancelled for 2020, our flagship Introduction to Bioinformatics Course (IBT) could still go on. Because the course was designed as a blended learning course it meant we could easily adapt the model to a fully online course. Face-to-face sessions were replaced with online zoom meetings across our local classrooms with some creating whatsapp groups and slack channels to remain in constant communication with each other. We applaud the over 40 classrooms who have committed to bring this training to their participants! It will be the first time the course goes fully online and with over 1000 participants it promises to be a really interesting experience.

Left: Training and Outreach Coordinator Paballo Chauke get staff ready for IBT via an online session, Right: Fouzia who runs an IBT classroom every single iteration goes above and beyond to continue to support her participants even if she cannot see them anymore.

The "working from home" hashtag on twitter

Our social media team, headed up by our Training and Outreach Coordinator Paballo Chauke, started the hashtag "working from home" on twitter and asked the network to upload some photos of them working remotely. Below are some of the responses from the H3ABioNet community.

Twiiter post of the year definitely went to Scott for his creative teaching attire!

Keeping up with meetings

Working from home often means more but also longer meetings and many staff feel that meetings have just been getting longer and longer as lock-downs continue.

The H3Africa team has lots of meeting to stay on top of their work.

Despite the challenges we commend staff for pushing on with their tasks and attending the ever lengthy meetings with a great can-do attitude.

The role of the Tunisian node IPT in the fight against Covid-19

By: Melek Chaouch

In Tunisia the first case of Covid-19 contamination was noted on March 2nd 2020 within a Tunisian returned from Italy. As of April 26 2020, a total of 21,081 samples have reached virology laboratories and analyzed (suspect cases and close contacts of confirmed cases), of which 967 were positive for SARS-CoV-2. The average age is 43 years old. 40 deaths have been recorded. The average age of deaths was 67 years. The lethality is 4.13%.

Several strict measures have been taken by the government to contain the spread of the virus, including the establishment of total containment of the population from March 22 and this will continue until May 4. These measures with a targeted diagnostic policy have helped to curb the spread of the epidemic in Tunisia.

Since March 26th, the number of screening centers has been extended to several laboratories, including the Institut Pasteur de Tunis. At the same time, the number of tests performed daily is increasing and IPT is playing different roles in the fight against Covid-19 epidemic.

The role of the Institut Pasteur de Tunis in the management of the Covid-19 epidemic in Tunisia:

The IPT contributes to the management of the Covid-19 epidemic by participating in the national response plan set up by the Ministry of Health, on two aspects:

  • Epidemiological monitoring of the disease, to which the medical epidemiology service and the clinical virology laboratory of the IPT contribute.
  • Receipt of samples sent by the Ministry of Health for RT-PCR diagnostic tests. The results are then sent to the ministry.
  • Carrying out Covid19 diagnostic tests for travelers whose country of destination requires a negative diagnosis to enter their territory.

The role of the Institut Pasteur de Tunis in local and international Covid-19 research activities:

  • The search for innovative solutions in the field of diagnostics, vaccinology, mathematical modeling…
  • The Institut Pasteur de Tunis is working, within the framework of a technological partnership with the Hong Kong University-Pasteur Research Pole and the Institut Pasteur in Paris, on an Elisa serological test that will detect SARS COV-2 antibodies. This test relies on targeting two viral antigens: the entire N protein or the extracellular domain of the splice S of the virus. The recombinant proteins produced will be made available to all IPIN institutes. This test will facilitate the large sero-epidemiological studies needed to understand how the virus spread over time and geographically.

Meet the PI: Faisal Fadlemola

By: Deborah Fasesan

1. Tell us a bit about yourself:

My name is Faisal Mohamed Fadlelmola, I specialize in molecular genetics, bioinformatics and Information Technology (IT). I am the Principal Investigator (PI) of the H3ABioNet node at the University of Khartoum. I am also the head and founder of the Centre for Bioinformatics and Systems Biology (CBSB) at the Faculty of Science, University of Khartoum. I started my scientific life at the University of Khartoum where I obtained my first degree in biological science. I worked briefly after that at the information center at the Islamic Research and Training Institute (IRTI) as a member of the Islamic Development Bank Group (IsDB). IRTI delivers cutting-edge research, capacity building and learning activities, advisory and information services in Islamic economics, banking and finance to achieve the Sustainable Development Goals (SDGs) in Muslim countries. IRTI has also the role of building databases and information systems (e.g. Muslims Experts and Islamic Banks), and conducted extensive training including online and distance learning programs, and organized conferences, seminars and workshops worldwide. During my work in IRTI, I took one year as sabbatical leave for conducting my post-graduate studies in the United Kingdom; I finished my first masters in medical molecular biology in one year, extended my sabbatical leave and finished my second masters in Computer-Based Information Systems (CBIS). Just two months from resuming my work at IRTI after the sabbatical leave, I got a PhD fellowship and proceeded to have my PhD in Human Molecular Genetics & Bioinformatics at the Institute of Human Genetics (IHG) at the University of Wurzburg in Germany (2000 – 2003). Before defending my PhD, I got an offer to work as a post doc fellow at the Centre for Translational and Applied Genomics (CTAG) in the British Columbia Cancer Agency (BCCA) in Vancouver, Canada on conditional completion of my PhD, which I finished in September 2003. In January 2004, I started my postdoctoral fellow training at the CTAG for three years and I had also worked at CTAG for another two years as a senior research associate.

2. Tell us a bit about your institution:

The history of the University of Khartoum (UofK) dates back to as far as 1898, when Lord Kitchener of Khartoum proposed establishing a college in memory of General Gordon who had been killed in Sudan. The college was officially opened in 1902 and later on, Henry Wellcome donated a fully equipped laboratory for bacteriological analysis. Then in January 1945, these schools were brought under the administration of a special arrangement with the University of London. The college was upgraded in 1951 as the University College of Khartoum. In 1956, when the country gained independence, it was converted to the University of Khartoum and is one of the oldest Universities in Africa. The University’s vision is to participate, through its role in the field of higher education and scientific research, in the creation of a unified, developed and advanced Sudanese Nation. The Faculty of Science was founded in 1937 as one of the Higher Schools of Gordon Memorial College. In 1945 these schools came under a single independent administration. In 1947 the School of Science became the Faculty of Science and continued to maintain this name until the University College of Khartoum became the University of Khartoum in 1956.

3. How did you get into bioinformatics?

While I was doing my master’s degree in medical molecular biology, I isolated and cloned Alpha-Galactosidase gene from Tritrichomonas foetus from bovine using public databases and Polymerase Chain Reaction. The main catch here was to identify short sequences of 3-9 amino acids conserved within the protein across a wide range of species and then design degenerate primers that would isolate them from those protozoan parasites. In addition, during my PhD in Germany, I blasted around 2379 clones from a bovine cDNA library of Retinal Pigment Epithelium (RPE) constructed utilizing the molecular biology technique of Suppression Subtraction Hybridization (SSH). SSH is a highly effective method for constructing subtracted cDNA libraries. The normalization step equalizes the abundance of cDNAs within the target population (RPE) and the subtraction step excludes the common sequences between target and driver populations. At that time, it was only the human genome draft available and there was no bovine genome available at the public databases. We picked those clones from the bovine cDNA library and sequenced them from both directions using Sanger sequencing and BLAST’eda high quality length of these sequences (100bp) against the human genome. About 50% clones were found to be human positive while 50% were negative, so we proposed that the non-positive ones were probably specific for bovine. Moreover, I developed a relational database management system in order to record and retrieve the outcome of those blasting outcomes, their do-blots, and Northern blot for gene expression analysis in a range of human tissue (Brain, Retina, RPE and Liver). The 50% of the positive clone sequences were subjected to dot-blot, Northern blot gene expression, and comprehensive in-silico analyses and we were able to narrow those 600 clones down to 25 candidate genes for Age-related Macular Degeneration. After 15 years, I gave the high quality sequences of those negative clones to one of my MSc students two years ago, he blasted them against the bovine genome, which is available now, and found all of them to be bovine-based clones. Moreover, during my postdoctoral fellow training at CTAG, I did a compressive Array-Comparative Genomic Hybridization (A-CGH) and Microarray cDNA data analysis of Hodgins Lymphoma (HL) and Anaplastic Large Cell Lymphoma cell lines seeking discovery of new biomarkers to differentiate between these two types of HL and non-HL.

4. What are your research interests?

After my PhD, I got an offer to work as a post-doc fellow at the British Columbia Cancer Research Center in Canada, so my research interests are in cancer genomics, bioinformatics, epigenetics, biomarkers identification and validation, microbial genomics, genomics of human population and health informatics. After my post-doc, I relocated to Botswana where I was one of the founding staff of the first School of Medicine in University of Botswana (SoM, UB); I was involved in teaching genetics, genomics and health informatics to the first and second year of the Medical School. During my work at SoM-UB, I was also involved in health informatics projects with the University of Pennsylvania and we managed to publish two papers in IEEE.

5. What does your typical workday look like?

The most interesting part about my current job is that there is no routine day. I worked in industry; and in a bank information center, in a routine environment. Nevertheless, in my current research work, there is no routine. Some days, I would be busy scheduling and attending meetings. Another day I would be supervising my post graduate students, reviewing their projects progress report or proposals. Another day might be that I am busy making a presentation for a meeting, mentoring trainees on how to speak efficiently in front of a crowd, giving advice for other students in the faculty seeking advice on how to pursue their career in genomics and/or bioinformatics. I do not like routine jobs, my type of work is such that it is a challenge, we face a problem and we have to find a solution to it and we would be busy sometimes for one week or even one month until we find a solution, so there is no routine typical day. I usually start my work by planning my day and ensure that most major work is done first. The good thing now is the Active Collab, which makes things quite easy, we already find what is to be done for each day.

6. What do you enjoy most about your job?

I like the fact that it is not a routine job, and it is full of challenges and surprises every day, and to find a solution, it needs thorough but critical thinking and cost effective analysis.

7. What do you enjoy least about your job?

I did have a job where there was lots of paperwork, an unusually large amount of paperwork that needed to be done with deadlines which could lead to stress; I had to delegate some paperwork and then still needed to review every one of them.

8. How has being a part of the H3ABioNet community influenced your research group?

After my post-doc in Canada, I had been thinking on how the advanced field of genomics, bioinformatics and information technology could be introduced into African universities and the research institutions. This was one of the reasons I left Canada and accepted an offer of work as a biomedical scientist and assistant professor at the then newly established school of medicine at the University of Botswana, this was in July 2009. Luckily, in March 2011, I attended three meetings in a row: 1. the kick-off meeting of the H3Africa in the Convention Center in Cape Town, South Africa, 2. the Genetics meeting of the African Society of Human Genetics (AfSHG) conference, 3. The International Society for Computational Biology (ISCB) and African Society for Bioinformatics and Computational biology (ASBCB) Joint Conference on Bioinformatics, where a group of senior African scientist agreed to submit a single proposal to develop Pan-African Bioinformatics Network (H3ABioNet) to serve H3Africa projects. For this initiative, one of the main aims of the network was to build human capacity in bioinformatics in Africa, which would make our dream come true. The network is involved in combining information on existing degree programs and courses. It is also working towards developing face-to-face training and online training bioinformatics courses, as well as training courses on genomic medicine for Nurses in Africa. All of these are what we had been dreaming of when we (PIs’) left the north (UK or North America) and now our dream has come true. When we did the proposal, we discovered there were existing bioinformatics degrees and courses in the continent, but in very few countries, but now we are more or less on the same level, thanks to the US National Institutes of Health (NIH), UK-based Wellcome Trust, and also the African Society for Human Genetics (AfSHG). In addition, H3ABioNet allows the younger generation to get involved in how to build bioinformatics tools, so this is a good shift. For example, if you are using a tool and it stops working, then there is a need to troubleshoot it, if you do not know how it was developed then it would be difficult to troubleshoot it.

9. What advice would you give a young person that is interested in pursuing a career in bioinformatics?

According to the International Society for Computational Biology recent paper, there are usually three persons involved in computational biology and bioinformatics: Users, scientists and there are engineers. The user can be a scientist or a doctor while the engineer can be the person doing the mathematical modelling and/or developing the tools etc. My advice for young persons is that they should use their early career in bioinformatics to learn as many techniques as possible, this would assist them in solving an array of problems in the future, they cannot learn everything, but at least the thing in their domain/field, and they should learn different techniques. Secondly, when deciding where to do post-doc, their decision should not be based only on whether the laboratory has a grant, they need to know who the mentor is, whom the supervisor is and if they can be in harmony. In terms of communication, they need to learn how to give presentations. I see many graduates not being confident during presentations in conferences, and they would merely read the slides, which is not good. In addition, some scientists do not like to attend seminars or move from their benches or computers, I would advise them to attend as many seminars as they can, because from there, they get to know and learn something new or probably find a solution to one of their ongoing problems in bioinformatics and genomics. The young ones can make a mark in the field by joining scientists and researchers and publishing in high profile journals. In addition, they also need to learn about statistics and scripting. As young researchers working in developing countries, they should solve a sort of life challenge by establishing relationships with senior researchers.

10. Final words:

To all those involved in H3ABioNet and H3Africa, I suppose they need to be proud of themselves, as they have been working hard during the last seven and a half years. In doing so they managed to prove to the funding agencies and others in the genomics and bioinformatics domain research community that we as Africans have worked together and secondly could deliver outcomes in science that are of high quality. For the young generation in H3ABioNet, they need to stay motivated, as this is what would drive them towards their goals in their career even when things get tough.

Q&A with grantmaster Victor Jongeneel - successful grant proposal submissions

1. Where to find information about funding opportunities?

The best way is to go to the Web sites of the major funding organizations such as NIH and NSF (US), the European Commission, the UK Research Councils and the charitable foundations such as the Gates Foundation, the Wellcome Trust, the Novo Nordisk Foundation, etc. Some of these (e.g. NIH, NSF, Grants.gov) also have RSS feeds that you can add to your mail client, so that you receive the funding opportunities in real time. Btw, this is what I do to receive the NIH calls. The real challenge is to be able to spot, among a mass of information that is irrelevant to your research, the calls that are relevant to your research agenda. This requires skill and patience. Some institutions, countries and professional organizations track funding opportunities that are relevant to their constituencies. In my experience, these can occasionally flag interesting opportunities, but should never be relied on to be comprehensive. Finally, your network of friends and colleagues will often find promising leads that are directly relevant to your work. Sharing is the key. To summarize: there is no good “single stop” shopping place for funding opportunities. Finding and selecting them takes a lot of time and energy.

2. Can I still submit a proposal even if I don’t meet all the criteria?

As a general rule, no. Funding agencies set out criteria for a reason. If for any reason you are unsure whether one of the institutional or personal criteria applies to you, the best thing to do is to contact the Program Officer in charge of the call and ask. Never, ever, prepare an application without being absolutely sure that you meet all of the conditions for applying. It may be returned to you without even having been sent out for review.

3. How much time do I need to prepare my application?

As much time as possible. When you see an opportunity, decide within a few days whether you want to apply, and produce a short outline (1-2 pages) of what you want to propose. You can then use that to engage collaborators, make a first budget estimate, contact the PO at the funding agency, etc. This information will allow you to decide whether you can produce a credible proposal. In my experience, about half the potential submissions die at this stage. How much time it will take to produce a full proposal will depend on the complexity of the RFA, the amount of ancillary material that is required, the number of collaborators, etc. In my experience, a simple, single PI proposal will take about 6 weeks of full-time work, while a complex proposal with multiple components can easily take 3 months or more. I once led the preparation of a Center proposal with five components, each the size of a typical NIH R01; it ran to over 400 pages and took us about 4 months to prepare.

4. When should I start contacting potential collaborators?

You should start contacting collaborators once you have a clearly formulated outline for your proposal. Potential collaborators should be chosen because they have specific expertise, or access to data or materials, that are essential to the successful completion of the project. You should also have a budget outline ready, so that you can tell them how much funding could be allocated to them, and what would be expected from them in return. It is a bad idea to include collaborators for personal or political reasons (your friends, your bosses’ friends, a big shot in the field).

5. Beginners usually lack preliminary data, would that be fatal for an NIH grant application?

This very much depends on the type of grant you are applying for, and on the role you would play in the project. R01 grants typically fund well-established research groups with a strong track record, and the PI will be expected to provide a solid body of evidence that their research plan will work and preliminary data to support it. Smaller R21 grants are targeted to beginning researchers, and do not require as many preliminary data. If you are a junior co-PI and your contribution is mainly based on your expertise, the burden will be on the main PI. But in general, having already done some work in the area for which you apply, and having data showing that your approach works and that your hypotheses are sound will make a big difference.

6. What aspects/ parts of an NIH grant application are especially critical in the review?

NIH proposals are scored on five criteria, all of which are important.

  • Significance (often called Impact by other funding agencies). This measures to what extent the results of the proposed project will make a difference in the field by generating new hypotheses, crucial data, better methods, etc.
  • Investigator(s). This evaluates how qualified the named investigators are to carry out the proposed research, based on their experience, publications, contributions to the field, etc. In multi PI proposals it also looks at how well the individuals have collaborated in the past. This is often the most subjective criterion. Having carefully crafted NIH Biosketches is key.
  • Innovation. This evaluates how innovative the approach is, both from a technical and an intellectual point of view. Does it contain truly new ideas? Does it propose a smart technical approach? Will it test hypotheses that have never been thought of before?
  • Approach. This tries to judge now likely the project is to produce the expected results, given the experimental approach, the available equipment, the requested funds, the preliminary data, etc. It also looks at how well you have mapped out all of the components and dependencies of your experimental approach, In other words, if the investigators do what they say they are going to do, how likely is it that they will produce data that will help answer the scientific questions they are asking.
  • Environment. This looks at the institutional environment in which the research will be performed. Do they have the right equipment and space? Are there people around who can help out if the project gets stuck? Do they have access to resources outside those of their individual labs?

Finally, the most important aspect of a successful proposal is that it lays out clearly and concisely the scientific questions it is addressing (Specific Aims) and proposes a well thought out plan to answer them.

7. Some calls come with multiple submission dates in their cycle - what cycle would be strategically best to target - 1st or later dates?

Unless one has insider knowledge about available funds, competing applications, composition of the review panels, etc., it should make no difference. This being said, for calls with an expiration date, it may be wise to submit early so that you have a chance at resubmission. However, you should never rush a submission before all of the pieces have fallen into place and you are completely happy with the Research Plan.

8. After one receives review scores after a submission round, what range below the funding cut off would be worth reworking for a future resubmission (i.e. for calls with multiple submission dates)?

About half of all proposals never make it to external peer review and are not scored. They do receive a summary statement explaining why. If yours is in that category it is probably not worth revising and resubmitting. The NIH scoring system goes from 10 (all reviewers gave maximum scores to all criteria) to 90. The funding cut-off is typically around 25 but scores up to about 35 indicate fundable projects; cut-offs are highly variable depending on the level of competition and available funding. It is not unusual to have one reviewer who scores much worse than the others, sending the proposal out of fundable territory. However, the score received by an application is not as important as the reviewers’ comments. Look carefully at the comments from all reviewers, and probably a pattern will emerge telling what was considered sub-par. Revisions should concentrate on those parts.

Finally, here are a few things not to do:

  • Basing a proposal on a set of activities rather than defining open scientific questions that need to be addressed
  • Planning a project that does not closely fit the scope of the FOA
  • Underestimating the length and complexity of the Research Plan; not structuring it correctly
  • Assembling a team based on one’s professional network rather than the needs of the project; making the team too large to be reasonably funded by the grant
  • Not producing a draft budget early enough in the proposal preparation phase, and then realizing that the project cannot be funded within budget limits; not allocating resources in line with contributions to the project
  • Waiting to produce ancillary documents (site descriptions, biosketches, letters of support, data management plans, project leadership plans, etc.) until too close to the due date
  • The Carpentries official guidelines for taking your workshop online has been released. You can find more information here . For the latest information follow "@thecarpentries" on Twitter.
  • ISMB Conference goes virtual in 2020. Register for the conference here.
  • ISID and Pfizer Global Medical Grants announce a new competitive grant challenge to support programs working on antimicrobial stewardship campaigns throughout Africa and the Middle East. They are seeking innovative quality improvement health services and/or educational research applications that identify and evaluate practices for successfully implementing key elements of antimicrobial stewardship campaigns. Programs designed for healthcare organizations, hospitals, tertiary care clinics, and educational settings are all applicable. Projects can request up to $100,000 USD of funds to support two-year initiatives. For complete details about this grant challenge and instructions to submit your project, please visit this link. All proposals are due by August 4, 2020.
  • Applications are now being accepted for the African Independent Research (FLAIR) Fellowships offered by the African Academy of Sciences (AAS) and the Royal Society. The fellowships are offered to early career scientists from sub-Saharan Africa. Deadline 27 May 2020. More information about this fellowship can be found here. Applications must be made through the Royal Society's grants portal.
  • The flagship H3ABioNet Introduction to Bioinformatics Course began on 12 May 2020 for all participants despite global lock downs.
  • The H3ABioNet 16S rRNA intermediate bioinformatics training course will begin accepting classroom applications shortly. A call will be circulated in the coming weeks.
  • L’Oréal-UNESCO For Women in Science International Awards. Created in 1998, the International Awards L'Oréal-UNESCO For Women in Science honours - every year - 5 eminent women scientists from 5 regions of the world. An award of €100,000 is given to each of the five laureates selected by a jury of internationally renowned experts. Deadline: 31st May 2020 Please follow this link for more information on the award.
  • The West African Genetic Medicine Centre, an African Centre of Excellence for Genetic Medicine, College of Health Sciences, University of Ghana (UG) is offering fellowships for graduate students to conduct research in genetics in UG, in collaboration with the School of Biomedical and Allied Health Sciences, University of Ghana Medical School, Department of Psychology and Department of Biochemistry, Cell and Molecular Biology. Deadline: 29th May 2020. Please follow this link for more information on the fellowships.
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Verena Ras
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