Read Between the Lines: Closing Gaps of Materials and Methods to Build Workflow from the Publication Tazro Ohta1, Osamu Ogasawara2, Yoshinobu Masatani3, Shigetoshi Yokoyama3, Kento Aida3 1. Database Center for Life Science, Chiba, Japan 2. DNA DataBank of Japan, Shizuoka, Japan, 3. National Institute of Informatics, Tokyo, Japan Background Increasing cost of translation from text to executable scripts Galaxy as an inter-laboratory workﬂow sharing platform workflow runs on any galaxy, and the galaxy runs anywhere Fig. 1. FANTOM5 (http://fantom.gsc.riken.jp/5/) data processing protocol descriptions. (a) Description of data processing in the main paper of FANTOM 5 project. (b) Online protocol published by FANTOM 5 project. Though this is helpful, it is still not enough to reproduce the exact same results. (c) A script we made with a help by members of FANTOM 5 project. There are some missing informations from materials and methods or online protocols. a b c Application: Community ‘Pitagora’ Galaxy VM Platform: ‘Overlay Cloud’ datacenters We have been trying to develop the system that we are able to share community’s workflows developed and used in the various studies which deal with NGS data, such as Exome-Seq, RNA-Seq, ChIP-Seq, or Bisulfite-Seq. We developed Virtual appliance that includes workflows and some tools to help execution of the workflows, and the Virtualbox image and Amazon Machine Image are distributed. We also maintain public server for the test use, and documents and test data are hosted on our project website. Challenges “Overlay Cloud” project led by National Institute of Informatics (Tokyo, Japan) is building large scale cloud computing infrastructure that can distribute computing tasks via their high-speed network system “sinet”. We are testing to build galaxy environment on their cloud system, which runs all the process or application as a docker container. Apache Mesos running over the nodes and datacenter is managing computing resource, and galaxy runs on it as a container, then run tools as a docker container. We have build some tool.conf and job runner for containerized tools and are still being tested and under the benchmarking. Fig. 2. Community Galaxy VM and Galaxty Community Japan. We have been organizing Japanese local community of the galaxy developers and users. The community is sharing the tools and workflows that are used in their labs. Workflows are implemented and fully documented online with the test data. Automated test of the workflow is being developed. Packed VM is distributed as a normal Virtualbox image and Amazon Machine Image via Amazon Web Service. The community is also hosting public server (listed on the page of galaxy project ‘virtual appliance’). 🐳! Mesos Master 🐳 Mesos Slave Node Node Node 🐳! Galaxy 🐳 Mesos Slave 🐳 BWA 🐳 samtools 🐳! CLI- manager 🐳! Marathon 🐳! SCS 🐳! NFS 🐳Mesos! Master 🐳 Mesos Slave Node Node Node 🐳! Galaxy 🐳 Aurora 🐳 Mesos Slave 🐳 BWA 🐳 samtools 🐳! CLI- manager 🐳! Chronos L2VPN 🐳 Docker Container • Performance Comparison and benchmarking • Connecting published workflows to the publication •Toolshed or other data repository • Standard description or annotation of workflows • Data transfer via internet • burst buffer like cloud volume? Fig. 3. Overlay cloud system and container-based galaxy and galaxy tools. (top-left) Current system which is fully containerized computing infrastructure for the galaxy. Each application runs as a container and connected by L2VPN. Data are stored in the NFS mounted on each node. (bottom-right) Current idea of ver. 2.0 system. Apache mesos and marathon container are detached from the network of the containers of galaxy and galaxy tools which are attached to the NFS via L2VPN. This enables more portability to the running system. Publishing and sharing data analysis workflow using the galaxy platform has spectacularly reduced the cost of reproducing one's research, but following the description of data analysis which had been performed