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Biosciences Working Group Report

Biosciences Working Group Report. Seok Jong Yu, KISTI Hosted by Kunkuk University Seoul, Korea, Oct 10-12, 2012. PRAGMA 23 Activities. Day 1 WG Breakout Session 1: 15 : 0 0 – 1 6 : 2 0 Computational Methods for Comparative Genomics (Dr. Jaebum Kim, KU)

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Biosciences Working Group Report

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  1. Biosciences Working Group Report Seok Jong Yu, KISTI Hosted by Kunkuk University Seoul, Korea, Oct 10-12, 2012

  2. PRAGMA 23 Activities • Day 1 • WG Breakout Session 1: 15:00 – 16:20 • Computational Methods for Comparative Genomics (Dr. Jaebum Kim, KU) • Eztaxon-e database (Dr.Bong-soo Kim , Chunlab Inc.) • Development of biosenser (Dr. Young Soo Yoon, YU)

  3. PRAGMA 23 Activities • Day 2 • Demo: Dr. Thai Quang Tung(KISTI), 10:15 ~ 10:35 • insilicoCell : biological network modeling and simulation system. • WG Breakout Session 2: 11:00 ~ 12:00 • Constructing Systems Biology platform on HPC, (Seok Jung Yu, KISTI) • Discussion about collaboration • WG Breakout Session 3: 14:00 ~ 16:00 • Future plan about Bioscience WG activities

  4. Day 1 Breakout Session Summary • Dr. Jaebum Kim, KU • Computational Methods for Comparative Genomics • Developing a post-assembly method for a de novo assembled genome

  5. Day 1 Breakout Session Summary • Dr. Bong-Soo Kim, • Introducing Eztaxon-e database and Chunlab services • Introducing Chunlab services. • Eztaxon and Eztaxon-e database • Application of Eztaxon-e database on microbial community analysis

  6. Day 2 Summary • Dr. Thai Qung Tung, KISTI • insilicoCell • Design the biological network model • (Boolean model/Kinetic model) • Simulating the biological model using VCellSim and BooleanSim tools

  7. Day 2 Breakout Session Summary • Dr. Seok Jong Yu, KISTI • Constructing Systems Biology platform on HPC • Constructing biological networks using Text-mining tool (Bioknowledge Viewer) • Analyzing the biological network (VCellSim/BooleanSim)

  8. Collaboration • Tianjin Instituteof Industrial Biotechnology – KISTI • Setup Bioworks system on the TIIB cluster • Construct workflows for analyzing genomics data including NGS data. • KU – NSCC (Tianjin) • NSCC supports the genomics researches in KU by providing HPC resource. • Collaboration on developing new algorithm on de novo assembly.

  9. Collaboration • KU – KISTI • Constructing de novo assembly analysis pipeline in KISTI with Dr. Jaebum Kim’s tools • KISTI – NSCC (Tianjin) • Planning an international project about NGS analysis research • Genomics research • Developing a NGS analysis platform • Making a novel analysis algorithm

  10. Future planning for next bioscience research • Research field • Molecular Dynamics (Protein) • Drug Discovery • Genomics • Microbiology • Systems biology • Computational biology • Bioinformatics

  11. Type of the researcher • Biologist ( focus on biological experiments ) • Bioinformatist ( developing analysis tools ) • Computer scientist ( developing research infrastructure)

  12. Where is the sandbox of cyber research environment for biologist. • Collaboration with Resources and Data WG • What is the exciting bioscience research in PRAGMA • HPC resources • Research frameworks • Bioinformatics tools • Biological Data (NGS/Proteomics/PPI/…)

  13. Candidate Research Topic • Drug Discovery • Genomics research • Systems biology • Education Program in PRAGMA • Introducing the developed system • Practice course of the software in the workshop for users

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