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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:
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.
Course Overview: The course aims to provide an introduction to the field of bioinformatics, with a focus on important bioinformatics tools, and resources. The course aims to use a combination of theoretical and practical sessions in order for 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 bioinformatics users. For an explanation on who 'bioinformatics users' might be, see Figure 2 in http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1003496. A baseline level of the understanding of the central dogma of biology (DNA -> RNA -> Protein) is a requirement.
Keywords: Genetics, Genomics, Nucleic acids analysis
Skill level of training: Beginner
Language: English
Credential awarded: Letter of completion
Type of training: Blended/hybrid learning
Venue of workshop: Local classrooms ( usually 30 physical sites across Africa) and online
Dates for the workshop:10 July – 15 October; Every Tuesday and Thursday from 10:30 CAT to 14:30 CAT.
Workshop organisers: Kim Gurwitz, Shaun Aron, Sumir Panji and Nicola Mulder
Participation: The course is available to any classroom who meets the requirements and to any participant who is able to attend a physical classroom, if one has been set up at a local institution, provided they have been selected via the selection process.
Workshop Sponsors: H3ABioNet
Syllabus and Tools:
The course curriculum will cover the following main themes (subject to slight changes):
**All modules make use of ONLY web-based tools such as NCBI, Ensembl, etc.
Prerequisites: A basic background/understanding of of biochemistry and/or genetics.
Objectives: After this workshop participants should be able to:
Workshop limitations: This workshop will only provide a foundation for continued learning in bioinformatics and will not teach any advanced coding.
Training Material Availability:
Training materials for this course are available here: https://zivahub.uct.ac.za/projects/Introduction_to_Bioinformatics_Training_Course_Materials/131552. Should you re-use any of these materials, please ensure that both the author/s of the material AND H3ABioNet are clearly credited.
Materials have been made available as a single archive per module containing lecture slides, transcribed videos, practical assignments and any other resources important to complete each module:
Module 1: Databases and Resources
Module 2: Linux
Module 3: Sequence Alignment
Module 4: Multiple Sequence Alignment
Module 5: Genomics
Module 6: Phylogenetics (2018 - 2021)
Module 6: Structural Biology (2016 only)
Introduction Week
Wrap Up week
Workshop overview:
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.
Intended audience: 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.
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
Topics (NGS):
Topics (Statistics):
Sponsors:
Training Materials Availability:
Training materials for this course are not currently available.
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.
Keywords: Genetics, Genomics. Nucleic acids analysis
Skill level of training: Introductory
Language: English
Credential awarded: course attendance certificate
Type of training: face-to-face / in person
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
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
Afternoon: two or three of the following modules will be covered, depending on the interest of the participants.
Objectives:
Training Materials Availability:
Training materials used for this course were not directly produced by H3ABioNet but may be accessed here: http://training.ensembl.org/events/2016/2016-06-07-Cape_Town. Please note, these materials may be governed by different sharing/re-use policies, and you are encouraged to follow the policies of the external providers regarding material re-use and/or sharing.
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.
Keywords: Genetics, Genomics, Nucleic acids analysis
Skill level of training: Beginner
Language: English
Credential awarded: Letter of completion
Type of training: Blended/hybrid learning
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
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
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 |
Training Material Availability:
Training materials for this course are available here: https://zivahub.uct.ac.za/projects/Introduction_to_Bioinformatics_Training_Course_Materials/131552. Should you re-use any of these materials, please ensure that both the author/s of the material AND H3ABioNet are clearly credited.
Materials have been made available as a single archive per module containing lecture slides, transcribed videos, practical assignments and any other resources important to complete each module:
Module 1: Databases and Resources
Module 2: Linux
Module 3: Sequence Alignment
Module 4: Multiple Sequence Alignment
Module 5: Genomics
Module 6: Phylogenetics (2018 - 2021)
Module 6: Structural Biology (2016 only)
Introduction Week
Wrap Up week
Page 4 of 5
Tools and Services
Resources
Communication