Bilkent University
Department of Computer Engineering


A cryptocurrency incentivized voluntary grid computing platform for DNA read alignment


Halil İbrahim Özercan
MS Student
(Supervisor: Asst. Prof. Dr. Can Alkan)
Computer Engineering Department
Bilkent University

The main computational bottleneck of High Throughput Sequencing (HTS) data analysis is to map the reads to a reference genome, for which clusters are typically used. However, building clusters large enough to handle hundreds of petabytes of data is infeasible. Additionally, the reference genome is also periodically updated to fix errors and include newly sequenced insertions, therefore in many large scale genome projects the reads are realigned to the new reference. Therefore, we need to explore volunteer grid computing technologies to help ameliorate the need for large clusters. However, since the computational demands of HTS read mapping is substantial, and the turnaround of analysis should be fast, we also need a method to motivate volunteers to dedicate their computational resources. For this purpose, we propose to merge distributed read mapping techniques with the popular blockchain technology. Cryptocurrencies such as Bitcoin calculate a value (called nonce) to ensure new block (i.e., “money”) creations are limited and difficult in the system, however, this calculation serves no other practical purpose. Our solution (Coinami) introduces a new cryptocurrency called Halocoin, which rewards scientific work with alternative minting. In Coinami, read alignment problems are published and distributed in a decentralized manner while volunteers are rewarded for their work. Authorities have two main tasks in our system: 1) inject new problem sets (i.e., “alignment problems”) into the system, and 2) check for the validity of the results to prevent counterfeit.


DATE: 06 September 2019, Friday @ 13:40