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Posted by 이승철 2017.01.11


Opentox Hackathon on Case-Driven Data Analysis


OpenTox is the leading global open platform for predictive toxicology supported by open standards that want to develop an predictive toxicology framework which may be used as an enabling platform for the creation of predictive toxicology applications. One of OpenTox’s plans is to develop OpenTox further as an infrastructure and community with annual events held in Europe, USA and Asia in the area of predictive toxicology and related fields.

Located at Megagen TOZ, Seoul, South Korea, OpenTox workshop was held for 2 days, 5-6th December. This workshop was the first OpenTox meeting organized in Asia. As the series meeting event of OpenTox, the workshop was aimed to advance the understanding of the application of new computational methods to practical case-driven questions on the toxicology and safety of compounds. The participants were expected to build and explore biological signatures for toxicity endpoints of interest using toxicogenomic data linked to chemical toxicities. The Hackathon places an emphasis on learning by doing. Groups working on case study problems, formulate questions to be addressed, and then attempt to generate answers combining different datasets and modelling tools into a scientific analysis.

                Dr. Hardy introduced OpenTox

On the first day, the workshop was opened by welcoming remark by Tae-Hyun Yoon (Professor at Hanyang University) and then continued by a presentation on advances in predictive toxicology and safety assessment methods by Dr. Barry Hardy, the coordinator of OpenTox project in predictive toxicology who is also the Managing Director of Douglas Connect (

Dr. Hardy introduced OpenTox as an association to promote the community-based  exchange and use of open knowledge, methods, tools, data, reference resources, and standards including OpenTox Software ( and the OpenTox API ( in the scientific activities of predictive toxicology, safety assessment and risk management, including the “3Rs” goal of the Reduction, Refinement and Replacement of Animal Testing.

After Dr. Hardy’s presentation, Johan Nyström-Persson, a bioinformatician and software engineer at Level Five Co.,Ltd (, gave his presentation about how to use Toxygate ( and others omics databases (ToxCast [], TG-Gate []) to do analysis and discover interesting and useful knowledge.

Participants of the workshop were researcher from several companies and institutes and master/P.hD student from South Korea and other Asian countries. In work using study case, participants were divided into 4 teams. Each groups decided their names based on the problem that they wanted to solve.

Team 1 : Pathos Team (using omics data to find key regulator (gene) responsible for certain toxic action)

Team 2 : GenePredict Team (using omics data to predict disease)

Team 3 : Target Team (using omics data to see the effect of a chemical compound on gene activity)

Team 4 : AOP Team (Finding biomarker candidates in metal oxide nanomaterials related AOP using metal oxide microarray)

Each team had internal discussion to make a problem as well as solution

Each teams had internal and external discussion during working. Each team members used his or her expertise to make contribution for solving the case. Dr. Hardy and Johan also offered suggestion that help participant to overcome problem found while working. Johan, as the developer of Toxygate, made many helps related to software utilization.

Discussion time was valuable. We can develop some idea about we can do by using genomic data”- Tung’s (Graduate student of Hanyang University) testimony for OpenTox Hackaton Asia.

          Dr. Hardy discussed with participant

On the second day, all teams continued their work and made preparation for their result presentation. After lunch, Johan introduce  Garuda as a platform to connect, discover and navigate through inter-operable gadgets with applications in biology, healthcare and beyond. Johan explain what Garuda can do as well as problem that can be solved using Garuda.

Johan introduced Garuda as a platform to connect, discover
and navigate through inter-operable gadgets

About 4 p.m, result presentation was started. The first presentation was performed by Target Team. Target team used  Toxygate to figure out the effect of Carbon Tetrachloride (CCl4) on gene level of on rat’s liver exposed for 4 and 29 days with single mode. They validated data obtained from Toxygate by using published journal.

The second presentation was from Pathos team. Pathos team presented their efforts using omics data from Toxygate, TG-Gate, ToxCast and Target Mining to find gene activity responsible for the same toxicity action in several chemical compounds. The third was GenePredict team. This team showed their idea about building prediction model based on gene signature from TG-Gate and structure to predict liver weight change.

The last was AOP team that presented SIRT1 as a biomarker candidate for mitochondrial function increase and oxidative stress decline which both mitochondrial and oxidative stress are included in AOP (Adverse Outcome Pathway) of nanoparticle. This team was the only team that shared their data (ZnO NP) to Toxygate which made Johan as the developer of Toxygate gave them more appreciation.

Dr. Hardy, Johan, Tae-Hyun Yoon and participants gave questions, suggestions and new ideas during presentation section. Some of them offered collaboration work with team that presented interested idea. It shows that OpenTox workshop can be mean that is not only for enlarging connection but also finding new thing to be discovered. Joeun Jung, a researcher from TO21 Co., Ltd ( said that, “OpenTox workshop gave me an opportunity to have practical experience in both toxicological and its analysis in molecular level. Also, it opened my sight to see that there are actually many things to be developed in this field. Even though, it was quite difficult for them who has no computer science or data analysis background, it is still challenging and interesting. Another thing is I was very happy to have discussion with professional people to get knowledge on adverse health effects by various chemical compound.”.



OpenTox workshop was ended by certificate awarding by Dr. Hardy and photo shoot of participant with all organizing committee. 

by Desy Maulina