Workshop Title: H3ABioNet / IBM Research Africa Hackathon on Malaria Drug Resistance for a DREAM challenge

    Venue of workshop: Johannesburg, South Africa

    Dates for the workshop: 5th September to 10th September 2016

    Workshop organisers: Amel Ghouila, Jean-Baka Domelevo Entfellner, Geoffrey Siwo, Darlington Mapiye, Pavan Kumar, Waheeda Saaib, Michael Ferdig, Sage Davis, Katie Button, Faisal M. Fadlelmola, Sumir Panji, Nicola Mulder

    Registration opens: 23rd June 2016

    Registration closes:  11th July 2016

    Notification date: 21st July 2016

    Application process:

    1. Complete the application form available at: https://docs.google.com/forms/d/18bWGjgxc2KIx2cXj9WVkJIfzDxJ78iFQM-scJMeoEBQ/viewform?edit_requested=true
    2. After submitting the application form, email a 2 pages CV to  in the format of FIRSTNAME_SURNAME_CV in order to complete your application

    Workshop Sponsors: H3ABioNet, IBM Research Africa and University of Notre Dame

    Workshop Overview: H3ABioNet, the University of Notre Dame and IBM Research Africa are organizing a joint hackathon on a complex biomedical research question on antimalarial drug resistance to prepare preliminary datasets for a future open collaborative challenge on drug combination prediction.

    While malaria, a disease caused most commonly by the protozoan parasite Plasmodium falciparum, remains a major global health challenge, with a global estimate of slightly less than half a million deaths in 2015 [WHO World Malaria Report 2015], the African continent carries a disproportionately high burden of the disease (88% of the world cases and deaths). Nowadays, the World Health Organization (WHO) recommends artemisinin-based combination therapies for the treatment of malaria cases due to P. falciparum. However, emerging resistance of P. falciparum to artemisinins has been observed over recent years in South-East Asia, and the WHO has stated that “The emergence of P. falciparum resistance to artemisinin is an urgent public health concern, threatening the sustainability of the global effort to reduce the malaria burden in all endemic regions.”
    In this context, it is the endeavor of consortia like H3ABioNet and IBM Research Africa to foster major breakthroughs in scientific research on diseases having a major impact on the African continent, hence the motivation for this collaboration.

    Syllabus and Tools: The Ferdig Laboratory at the University of Notre Dame (Indiana, USA) is generating transcriptional data sets from a range of the malaria parasite isolates exposed to artemisinin in culture. This data needs to be preprocessed and prepared for an open challenge that will be launched under the DREAM Challenges initiative within the next 2 years. The challenge will invite participation of the whole research community in developing computational models for malaria drug combinations. Therefore, H3ABioNet, the University of Notre Dame and IBM Research Africa are organizing a data analysis workshop to prepare data for the launch of part 1 of a two-fold future open challenge on drug resistance prediction from transcriptional response in the context of (1) single drug treatment and (2) multi-drug treatment. In this latter challenge, the scientific problem will involve the prediction of synergistic and/or antagonistic effects of drug combinations from transcriptional responses to individual drugs.

    Some work has already been published on drug sensitivity prediction using genomics data sets, including results from a previous DREAM Challenge [Costello et al, Nat. Biotechnol. 2014] or [Liu et al, Sci. Rep. 2016]. As part of the workshop, we also plan to review the biological foundations and hypotheses for predicting drug combinations.

    Objectives:  The main objective of this workshop is to normalize, pre-analyse and curate the microarray data generated in order to prepare for the launch of the two-fold DREAM Challenge that will be open in the near future to the research community.

    After the data have been processed, workshop participants will be tasked with developing baseline models for predicting drug sensitivity and assessing the viability of the challenge. The specific aim is to evaluate the predictability of the level of drug resistance of P. falciparum isolates exposed to dihydroartemisinin (DHA), the active form artemisinin, based on their transcriptional response measured at two time-points in red blood cell cultures. The genetic background information on the isolates will be provided to the participants. The genome-wide transcriptional profiles will come in the form of microarray data.

    Developing a satisfactory solution to this complex prediction problem will require participants to make use of a mix of skills pertaining to various areas of the broad bioinformatics field: microarray data analysis, drug response (drug mechanism of action and drug resistance), pharmacogenomics, vector-host interactions, discrete modeling, machine learning, biostatistics and computer programming. Therefore, we seek to gather a few motivated participants originating from the H3ABioNet/H3Africa consortium for a five-day workshop.

    Intended Audience: Participants should demonstrate confirmed expertise in one or several of the above-mentioned domains and that they will bring an added value in the data analysis process.

    This workshop is clearly results-oriented, and training during the workshop will be limited to topic-specific sessions to implement efficient cross-talking between the different subgroups of expertise that will make up the group of workshop participants. It is NOT designed to be a training course. Participants are expected to benefit from learning to integrate skills from statistics, computing and biology to seeking solutions to biological problems in a collaborative manner and within a limited span of time. We anticipate that participants will work openly with each other and will therefore have the chance to learn from each other and develop critical thinking and may develop close collaborations and that the experiences on collaboration and scientific insights obtained will be published at a later date with participants as authors.

    Application: All potential applicants must complete the application form (https://docs.google.com/forms/d/18bWGjgxc2KIx2cXj9WVkJIfzDxJ78iFQM-scJMeoEBQ/viewform?edit_requested=true) and email their 2 pages CV to Sumir Panji ( ) before 11th July 2016.  incomplete applications will NOT be reviewed. 
    Successful applicants will be brought together to start group discussions prior to the workshop, to ensure that they familiarize themselves with the data at stake and with the collaborative work platform that will be used during the workshop, namely Sage Synapse. Pre-selected applicants might be invited by the organizing committee to take part in a Skype interview between the 25th and the 28th of July.

    H3ABioNet will provide travel fellowships that cover travel and accommodation costs for selected participants. Once being successfully chosen for the workshop, participants will be contacted to complete an airline ticket booking form, a short biosketch with a recent picture and the H3ABioNet workshop policy.

    **Please note, if a participant is unable to attend this workshop after acceptance, their place will be passed onto to applicants on the waiting list and not to other recommended members from their H3Africa programme.



    Workshop dates: Monday 6th June 2016

    Venue: Health Teaching Labs 1-2, Basement of Anatomy Building, UCT Medical School, Anzio Rd, Observatory, Cape Town, South Africa

    Workshop organisers and sponsors: Ben Moore, Nicola Mulder, CBIO@UCT

    Workshop trainers and support: Ben Moore, CBIO@UCT

    Course Overview: The Ensembl project at www.ensembl.org provides a comprehensive and integrated source of annotation of mainly vertebrate genome sequences. This 1-day workshop offers participants the possibility of gaining hands-on experience in the use of the Ensembl genome browser but also provides them with the necessary background information. Our sister project at www.ensemblgenomes.org can also be covered if participants are working with bacteria, plants, fungi, protists or (invertebrate) metazoa.

    Intended Audience: The workshop is primarily targeted at wetlab researchers, and we customise the course for species of interest and to include total beginners to our browser up through frequent users.

    Prerequisites: Participants should complete the application form to attend the workshop. Participants should have a general knowledge of molecular biology / genomics and a familiarity with web browsers. As there is no workshop fees, participants must take care of their own catering needs.

    Workshop format: Most modules consist of a presentation and demo, followed by an opportunity to complete exercises and explore Ensembl with assistance. Participants are encouraged to bring problems/questions about their research to try to tackle these during the workshop using Ensembl.

    Note: Most examples and exercises in the workshop will be focused on human as this is by far the most richly annotated species. However, most of what is taught in the workshop can be applied to other species in the Ensembl browser (http://www.ensembl.org), as well as to the species in the Ensembl Genomes browser, that contains genomes of invertebrates, protists, plants, fungi and bacteria www.ensemblgenomes.org.

    Syllabus: Morning

    • Introduction to Ensembl: origin, goals and organization of the Ensembl project
    • Genes and Transcripts: guided tour of the most important pages of the Ensembl website
    • Data retrieval with BioMart: retrieving complex / large datasets using the data retrieval tool BioMart

    Afternoon: two or three of the following modules will be covered, depending on the interest of the participants.

    • Comparative genomics: gene trees, orthologues and paralogues, whole genome alignments and syntenic regions
    • Variation: sequence variants, structural variants, Variant Effect Predictor
    • Regulation: annotation of regulatory elements using data from ENCODE, Roadmap Epigenomics and BLUEPRINT projects.
    • Custom annotation: uploading / attaching your own data (BED, GFF, BAM, VCF files) to Ensembl
    • Advanced access: other ways to access Ensembl data (MySQL, Perl API, REST API)

    Objectives:

    • Learn about the data types in Ensembl
    • Learn how to view data in the Ensembl browser
    • Learn how to mine Ensembl data using BioMart

    Workshop materials:

    Attachments:
    Download this file (Exercise_BM2.txt)Exercise_BM2.txt [ ] 0.1 Kb
    Download this file (Exercise_BM3.txt)Exercise_BM3.txt [ ] 0.2 Kb
    Download this file (Exercise_BM5.txt)Exercise_BM5.txt [ ] 0.2 Kb
    Download this file (Exercise_V4.vcf)Exercise_V4.vcf [ ] 319 Kb

    Course websitehttp://training.h3abionet.org/IBT_2016/

    Venue of course: 19 classrooms across 11 African countries. Classrooms connect to the trainer via Mconf (‘virtual classroom’).

    Dates for the course: 6th July – 9th October 2016, every Wednesday and Thursday, 10:00-14:00 CAT each day

    Course organisers: H3ABioNet Education and Training working group and the IBT core team (Kim Gurwitz, Shaun Aron, Sumir Panji and Nicola Mulder)

    Participation via Classrooms: A call was sent out for institutions to apply to host a classroom. Classroom selection was based on the availability of certain infrastructure requirements, as well as the availability of dedicated, local teaching assistants. Classrooms hosted at both H3ABioNet and non-H3ABioNet institutions.

    Participants: Participants applied to a particular classroom via a centralised application form and were informed of the outcome of their application.

    Course Sponsors: H3ABioNet

    Course Overview: The IBT_2016 course is an introduction to the field of Bioinformatics, with a focus on important Bioinformatic tools, algorithms and resources. Over a period of 3 months of intensive biweekly contact sessions, the course combines theoretical and practical sessions to allow participants to gain practical experience in using various tools and resources.

    Intended Audience: The course is aimed at individuals from a Molecular Biology background who have a basic understanding of Biochemistry and/or Genetics and would like to become basic Bioinformatics users.

    Syllabus and Tools: The participants will cover an introduction to various Bioinformatics topics, namely; Databases and Resources, Genomics, Linux, Sequence alignment theory and application, Multiple sequence alignment, Protein structural Bioinformatics, Phylogenetics and molecular evolution. For practical sessions, web-based tools are used as far as possible.

    Prerequisites: A base line level of the understanding of the central dogma of molecular biology (i.e. DNA to RNA to Protein) is a requirement.

    Objectives: By the end of the course participants should be able to:
    • Explain the use of Bioinformatics
    • Name the key Bioinformatics techniques and tools
    • Locate important biological databases and retrieve data
    • Use selected tools effectively to run specific Bioinformatics analyses
    • Understand the strengths and limitations of the various techniques

    Course limitations: This course will provide an introduction to the field of Bioinformatics. Participants must be able to attend biweekly contact sessions at one of the classroom sites.

    Course costs: There is no application or participation fee. Local sites provide the physical resources for the course and the course core team provides logistic and course management support

     

    IBT_2016 course schedule(*subject to slight changes)

     

    Date Topic Trainer
    Welcome to the course!

    Wednesday,

    6 July

    Introductory session (+- 1 hour)

    - get to know where your classroom is and meet your teaching assistants and fellow participants

    (NOTE: a repeat of this session will be held on Monday, 11 July for those unable to make the session on the 6 July. A written document detailing the logistics of the course will also be available)

    IBT core team
    Introduction to databases and resources
    Wednesday, 13 July Guest lecturers: ‘What is bioinformatics and why is it important?’

    Pedro Fernandes

    Instituto Gulbenkian de Ciência, Oeiras, Portugal

    and

    David P Judge

    Freelance independent Bioinformatics instructor

    Thursday,

    14 July

    Biological databases and resources (NCBI, EBI)

    Shaun Aron

    University of Witwaterstrand, South Africa

    Wednesday, 20 July

    Advanced literature searching – PubMed

    Shaun Aron

    Thursday,

    21 July

    DNA analysis – e.g. sequence features, start site, restriction sites etc

    Nicola Mulder University of Cape Town, South Africa

    *Thursday,

    21 July

    Assessment available for the ‘introduction to databases and resources’ module via Vula ‘Tests and Quizzes’ tab individual

    *Tuesday,

    26 July

    FINAL hand-in date for ‘introduction to databases and resources’ assessment

    individual
      Genomics  

    Wednesday,

    27 July

    Genome sequences – sequencing technology and NGS overview

     

    Fatma Guerfali Institute Pasteur de Tunis, Tunisia

    Thursday,

    28 July

    Genome annotation including genome browsers (feature finding etc)

     

    Colleen Saunders

    South African National Biodiversity Institute, South Africa

    Wednesday,

    3 August

    Comparative genomics

     

    Fatma Guerfali

    Thursday,

    4 August

    Human variation

     

    Colleen Saunders

    *Thursday,

    4 August

    Assessment available for the ‘genomics’ module via Vula ‘Tests and Quizzes’ tab individual

    *Tuesday,

    9 August

    FINAL hand-in date for ‘genomics’ assessment individual
    Linux
    Wednesday, 10 August

    Introduction to Linux and UNIX and the command line

    Amel Ghouila

    Institute Pasteur de Tunis, South Africa

    Thursday,

    11 August

    Manipulating files. Useful commands and tips

    Amel Ghouila
    Wednesday, 17 August

    Permissions, groups and process control

    Amel Ghouila
    *Wednesday, 17 August Assessment available for the ‘Linux’ module via Vula ‘Tests and Quizzes’ tab individual

    *Wednesday,

    24 August

    FINAL hand-in date for ‘Linux’ assessment individual
    Sequence alignment theory and application

    Thursday,

    18 August

    Introduction to searching and sequence alignment

    Pandam Salifu

    Kumasi Centre for Collaborative Research, Ghana

    Wednesday, 24 August

    Pairwise sequence alignment

    Pandam Salifu

    Thursday,

    25 August

    BLAST algorithm

    Pandam Salifu

    *Thursday,

    25 August

    Assessment available for the ‘sequence alignment theory and application’ module via Vula ‘Test and Quizzes’ tab individual

    *Wednesday,

    31 August

    FINAL hand-in date for ‘sequence alignment theory and application’ assessment individual
    Multiple sequence alignment
    Wednesday, 31 August Overview of multiple sequence alignments applications

    Ahmed Mansour Alzohairy

    Zagazig University, Egypt

    Thursday,

    1 September

    Choosing the right sequences with the right software

    Ahmed Mansour Alzohairy

    *Thursday,

    1 September

    Assessment available for the ‘multiple sequence alignment’ module via Vula ‘Tests and Quizzes’ tab individual

    *Wednesday,

    7 September

    FINAL hand-in date for ‘multiple sequence alignment’ assessment individual
    Protein structural bioinformatics

    Wednesday,

    7 September

    (To be confirmed) TBC

    Ruben Cloete

    South African National Biodiversity Institute, South Africa

    Thursday,

    8 September

    TBC Ruben Cloete
    Wednesday, 14 September NO SESSION NO SESSION

    Thursday,

    15 September

    TBC Ruben Cloete

    *Thursday,

    15 September

    Assessment available for the ‘protein structural bioinformatics’ module via Vula ‘Tests and Quizzes’ tab individual

    *Wednesday,

    21 September

    FINAL hand-in date for ‘protein structural bioinforamtics’ assessment individual
                                                     Consolidation week

    Wednesday,

    21 September

    TBC TBC

    Thursday,

    22 September

    TBC TBC
    Molecular evolution and phylogenetics
    Wednesday, 28 September TBC

    Jean-Baka Domelevo Entfellner

    University of the Western Cape, South Africa

    Thursday,

    29 September

    TBC Jean-Baka Domelevo Entfellner

    Wednesday,

    5 October

    TBC Jean-Baka Domelevo Entfellner

    Thursday,

    6 October

    TBC Jean-Baka Domelevo Entfellner

    Thursday,

    6 October

    Assessment available for the ‘molecular evolution and phylogenetics’ module via Vula ‘Tests and Quizzes’ tab individual

    Wednesday,

    12 October

    FINAL hand-in date for ‘molecular evolution and phylogenetics’ assessment individual
         

    Wednesday,

    12 October

    Course end  

    Workshop Venue: Mbour, Senegal

    Workshop Dates: October 3rd - 14th, 2016

    Application deadline: Extended to the 22nd of August 2016

    Link to application form: https://together.pasteur.fr/inda/event/inda-hands-ngs-statistics-course-senegal-2016

    Workshop description:

    This theoretical and practical course is aimed at researchers that would like to get the most out of their Next Generation Sequencing datasets. We will tackle several topics, encompassing theoretical NGS approaches and statistical analysis of NGS data.

    The first week of this course (Oct 3rd – 7th) will be devoted to theory and practical examples for a broad audience (100 participants), while the second week (Oct 10th – 14th) will be dedicated to practical analysis for a selected group (30) of participants. Prospective students for the hands-on section should apply and will be selected on the basis of their data and the analyses they wish to perform. The exact syllabus will depend on the interest of the attendees, we want this course to be of immediate value.

    The course will be held in Mbour in the AIMS Senegal facilities. The official language for the theoretical and hands-on session will be English. This hands-on NGS course is open to the whole Pasteur International Network, Senegalese Universities (CEA-MITIC), H3ABioNet and AIMS Senegal.

    Eligibility: This hands-on NGS course is open to the whole Pasteur International Network, Senegalese Universities (CEA-MITIC), H3ABioNet / H3Africa members and AIMS Senegal. Selections will be made via review of competitive applications.

    Topics (NGS):

    • Basic statistics and probability concepts applied to NGS
    • Experimental design applied to NGS Quality analysis NGS data
    • Mapping and assembling algorithms
    • Variant calling algorithms, statistical models and approaches / strategies used
    • Resequencing and variant analysis

    Topics (Statistics):

    • Multidimensional Statistics
    • Principal Component Analysis
    • Correspondence Analysis (simple and multiple)
    • Multivariate Generalized Linear Models Bayesian models for NGS

    Sponsors:

     

    The original workshop call can found here.

    ,

    The H3Africa initiative is aimed at studying the genomic and environmental determinants of disease in Africa. The goals of H3Africa are to enhance the necessary genomic expertise among African scientists and to encourage collaborations between African investigators by supporting infrastructure development and research projects. H3ABioNet aims to create a sustainable African Bioinformatics Network to support H3Africa researchers through the development of bioinformatics capacity on the continent.

    Course Overview
    Catalogues on human genome variants produced by large-scale human genome variation projects provide a wealth of genome variation datasets to conduct research on the genomics and environmental determinants of common diseases with the goal of improving the health of African populations. A recognized need is to promote computational skills among African researchers to facilitate genomics-based research on human disease and health across the continent. Visual analytics, the science of analytical reasoning supported by interactive visual interfaces, provides computational tools and techniques to foster collaboration in making sense of data of any size. Participants will be introduced to the focus areas of visual analytics and learn visual analytics skills by working with datasets from catalogues on human  genome variation such as 1000 genomes, National Human Genome Research Institute (NHGRI) GWAS Catalog and the Database of Genomic Variations. The expectation is that participants will initiate collaboration among the H3Africa consortium projects. The course is open to staff and students in the H3Africa Consortium projects

    The successful applicant’s home institution/project shall be responsible for transportation (to and from Abuja), and accommodation (Bed and Breakfast) at Abuja, and dinners during their stay. The host institution (NABDA/FMST) shall provide, in addition to free tuition, Tea Breaks and lunches during the course. 

    Course Trainers
    Dr. Raphael Isokpehi, Visual Analytics in Biology Curriculum Network, USA
    Dr. Oyekanmi Nash, NABDA, Nigeria
    Dr. Segun Fatumo, NABDA/SANGER
    Atinuke Hassan, NABDA, Nigeria


    Course Programme
    Day 1: Monday, 29 July, 2013
    Bioinformatics Research Categories
    Definition, Focus Areas, Scope and Process of Visual Analytics
    Hardware and Software for Visual Analytics
    Hands-on Exercises

    Day 2: Tuesday, 30 July, 2013
    Introduction to Datasets of Catalogues on Human Gene Names
    Hands-on Exercises

    Day 3: Wednesday, 31 July, 2013
    Introduction to Datasets of Catalogues on Human Genome Variation
    Hands-on Exercises

    Day 4: Thursday, 1 August, 2013
    Collaborative Visual Analytics
    Day 5: Friday, 2 August, 2013
    Collaborative Visual Analytics
    Course Evaluation

    How to apply

    To apply to attend the course please complete the application form found here:
    http://surveys.h3abionet.org/visualanalytics
    The application form will open on the 25th June and the deadline for applications is the 15th July 2013.
    Please ensure that all required information is completed on the application and that a motivation letter from your PI is attached


    Subcategories

    Page 4 of 4

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