BioHackathon 2015 in Nagasaki
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1. This document outlines BioHackathon 2015 which was held in Nagasaki, Japan. 2. It provides a brief history of Nagasaki and Nagasaki University, including its origins as a trading port and the establishment of its medical school. 3. It discusses challenges in gene hunting for rare and undiagnosed diseases even with new sequencing technologies, and proposes that semantic web technologies can help address these challenges by facilitating knowledge sharing across databases.
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CHAPTER 1 Microbiology: Then and Now
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Leeuwenhoek, attached any practical significance to the microorganisms, but
during the next three centuries, scientists would discover how profoundly these
organisms influence the quality of our lives and the environment around us.
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understanding of microorganisms continues to grow even as you read this book. Chapter 1, therefore, is an important
introduction to microbiology then and now.
Part 1 also contains a chapter on basic chemistry, inasmuch as microbial growth, metabolism, and diversity
are grounded in the molecules and macromolecules these organisms contain and in the biological processes they
undergo. The third chapter in Part 1 sets down some basic concepts and describes one of the major tools for study-
ing microorganisms. Much as the alphabet applies to word development, in succeeding chapters we will formulate
words into sentences and sentences into ideas as we survey the different groups of microorganisms and concentrate
on their importance to public health and human welfare.
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on the bacterial organisms in Chapter 4, where we survey their structural frameworks. In Chapter 5, we build on these
frameworks by examining microbial growth patterns and nutritional requirements. Chapter 6 describes the metabolism
of microbial cells, including those chemical reactions that produce energy and use energy. Part 1 concludes by consider-
ing the physical and chemical methods used to control microbial growth and metabolism (Chapter 7).
I
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BioHackathon 2015 in Nagasaki
- 1. BioHackathon 2015 in Nagasaki Department of Human Genetics, ABDI, Nagasaki University MISHIMA, Hiroyuki CC BY 4.0
- 3. 1.Brief history of Nagasaki and Nagasaki University 2.My TO-DO LIST for BH15
- 4. 1641 – 1859: Dejima – the sole place of direct trading between Japan and outside world
- 5. The Medical School (1857-) J. L. C. Pompe van Meerdervoot from the Netherlands A. F. Bauduin from the Nerherlands B. Ryojyun Matsumoto
- 6. Nagasaki Medical College (about 1900) College Hospital (about 1920)
- 8. 1967- Atomic Bomb Disease Institute, Nagasaki University • Radiation risk control unit • Cellular function analysis unit • Genomic function analysis unit • Dept. of Human Genetics • Atomic bomb disease and Hibakusha medicine unit • Center for promotion of collaborative research
- 9. Human Genetics ::= Science of heredity and variation in humans
- 10. Dr. Toshihisa Takagi Director-General, National Bioscience Database Center The goal of life sciences is building databases! “Database Biology”
- 11. Human Genetics ::= “Database Biology” “Database Medicine”
- 12. Gene Hunting: Finding causal genes of rare and undiagnosed diseases
- 13. NGS - the break-through 1. Massive Parallel Sequencing technology (biologists) 2. Nagasaki (IATA)
- 14. Combination of NGS + public databases has achieved a triumph in gene hunting
- 15. Is “NGS + huge sample sets + huge databases” a silver bullet for gene hunting?
- 16. Answer: NO for rare and undiagnosed diseases 1.Heterogeneity – same phenotype, different causal genes 2.Only one patient in the world 3.Can be a non typical case of known rare disease
- 17. Knowledge network – like a brain of a remarkable researcher who knows everything in a field Togo picture gallery by DBCLS is licensed under a Creative Commons Attribution 2.1 Japan license (c)
- 18. Biohackers’ answer: The Semantic Web Technology
- 19. American Journal of Human Genetics, 2015 Dr. Tudor Groza (1:15pm -)
- 20. Initiative on Rare and Undiagnosed Diseases (IRUD) Dr. Kenjiro Kosaki (1:00pm -)
- 21. Mishima’s TO-LIST • Develop Docker “data containers” for my favorite RDFs and the Virtuoso engine (BioVirtuoso) • RDFize “HPO Annotation” • Play with SPARQL and the Knowledge Network • Japanese Translation of HPO • Liftover several databases from hg19 to hg38
Editor's Notes
- Welcome to Japan, welcome to Nagasaki It gives me great pleasure to talk to you as a local organizer of Biohackathon 2015.
- I’d like to talk about two topics, brief history of Nagasaki and What I expect BH15 and myself
- From middle of 17c to middle of 19c, under the Sakoku or locked-country policy, an artificial island in Nagasaki called Dejima was the sole place of direct trading between japan and outside world. Thus, Nagasaki was entrance of western items as well as knowledge, science and medicine.
- In 1857, Japan’s first western medical school was established in Nagasaki, the medical school. First and second principal were Dr Pompe and Dr Bauduin from the Natherlands. One of student was Ryojun Matsumoto who became Surgeon General later. This hall ls Bauduin hall. This building is Ryojun auditorium. And a builiding over there is Pompe Hall
- The medical school was changed its name to Nagasaki medical school.
- At the end of World War II, on 1945bAugust 9th 11:02am, Nagasaki had a atomic bombing. Here is Nagasaki medical college. The hypocenter is about 600M far from here. The college was totally destroyed.
- Just after bombing, survived doctors in the college played important roles in reconstruction of Nagasaki. In 1967, Atomic bomb disease institute was established for clinical and basic research for atomic bomb survivors or Hibakusha. The Institute has 5 units.