Pan African Bioinformatics Network for H3Africa

H3ABioNet / IBM Research Africa hackathon on Malaria Drug Resistance for a DREAM challenge

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 This email address is being protected from spambots. You need JavaScript enabled to view it. 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 ( This email address is being protected from spambots. You need JavaScript enabled to view it. ) 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.