issue 25: may 2018 foreword - aibstaibst.com/wp-content/uploads/2019/07/h3abionet...issue 25: may...

Issue 25: May 2018

Work package introductions

• Data & standards

• Health informatics

• Pipelines & computing

• Tools & web services

• Databases & resources

• Data integration

• Training

• Sustainability & outreach

News

• Report: H3ABioNet 2.0kick-off meeting

• Report: software & datacarpentry training

• Announcements

• Upcoming events

ForewordWelcome to the first official newsletter for phase 2.0 of

H3ABioNet. We are already more than 6 months into the renewal,but have had delays in preparing the newsletter as our trainingcoordinator and newsletter editor, Kim Gurwitz, left to take up anew position in Cambridge.

This has been a busy period of setting up the many new andexisting projects in Active Collab, a project management system.This will help us to more easily track tasks and deliverables. Theexisting projects from phase I have continued and many of thenew projects have already made good progress.

During this period weheld a kick-off meeting for therenewal, which welcomed oldfriends and introduced newnodes into the consortium.A report on the meeting canbe found later in this issue.Many H3ABioNet membersalso attended the 11th H3Africaconsortium meeting in Ugandawhere we met some of thenew H3Africa grant awardees..We look forward to working with them to provide informaticssupport for their projects.

In this issue of the newsletter you will notice a new look,which has been assembled by Kirsty Lee Garson from CBIO atUCT. We felt it was important to refresh the look and feel of thenewsletter for phase 2.0. The pages all have links between them,and to our social media platforms. In this first issue we intro-duce the 8 work packages which are responsible for driving all theprojects in H3ABioNet, together with their chairs and co-chairs.This should provide an overview of the focus areas and projectsof the network for the next 5 years. We also feature report backsfrom the kick-off meeting and a software/data carpentry trainingworkshop attended by some of the H3ABioNet staff.

I invite you now to read on to find out more about our plansfor H3ABioNet phase 2.0.

Nicky MulderH3ABioNet PI

Join the conversation:

g 7#bioinformatics #Africa

@H3ABioNet

http://www.h3abionet.org/

https://www.facebook.com/H3ABioNet-1388050288174486/?fref=ts

https://twitter.com/h3abionet

H3ABioNet Newsletter | Issue 25: May 2018

Data & Standards Work Package

Original image:parthenos-project.eu

CHAIR:

Judit Kumuthini

Dr Judit Kumuthini received her BSc inBiomedical Science, and MSc in Bioinformatics inthe UK. She completed her PhD in Bioinformat-ics at the University of Cranfield, UK, investigatinggenetic network extraction using a Bayesian beliefframework. After completing a post-doctoral re-search fellowship at the University of Cape Town,she became the Bioinformatics Manager at theCPGR and is currently the PI and node manager ofthe CPGR node in South Africa.

Judit is actively involved as a member or nodemanager in various other networks and societies,including EMBnet, GOBLET, SASBi, ITFoM, PGENI,ASBCB, ISCB and the Genomic Standards Consor-tium. She has also trained and supervised manypostgraduate students in Europe and in Africa. Herresearch interests include African genetic rare dis-eases, personalized medicine, pharmacogenomics,standardization and good practice, informationmanagement and visualization, and e-learning.

Contact: [email protected]

CO-CHAIR:

Raphael Sangeda

Dr Raphael Sangeda is a lecturer in the De-

partment of Pharmaceutical Microbiology at theMUHAS node in Tanzania. He graduated with a B.Pharm from Dr MGR Medical University, Chennai,India in 1998. In 2005, he obtained his MSc in Med-ical Microbiology at the Jomo Kenyata Universityof Agriculture and Technology. In 2005, he joinedKatholieke Universiteit Leuven, now KU Leuven, inBelgium, where he graduated with an M. Pharm(2006), an MSc. in Bioinformatics (2008) and a PhDon the use of bioinformatics approaches to predictHIV drug resistance (2013).

Raphael’s research interests include the useof Genome Wide Association Studies (GWAS) in in-vestigating the genetic epidemiology of Human Im-munodeficiency Virus, Hepatitis B virus and Hepati-tis C virus infections in individuals with Sickle CellDisease.

OBJECTIVE:

The objective of the Data & Standards WorkPackage is to design and implement guidelines andtools to allow for effective standardisation and har-monisation of H3Africa data (including genomic,experimental, clinical and disease-specific data).

This will involve the use of appropriate stan-dards (e.g. GA4GH, FAIR) and ontologies, in orderto add value to all data produced by the H3Africaconsortium.

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https://h3abionet.org/cpgr

https://h3abionet.org/muhas

https://www.ga4gh.org/

https://www.go-fair.org/go-fair-initiative/

PROJECTS:

1. Ontology Mapping

This project is carried over from the previousround of H3ABioNet. The purpose of the projectis to:

• select the ontologies that will be used for themapping of H3Africa data

• identify and address gaps in these ontologies• develop guidelines for the mapping of

H3Africa data• implement ontology mapping and valida-

tion

2. Minimum Data & Data Dictionaries

This project aims to identify and developdomain-specific minimum information collec-tions and reporting guidelines, as well as iden-tify and/or develop data dictionaries relevant toH3Africa research projects. The project is asso-ciated with the Standard CRF Project (led by DrAlia Benkahla), which aims to expand on stan-dard patient information in a domain-specificmanner.

The project will involve H3Africa commu-nity engagement. It is currently driven by twostandardisation projects relevant to H3Africa -stroke and kidney disease research, and clinicaldata reporting.

3. Data Management Plans

This project consists of several activities, includ-ing:

• the review of existing data management andgovernance plans

• the development of new or updated guide-lines

• the development of common repositories fordata management plans

• recommending and providing assistancewith tools for managing data and metadata.

The project will also investigate the useof the integrated Rule-Oriented Data System(iRODS) for data transfer and provenance.

4. FAIR Data

This project aims to develop capacitywithin H3ABioNet and H3Africa for producingdata that is findable, accessible, interoperableand reproducible (FAIR). Activities include theidentification of relevant literature and SOPs. Inaddition, the project will involve developing newSOPs where necessary, as well as developing aprocess for making data FAIR. The SOPs willbe implemented once sufficient H3Africa datahas been generated and adequate metadata cap-tured.

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Data & Standards Work Package

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Work packageintroductions


• Health Informatics

• Pipelines &computing



• Databases &resources


• Training

• Sustainability &outreach

News


• Report: Software &data carpentrytraining

• Announcements

• Upcoming events

Continue theconversation

Follow us:


@H3ABioNet

https://irods.org/




Health Informatics Work Package

Original image:bol.com

CHAIR:

Nicki Tiffin

Nicki started her research career in paediatricmolecular genetics and molecular endocrinologyresearch. She then shifted her focus to health ge-nomics and bioinformatics approaches to investi-gating disease in African populations, as well as re-lated ethical issues.

Nicki completed a Master’s in Public Healthin epidemiology, and worked on secondment to theWestern Cape Government Health Department toassist with developing the infrastructure and gover-nance for the Provincial Health Data Centre.

Nicki is currently part of the data integrationplatform with CIDRI-Africa and the CBIO node atthe University of Cape Town.

CO-CHAIR:

Katherine Johnston

With a long-standing desire to play a role

in advances in genetic research, Katherine movedfrom a position as Head Clinical Data Managerat AHRI, Durban to join the CBIO node as anH3ABioNet Software Developer.

She completed an honours degree in Com-puter Science and Economics, and started her ca-reer working in EHR systems development. Havingdeveloped a passion for helping medical profession-als in the field of patient care, by building usefulelectronic tools for them, she joined CAPRISA as aClinical Data Manager in 2004 and worked with en-joyment in this field for the next 13 years.

During this time, she got married and hadthree precious babies, the first of whom has DownSyndrome. As a result, she finds herself unexpect-edly combining her interest in genetics, health in-formatics and patient care with her love for herchildren, advocating for inclusivity and research ad-vancements in medical care and software develop-ment to benefit all genetically diverse people inAfrica.

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https://h3abionet.org/cbio

https://h3abionet.org/cbio

OBJECTIVE:

The Health Informatics Work Package con-sists of three projects, which are focused on clinicaldatabasing as well as data management best prac-tices and their implementation.

PROJECTS:

1. Phenotype harmonisation and establishingstandardised case report forms (CRFs)

This project, lead by Alia Benkahla, willbuild upon the phenotype harmonisation whichwas undertaken during the first five years ofH3ABioNet.

It will involve defining core CRF fields foruse across the H3A Consortium using PhenXstandardisation. In addition, Africa-centric eth-nic and linguistic ontologies will be developed.

fff

2. Guidelines for RedCAP clinical databasing

The second project, led by Katherine John-ston and Sumir Panji, will include the develop-ment of guidelines for principles and best prac-tice, minimum data standards, functionality fordata export and logging of data use, templateCRFs, clinical data governance, data presenta-tion and interoperability (e.g. HL7 and FHIRspecifications).

3. Meta-analysis databasing

Thirdly, Katherine Johnston will lead aproject that will involve developing and proto-typing metadata analysis principles, guidelinesand implementation, in collaboration with theH3Africa Cardiovascular Disease (CVD) WorkingGroup. The project will combine data from sev-eral H3Africa projects for meta-analysis of CVDacross those studies.

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Health Informatics Work Package

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• Training


News



• Announcements

• Upcoming events


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https://www.phenxtoolkit.org/

https://www.phenxtoolkit.org/

http://www.hl7.org/

https://www.hl7.org/fhir/overview.html




Pipelines & Computing Work Package

Original images:sigmatek-automation.comdipayan90.wordpress.com

CHAIR:

Christopher Fields

Chris Fields is the Associate Director of theHigh Performance Computing in Biology (HPCBio)group at the University of Illinois at Urbana-Champaign (UIUC), and is the PI of the UIUCnode. We are collaborating with Victor Jongeneel,the former PI of the UIUC node, in this round ofH3ABioNet.

In the first round of H3ABioNet, Chris, alongwith HPCBio/NCSA members Liudmila Mainzer,Jenny Drnevich, Jessica Holmes and RadhikaKhetani participated in the Node Assessment TaskForce. This included writing SOPs, choosing initialdata sets for testing and evaluation, and assistingwith assessment reviews.

Liudmila and HPCBio group member GloriaRendon also played a key role, in collaboration withGerrit Botha and H3Africa members, in processingthe initial H3Africa sequence data on NCSA’s BlueWaters supercomputer; this data would later proveinstrumental in the design of the H3A genotypingarray.

CO-CHAIR:

Shakuntala Baichoo

Shakuntala Baichoo is a Senior Lecturer at theUniversity of Mauritius. She is also the PI of the Uni-versity of Mauritius SANBio node. In the first roundof H3ABioNet, she was a member of the Education& Training Working Group and the Cloud Comput-ing & Pipelines Taskforce. Shakuntala has been in-volved in the development of the H3ABioNet 16SrDNA analysis package using the Common Work-flow Language (CWL).

SECRETARIAT:

Azza Ahmed

Azza Ahmed is a PhD student and member ofthe University of Khartoum node in Sudan, and alecturer in the Department of Electrical and Elec-tronic Engineering at the same institution. Duringthe first phase of H3ABioNet, she contributed to itsactivities through involvement in the Research andInfrastructure Working Groups. She is continuingher involvement in these areas during the currentphase.

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https://www.h3abionet.org/hpcbio

https://www.h3abionet.org/hpcbio

http://www.ncsa.illinois.edu/

https://www.h3abionet.org/uom

https://h3abionet.github.io/h3abionet16S/

https://h3abionet.github.io/h3abionet16S/

https://www.h3abionet.org/fus

PROJECTS:

1. Provision of computing infrastructure

Project Lead: Suresh MaslamoneyStatus: The development of the single

sign-on and infrastructure draftproject plan is in progress. Ac-tivities have begun with workfrom the previous round beingcarried over.

2. Node accreditation

Project Lead: Victor JongeneelStatus: Activity is underway.fff

3. Development and deployment of workflows

Project Lead: Sumir PanjiStatus: In progress. Work from the previ-

ous round is being carried over.

4. Single sign-on system for H3ABioNet systems/portals

Project Lead: Suresh MaslamoneyStatus: In progress.

5. Data QC

Project Lead: Gerrit BothaStatus: To be merged with project 3 as an

integrated part of workflows.

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• Training


News



• Announcements

• Upcoming events


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@H3ABioNet




Tools & Web Services Work Package

Original image:waferwire.com

CHAIR:

Scott Hazelhurst

Scott Hazelhurst is based at the School of Elec-trical & Information Engineering at the University ofthe Witwatersrand, with a cross-appointment at theSydney Brenner Institute for Molecular Bioscience.He is a computer scientist by training, having re-ceived his BScHons and MSc degrees from Wits andhis PhD from the University of British Columbia.

Scott has been involved in bioinformatics re-search since 2002. His bioinformatics interests in-clude population structure, GWAS and the micro-biome; his computing interests include high per-formance computing and pipelines. He has beeninvolved with H3ABioNet since its inception andwas previous chair of the Infrastructure WorkingGroup. He is also a collaborator on the H3A AWI-Gen project exploring cardio-metabolic disorders inAfrican populations.

CO-CHAIR:

Itunu Isewon

Itunu Isewon is based at the Covenant Univer-sity node in Nigeria.

PROJECTS:

1. Human Mutation Analysis (HUMA) databaseand web server

The HUMA database and web server(Brown et al.) was developed at Rhodes Univer-sity as a platform for the analysis of genetic vari-ation in humans.

This project, led by Ozlem Tastan Bishop,will extend the work.

2. Big data analytics and machine learning toolsfor application to biomedical data

The main aim of this project, led by AmelGhouila, is to promote the use of Machine Learn-ing techniques to analyse different kinds of bio-logical data, in order to solve various biologicalproblems. It will provide resources, guidelinesand developmental support to facilitate the useand integration of existing packages and also de-velop new tools where needed.

In addition, big data analytics methodswill be incorporated into bioinformatics analyseswhich are related to H3Africa projects, in orderto improve the efficiency and accuracy of theseanalyses.

3. Genesis visualisation tool

Genesis is a tool that was developed at Witsfor the visualisation of population structure andadmixture. This project, led by Scott Hazelhurst,will further develop the tool.

Continued

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https://h3abionet.org/cubre

https://h3abionet.org/cubre

https://huma.rubi.ru.ac.za

http://doi.org/10.1002/humu.23334

http://www.bioinf.wits.ac.za/software/genesis

3. Integrative multi-omics-based simulationframework

This project, led by Emile Chimusa, willdevelop tools to enable sequencing data simu-lations, with the aim of furthering our under-standing of the effect of evolutionary and demo-graphic characteristics on omics variation. Thiswill give researchers the capacity to assess anddesign novel analytical approaches which lever-age the characteristics of genomes of popula-tions with African ancestry. Similarly, a syntheticmetagenomic dataset with diverse taxonomiccomposition will assist in improving metage-nomic tool development and metagenomic dataanalysis design.

An existing tool which we have developedwill serve as the basis for the project. Fractal-SIM (Mugo et al.), is an integrative whole multi-omics-based simulation framework, emulatingvarious properties of human NGS datasets. Us-ing similar principles, we will develop metage-nomics mock scenario-based sample simula-tions, mimicking the interactions between hu-man genotypes, environments and microbialcommunities, which could impact human dis-ease susceptibility.

4. Reference graphs and methods for large-scalestructural variant calling

The primary aim of this project is todevelop methods of representing genomes as

graphs, in particular, a reference graph suitablefor African populations. This will form the ba-sis for developing techniques for detecting large-scale variants.

5. African reference panel and imputation service

This project will involve building a servicewith a curated reference panel and providingthe necessary HPC facilities to enable H3Africaprojects genotyping large cohorts to accuratelyimpute from this data.

6. Development of a statistic for genetic associ-ation testing on multifactorial phenotypes infamily-based design

The goal of this project is to develop anopen source program which computes a family-based statistic testing for association between aphenotype (regardless of the distribution) and aset of independent multi-allelic markers.

In doing so, we will address challengessuch as non-specified distribution of traits, re-lated individuals, population admixture andlinkage disequilibrium among markers.

The purpose of the tool is to contribute todetecting single effect as well as joint effects ofgenetic mutations on infectious disease traits, ei-ther qualitative or quantitative, in family-baseddesign.

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• Training


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• Announcements

• Upcoming events


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https://omictools.com/fractalsim-tool

https://omictools.com/fractalsim-tool

http://doi.org/10.1093/bioinformatics/btx369




Databases & Resources Work Package

Original image:globalids.com

CHAIR:

Faisal M. Fadlelmola

Professor Faisal M. Fadlelmola is the PI of theUniversity of Khartoum node in Sudan.

CO-CHAIR:

Kais Ghedira

Dr Kais Ghedira is an Assistant Professor inBioinformatics and co-investigator of the InstitutePasteur de Tunis node in Tunisia.

SECRETARIAT:

Deborah Fasesan

Ms Deborah Fasesan is a member of theNABDA node in Abuja, Nigeria and a PhD candidateat the University of Ibadan.

PROJECTS:

1. African Microbiome Portal

This project involves:

• collecting information about African micro-

biome data, including the wide variety ofdata produced by H3Africa projects

• creating a web portal integrating tools and re-sources for microbiome data analysis

• maintaining and updating this web portal

2. African Precision Medicine Portal

This project will develop a web portal thatgathers information on clinical and pharmacoge-nomic data relevant to Africa, with the aim of fa-cilitating the study and development of precisionmedicine for African populations.

3. African Variation Database

This project will involve creating adatabase of the African genetic variation de-tected and identified by research projects inAfrican populations.

4. Data & Biospecimen Access Committee (DBAC)Support Resources

This project will develop the tools neededby the DBAC to carry out their duties.

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https://www.h3abionet.org/fus

https://www.h3abionet.org/ipt


https://www.h3abionet.org/nabda

5. H3Africa Archive

This project will be centred around host-ing H3Africa data and facilitating submission tothe EGA and other public repositories for long-term archival storage. The project will involveassisting users to submit data to the H3AfricaArchive and to format data as required for sub-mission to the EGA.

6. Patient Recruitment Database

This is an ongoing project, aimed at creat-ing a database to monitor the progress of patientrecruitment for the different H3Africa projects.

7. Pharmacogenomics Portal For African Popula-tions

This project will:• report pharmacovigilance• consolidate and provide documentation for

available data• extend the Pharmacogenetic Database of

African Populations - this will form part ofthe African Precision Medicine Portal

These projects are led by 12 project co-leads and involve more than 60 H3ABioNet mem-bers. While some projects have already startedhaving meetings and exchanging ideas using theSlack platform, most of the project leads are still

working on their project plans offline.

One project has been submitted to the MCfor review and approval thus far (Data ArchiveManagement System). It was agreed that projectplans would be finalized by the end of March.

Title Status

African MicrobiomePortal

Ongoing, project planbeing developed

African PrecisionMedicine Portal


African VariationDatabase

Not started yet

Data & BiospecimenAccess CommitteeSupport Resources

Continued from firstphase of H3ABioNet

H3Africa ArchiveOngoing, project plansubmitted

Patient RecruitmentDatabase


PharmacogenomicsPortal For AfricanPopulations


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Databases & Resources Work Package

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• Training


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https://www.ebi.ac.uk/ega/home




Data Integration Work Package

Original image:lendinglink.com

CHAIR:

Cheikh Loucoubar

Mathematician, PhD in Statistical Geneticsand specialized in statistical methods for complexdiseases traits. Head of the Biostatistics, Bioinfor-matics and Modeling Group at the Institut Pasteurde Dakar - a group whose research focus is the devel-opment of statistical methods and tools for geneticassociation analysis of infectious diseases. Teacherin Statistical Genetics, Biostatistics and R Statisti-cal Software at the Gaston Berger and Cheikh AntaDiop universities in Senegal.

CO-CHAIR:

Segun Fatumo

Research Fellow in Statistical Genetics, work-ing in two distinct research areas. The first involvesimplementing approaches in genetics research toassociate specific genetic variations with cardio-metabolic traits in Ugandan participants. The sec-ond area of research involves characterizing thetrans-generational genomic impact of genocide ex-posure and post-traumatic stress disorder (PTSD) infemale survivors of the Rwandan genocide and theiroffspring.

OBJECTIVE:

To identify existing data integration tools andto make these available via a portal. This mayinclude tools for protein-protein interaction net-works, pathway analysis, regulatory networks andintegration of different types of omics data.

PROJECTS:

The work package is made up of threeprojects:

Title Project lead

Systems biology analysistools/portal

Ezekiel Adebiyi

Statistical modeling ofcomplex genomic andenvironmental data

Nicki Tiffin

Meta-analysis tools Gaston Mazandu

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CONTRIBUTORS:

Alia Benkahla Gerrit Botha Nicki Tiffin

Anisah GhoorahGhaith BenAbdessalem

Postdoctoral fellow(Nicki Tiffin)

Azza Ahmed Hager Jaouadi Nihad H. Alsayed

Boutaina Ettetuani Ichrak Benamri Oumar Thiero

Cheikh Loucoubar Kais Ghedira Parker Lamptey

Graduate student(Cheikh Loucoubar)

Lilia RomdhanePhD candidate AB(Gaston Mazandu)

Cherif Ben Hamda Maia Lesosky Postdoc TBH

Dare Falola Mamadou Diop Rahma Mkaouar

Ebo Turkson Marion Adebiyi Samah Sami

Ezekiel Adebiyi Maroua Boujemaa Segun Fatumo

Faisal Fadlelmola Maryam Diarra Somia Mohamed

Fatma GuerfaliNana KenaFrempong

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• Training


News



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Training Work Package

Original image:parchmentsupport.force.com

CHAIR:

Nicky Mulder

Prof Mulder is PI of H3ABioNet and has beeninvolved in bioinformatics training and educationfor more than 10 years. She is involved in the GlobalOrganisation for Bioinformatics Learning, Educa-tion and Training (GOBLET), and is co-chair of theISCB Education Committee. Nicky also initiatedthe development of the African Bioinformatics Ed-ucation Committee, to provide guidelines for thedevelopment of bioinformatics degrees in Africa.

CO-CHAIR:

Shaun Aron

Shaun Aron is based at the University of theWitwatersrand node and has been involved in theeducation and training activities of the networksince its inception. He has developed and taughta number of courses, ranging from the online In-troduction to Bioinformatics (IBT) course to GWAScourses. He is involved in research aimed at ex-ploring the historical movements and interactionsof African populations.

OBJECTIVE:

The Training Work Package will be continu-ing and expanding on the initial work carried outby the Education and Training Working Group dur-

ing phase I of H3ABioNet. A major focus of the firstphase of H3ABioNet was the development and im-plementation of a number of training programs andproducts to improve bioinformatics capacity withinthe network and other H3Africa projects. A selec-tion of these projects have been carried over intothe new round of the project for completion, to-gether with the identification of new projects aimedat continuing to build a sustainable environmentfor providing high-quality bioinformatics trainingon the continent.

PROJECTS:

1. Specialized short-courses

The work package will still be responsiblefor assessing the need for short, topic-specificworkshops within both the network and thegreater H3Africa community.

Currently, we are gauging interest in aworkshop to develop skills in analysing data gen-erated by the new H3Africa Genotyping Array.

We have also identified a number of poten-tial workshops/jamborees/hackathons for theupcoming year and will continue to assess whereand when would be best to host these.

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https://www.mygoblet.org/

https://www.iscb.org/iscb-education-committee

https://www.h3abionet.org/training-and-education/african-bioinformatics-education-committee

https://www.h3abionet.org/training-and-education/african-bioinformatics-education-committee

https://www.h3abionet.org/wits

https://www.h3abionet.org/wits

2. Online Courses

Although there has been some delay instarting the online Introduction to Bioinformat-ics (IBT) Course this year, this is another majorproject for the work package.

In addition, we would like to trial the plat-form for running a more advanced short course,with an already-developed 16S rDNA course ear-marked for this.

As a separate project, we are also plan-ning on running the Genomic Medicine Courseagain, which utilises the same platform as theIBT course.

3. Managing Training Initiatives & AssessingTheir Impact

Some additional ongoing projects includeupdating and further developing HTrainDB, asystem used for tracking the careers and devel-opment of trainees, and for managing trainingworkshop calls and applications.

4. Projects Related To H3ABioNet Training Mate-rial

Another ongoing project is the curationand transcribing of existing H3ABioNet train-ing material, with a separate group lookinginto defining and mapping competencies to

H3ABioNet training material.

5. Partnering With Fogarty Training Grants Recip-ients

One of the major new projects for the workpackage is aimed at establishing a close collabo-ration with the Fogarty Training Grants in orderto assess possible synergies and areas where thecapacity developed within H3ABioNet could beleveraged to assist the training programs.

6. Projects To Ensure Sustainability

The final two new projects are both aimedat continuing to develop sustainable trainingprograms within the network.

The Train-the-Trainer Project aims to de-velop a platform to train and create a network ofexperienced trainers in a variety of bioinformat-ics areas.

In addition, the Software and Data Car-pentry Project will assess the need for provid-ing these specialized training courses withinthe larger H3Africa community, will establisha framework for presenting the training eventsand will train local trainers for presenting futureworkshops.

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Training Work Package

15









• Training


News



• Announcements

• Upcoming events


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Sustainability & Outreach Work Package

CHAIR:

Jonathan Kayondo

Dr. Jonathan Kayondo is a Senior Research Of-ficer (SRO) at the Uganda Virus Research Institute(UVRI), with a training background in Biochemistry,Chemistry and Molecular Genetics. His research in-volves investigating disease vectors and pathogens,with a focus on the genetics of malaria-transmittingmosquitoes and HIV drug resistance. He is cur-rently involved in research which explores thecontrol of malaria vectors using engineered endo-nucleases, profiling potential arboviral vectors inUganda, and the design of more sensitive molecular

assays for detection ofHIV-drug resistanceminority variants.

Jonathan alsocontributes to bioin-formatics capacity de-velopment and train-ing through a num-ber of partnerships atthe institute. Variousanalysis pipelines formetagenomics andvariant calling are be-ing developed to en-hance pathogen de-tection for research

purposes or disease outbreak investigations.

Jonathan served H3ABioNet I in various ca-pacities, including the roles of UVRI node PI, chairof the User Support Working Group (USWG), mem-ber of the Education and Training Working Group(ETWG) and facilitator in the Introduction to Bioin-formatics course series (IBT-2016 and IBT-2017).


[email protected]

CO-CHAIR:

Amel Ghouila 7 @AmelGhouila

A computer sci-entist by background,Amel Ghoulia earnedher PhD in Bioin-formatics from theLIRMM Laboratory,Montpellier, France.She is currently a bioin-formatician at the In-stitut Pasteur de Tunisnode in Tunisia, whereshe works on the frameof the H3ABioNet con-sortium.

Amel served asthe co-chair of the Research Working Group for thepast three years and contributed to various activi-ties within the consortium such as education andtraining. She is an open science advocate who ispassionate about knowledge transfer. Her main re-search interests are in Data Science and Bioinfor-matics of Pathogens using NGS data.

In her spare time, Amel runs the Technova-tion program in Tunisia, which teaches girls how toaddress challenges in their communities using cod-ing.


OBJECTIVE:

The Sustainability & Outreach Work Packageis designed to disseminate H3ABioNet outputs andactivities across and beyond the consortium, anddevelop plans for long-term sustainability.

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(https://www.h3abionet.org/uvri)

https://twitter.com/amelghouila?lang=en




PROJECTS:

This year we will reach out through a combination of new projects and selected activitiescarried over from the previous round of H3ABioNet, as follows:

Description Status

Managing an integrated social media platformfor promoting consortium events and products

Ongoing, continued from pre-vious round

Designing marketing materials as communica-tion tools for consortium outreach and publicity


Coordinating Open Science groupsStarting in April, building onactivities from previous round

Management and development of the Help DeskOngoing, continued from pre-vious round

Preparing and publishing the H3ABioNetnewsletter


Additional activities including:• improving the website• connecting H3ABioNet with other interna-

tional consortia and initiatives• public engagement• Women in Data Science activities


CONTRIBUTING TO THE WORK PACKAGE:

The Sustainability and Outreach Work Package monthly meetings will take place on thethird Thursday of every month at 12PM CAT. There is still opportunity for volunteersto sign up for any of these projects/activities. If you are interested in becoming involved,please contact the chair and co-chair.

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Sustainability & Outreach Work Package

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• Training


News



• Announcements

• Upcoming events


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@H3ABioNet




Report: H3ABioNet 2.0 Kick-off Meeting

The H3ABioNet 2.0 kick-off meeting tookplace at the Victoria and Alfred Waterfront in CapeTown, during the third week of November 2017. Itwas attended by 48 H3ABioNet personnel from 26of the 28 H3ABioNet nodes. Many of the attendeeswere PIs and personnel continuing from H3ABioNet1.0, while others were from new H3ABioNet nodesjoining for the first time as part of H3ABioNet 2.0.The new nodes had met in October 2017 to proposeand brainstorm projects in anticipation of the kick-off meeting.

The first day of the meeting commenced withwelcomes and introductions by Prof. Nicky Mul-der. This was followed by 10-minute presenta-tions from each of the research groups which makeup the H3ABioNet nodes, as a way of introduc-ing themselves. Each H3ABioNet node presenta-tion provided descriptions of (i) the background ofthe node, (ii) their research focus area, (iii) theircomputational- and training-related resources, (iv)current staff and their expertise, (v) the node’s ex-pected contributions to the various work packages

and projects within H3ABioNet and (vi) their expec-tations from H3ABioNet. The final node presenta-tion was completed up by late afternoon, leavingtime for Scientific Advisory Board (SAB) nomina-tions.

In the close-out meeting of H3ABioNet 1.0 inOctober 2017, the existing H3ABioNet SAB was dis-solved and node PIs were asked to think of suitablenominees for the new SAB, based on the expertiserequired. The categories of expertise deemed to benecessary for H3ABioNet 2.0 were Bioinformatics,African Population Genetics, Bioinformatics Educa-tion, Health Informatics, Big Data and Ethics. Toend off day one of the meeting, brief oral motiva-tions about the suitability of the proposed candi-dates were provided by the nominating PIs. There-after, an online poll was opened in which each nodecould provide a single vote for their preferred candi-date before the close of the kick-off meeting.

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The morning session of day two involvedtalks about the administrative and reporting as-pects of H3ABioNet. Prof. Mulder closed offthe morning session by providing a recap onH3ABioNet 1.0. The remaining sessions had beenset aside for brainstorming the various projects pro-posed since the close-out meeting. This discus-sion involved all personnel with input on possiblecontributions by each node, interspersed with 10-minute presentations on work carried over fromH3ABioNet 1.0. Three of the eight H3ABioNetwork packages (Data & Standards, Health Informat-ics, and Pipelines & Computing) were discussed indepth. The various projects and their progress willbe periodically reported in subsequent issues of theH3ABioNet newsletter.

The remaining five H3ABioNet 2.0 work pack-ages (Databases & Resources, Tools & Web services,Data Integration, Training and Sustainability & Out-reach) were discussed on day 3. Various projectswere proposed before being narrowed down, withshorter activities being separated from stand-aloneprojects. Attendees were asked to list the names

of members of their node who could contribute toeach project along with an indication of how muchtime they could devote. They were also asked to dis-seminate information about the available projectsand the related discussions, so that node mem-bers who were not in attendance could become in-volved.

The meeting ended with the announcementof the SAB nominees who had been selected. Thetop-ranked candidates were then were then ap-proached to serve as members of the SAB forH3ABioNet 2.0 and accepted their positions. The se-lected members of the H3ABioNet 2.0 SAB are Prof.Michele Ramsay (African Population Genetics), Dr.Janet Kelso (Bioinformatics), Prof. William Hersh(Health Informatics), Prof. Terri Attwood (Bioinfor-matics Education), Dr. Odile Ouwe Missi Oukem-Boyer (Ethics) and Dr. Francis Ouellette (Big Data).

Sumir PanjiNode Manager

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Report: H3ABioNet 2.0 Kick-off Meeting

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• Training


News



• Announcements

• Upcoming events


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@H3ABioNet




Software & Data Carpentry Training

Four members of H3ABioNet attended arecent Software and Data Carpentry Workshop,which took place from 21 to 23 February. The work-shop was aimed at individuals who wanted get in-volved in Software and Data Carpentry or similartraining initiatives. The objective was for partici-pants to develop the skills required to present thesecourses. The workshop covered the basics of edu-cational psychology and lesson design, and demon-strated the use of these concepts in intensive work-shops and regular classes. The workshop was spon-sored by the DHET’s Rural Campus Connectivity

Project II and was offered to participants at no cost.

The course included daily lectures presentedby a variety of trainers, interspersed with practicalactivities and opportunities for feedback. Partici-pants were able to interact with researchers fromother disciplines. An especially interesting aspectwas comparing how common tools are applied dif-ferently across these disciplines. The practical ac-tivities and short lessons presented were very effec-tive, giving trainees room to practice what they hadlearnt.

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https://tenet-rccpii.github.io/2018-02-21-South-Africa-ttt/

The workshop took place along South Africa’ssouthern coastline, in the quiet town of Kleinmond.It provided trainees with a satisfying break from thebustling city. The training was both valuable andextremely enjoyable. Breakfasts and lunches wereprovided, as well as a group dinner at KabelJoe’sseafood restaurant.

As part of the training, participants preparedlessons involving Data Carpentry (R programming)and Software Carpentry (Unix Shell) topics of their

choice. These short lessons were presented at theend of the workshop. As a result, the four membersof H3ABioNet who attend the course are now certi-fied Software and Data Carpentry instructors.

Lyndon ZassCPGR node

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Software & Data Carpentry Training

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• Training


News



• Announcements

• Upcoming events


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@H3ABioNet

https://h3abionet.org/cpgr



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1. SELECTED RECENTLY-PUBLISHED ARTICLES

(a) Projects Initiated By Or Contributed To ByH3ABioNet

• Hackathons as a means of accelerating scien-tific discoveries and knowledge transfer

Ghouila A et al.

• HUMA: A platform for the analysis of geneticvariation in humans

Brown DK et al.

• Organizing and running bioinformaticshackathons within Africa: The H3ABioNetcloud computing experience

Ahmed A et al.

• Whole-genome sequencing for an enhancedunderstanding of genetic variation amongSouth Africans

Choudhury A et al.

(b) ISCB Publications Involving H3ABioNet

• Highlights of the second ISCB Student CouncilSymposium in Africa, 2017

Rafael CN et al.

• The development and application of bioinfor-matics core competencies to improve bioinfor-

matics training and education

Mulder N et al.

(c) Research Perspectives Related To H3Africa &H3ABioNet

• Genomic Research Data Generation, Analysisand Sharing - Challenges in the African Setting

Mulder N et al.

• H3Africa: current perspectives

Mulder N et al.

Thank you to the numerous contributors to theefforts and insights described in these publica-tions.

Congratulations to all the authors.

2. NODE ACCREDITATION

Congratulations to the the following nodes fortheir recent accreditation:

• NABDA: 16S rRNA, GWAS

• Institut Pasteur de Tunis: 16S rRNA

• Stellenbosch University: variant calling fromNGS data

Continued


Worker & Ev Announcements jjjs Package

Original images:desotohs.desotoisd.orgnorthviewbandboosters.net

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http://doi.org/10.1101/gr.228460.117

http://doi.org/10.1101/gr.228460.117



http://doi.org/10.12688/aasopenres.12847.1



http://doi.org/10.1038/s41467-017-00663-9

http://doi.org/10.1038/s41467-017-00663-9

http://doi.org/10.1038/s41467-017-00663-9

http://doi.org/10.12688/f1000research.13463.1

http://doi.org/10.12688/f1000research.13463.1

http://doi.org/10.1371/journal.pcbi.1005772



http://doi.org/10.5334/dsj-2017-049

http://doi.org/10.5334/dsj-2017-049

http://doi.org/10.2147/PGPM.S141546

3. COURSE IN APPLIED BIOINFORMATICS

In March this year, the ECBAG node atZagazig University started a training course inApplied Bioinformatics at the Training Unit forBiotechnology and Genomic Informatics.

The course is comprised of 12 modules,with each module made up of a series of lecturesand practicals.

The course content is presented by Prof.Ahmed M. Alzohairy, with assistance from Med-hat Radi and Mohammed A. Farahat.

The topics covered include:

• The potential of bioinformatics

• Manipulating biological sequences

• DNA sequence analysis

4. WORKING WITH PATHOGEN GENOMESCOURSE

In June this year, the University of CapeTown will host the above-mentioned course.

It will be presented by members of the In-fection Genomics teams at the Wellcome TrustSanger Institute, as well as local trainers.

The course begins with training in the use

of genome analysis software (Artemis and ACT),developed at the Sanger Institute for genome ex-ploration and comparative genomics.

It goes on to cover the mapping of Illu-mina sequence data, SNP calling, phylogenetics,genome assembly, genome annotation and RNA-seq.

5. YOUNG RESEARCHERS’ SYMPOSIUM

This event, the second of its kind, tookplace at the Institut Pasteur de Tunis from 18 to20 April 2018.

It showcased the work of young re-searchers and provided a platform for exchangewith more established researchers.

The symposium involved four themes:

• Cancers, genetic diseases andpredispositions

• Bioinformatics, biostatistics andbiomathematics

• Infectious diseases

• Applied biotechnology

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• Training


News



• Announcements

• Upcoming events


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https://h3abionet.org/egypt



1. RESEARCH SUPPORT & FUNDING OPPOR-TUNTIES

(a) Addressing the Burden of Antimicrobial Re-sistance

The African Academy of Sciences (AAS) andthe South African Medical Research Council(SAMRC) are funding research to achieve thisaim.

To apply: AAS, SAMRC.

View open calls from Grand Challenges part-ners here.

Application deadline: 16 May 2018

Deadline for pitches: 5th of every month

(b) Africa Science Desk

This project provides funding to journalists inselected African countries to produce sciencestories aimed at local or global news markets.

Learn more or apply.

(c) Africa-India Mobility Fund

This programme funds short-term visits forresearchers from Africa and India to travel be-tween the two.

To find out more: English, French.

(d) African Career Accelerator Awards

These awards, from the UK Global ChallengesResearch Fund, provide support for Africanpost-doctoral researchers who are making thetransition to being independent researchers.

Application deadline: 1 Jul 2018

(e) African Postdoctoral Training Initiative

This program is a partnership between theAfrican Academy of Sciences (AAS), the U.S.National Institutes of Health (NIH) and theBill & Melinda Gates Foundation (BMGF).

Find out more at the links above or applyhere.


(f) Science and Language Mobility SchemeAfrica

This scheme offers travel grants for short-term visits for researchers in Franco and An-glophone Africa.

To find out more: English, French.


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http://www.aasciences.ac.ke/aesa/programmes/grand-challenges-africa/funding-opportunities/



http://www.samrc.ac.za/request-for-applications/grand-challenges-south-africa-call-proposals-antimicrobial-resistance

https://grandchallenges.org/grant-opportunities

https://www.aasciences.ac.ke/aesa/en/programmes/africa-science-desk/call-for-pitches/

https://www.aasciences.ac.ke/aesa/en/programmes/africa-science-desk/call-for-pitches/

https://aasishango.ccgranttracker.com/

http://www.aasciences.ac.ke/aesa/en/programmes/africa-india-mobility-fund/

http://www.aasciences.ac.ke/aesa/en/programmes/africa-india-mobility-fund/

http://www.aasciences.ac.ke/aesa/en/programmes/le-fonds-de-mobilit-afriqueinde/

https://crick.ac.uk/research/crick-african-network/african-career-accelerator-awards/


http://www.aasciences.ac.ke/about/about-us/about-the-aas/

https://irp.nih.gov/our-research/scientific-focus-areas

https://www.gatesfoundation.org/What-We-Do


http://www.aasciences.ac.ke/aesa/en/programmes/science-and-language-mobility-scheme-africa/



http://www.aasciences.ac.ke/aesa/en/programmes/programme-de-mobilit-science-et-langue-en-afrique/

2. RESEARCH EVENTS & TRAINING OPPORTUNI-TIES

(a) 17th European Conference on Computa-tional Biology

Athens, Greece, 8-12 Sep 2018

This is the leading European event of its kind.

Deadline for abstracts: 15 May 2018Early registration deadline: 29 Jul 2018

(b) 18th NETTAB Workshop: Building a FAIRBioinformatics Environment

Genova, Italy, 22-26 Oct 2018

Deadline for oral abstracts: 20 May 2018Early registration deadline: 28 Sep 2018

(c) 2nd International Congress on PersonalizedHealth Care

Montreal, Canada, 23-26 Sep 2018

Deadline for abstracts: 27 May 2018Early registration deadline: 22 June 2018

(d) Bioinformatics and Genome AnalysisCourse

Tunis, Tunisia, 10 Sep-14 Dec 2018

Application deadline: 23 Jun 2018

(e) ISCB Conference

Chicago, USA, 6-10 Jul 2018

This is the leading conference in the field.

Early registration deadline: 7 Jun 2018

(f) Research Data Science Summer School &Workshops

Trieste, Italy, Aug 2018

These events are co-organised by H3ABioNet.


i. Summer School, 6-17 Aug 2018

ii. Advanced Workshops, 20-24 Aug 2018

(g) SASBi-SAGS Joint Congress

Free State, South Africa, 16-18 Oct 2018

Deadline for abstracts: 29 Jun 2018Registration deadline: 1 Jun 2018

(h) SciDataCon-IDW Conference

Gaborone, Botswana, 5-8 Nov 2018

Deadline for abstracts: 31 May 2018Registration deadline: To be announced

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• Training


News



• Announcements

• Upcoming events


Follow us:


@H3ABioNet

http://eccb18.org/

http://eccb18.org/

http://www.igst.it/nettab/2018/

http://www.igst.it/nettab/2018/

http://www.icphc.org/index.html

http://www.icphc.org/index.html

https://webext.pasteur.fr/tekaia/BCGAIPT2018.html

https://webext.pasteur.fr/tekaia/BCGAIPT2018.html

https://www.iscb.org/ismb2018

https://www.ictp.it/scientific-calendar.aspx

https://www.ictp.it/scientific-calendar.aspx

http://indico.ictp.it/event/8329/

http://indico.ictp.it/event/8561/

http://sagene.co.za/sasbisags2018/

https://www.scidatacon.org/IDW2018/



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