若手研究者インターナショナル・トレーニング・プログラム(ITP)
バイオインフォマティクスとシステムズバイオロジーの国際連携教育研究プログラム
ワークショップ参加レポート

Report: International Workshop on Bioinformatics and Systems Biology (IBSB) 2011
Timothy Hancock1) Overview
IBSB is a workshop held annually since 2000 as part of an international educational collaboration
between several research in Japan, the United States and Germany: Boston University in the
United States, Charité-Universitätsmedizin Berlin, Humboldt-Universität zu Berlin, Kyoto
University, University of Tokyo. The workshop is forum for doctoral and post-doctoral researchers topresent their current research and discuss their objectives with peers at a similar stage within theiracademic career.

This year was the 10th IBSB workshop and was held in Humboldt-Universität

Berlin.
2) Conference Summary
The work I presented were methods developed during the past two years my of research in Japan.
Specifically two optimization strategies for optimizing a network classifier – Boosted Expectation
Propagation (BEP) and Boosted Message Passing (BMP).

These optimization strategies focus onefficiently combining local network information to construct a global network classifier. My
presented work is in line with the a major conference theme of biological network analysis.
Examples of complementary work presented at IBSB include "Modeling Cancer Signaling: A

Boolean Approach” by Thomas Handorf who presented an approach to incorporate statistical andphysical network models and "Identifying key regulators in ovarian cancer by analysis of correlatedtranscription in context of a literature-derived causal network” by Chia-Ling Huang who overlaidtranscription information onto a potential disease mechanism network derived from literaturesources.
3) Response and Feedback
My presentation generated several queries from both biological and machine learning areas. Thequestions focused on the wider application of the presented method to different types networks,
such as protein interaction networks. Specifically questions were on the assumption that local
correlated structure is dictating global network performance and whether this is a valid assumption
for other networks such as protein protein interaction networks (PPI) and the effect of network
hubs on the model.

In response to these queries, it is possible we may shift the application of our

method from PPI networks more towards evaluating the effect of proposed network edges to anotherwise known and validated network structure.

These discussion help put our proposed

method into a more biologically applicable context and will certainly be taken into consideration in
our future research plans.

若手研究者インターナショナル・トレーニング・プログラム(ITP)
バイオインフォマティクスとシステムズバイオロジーの国際連携教育研究プログラム
ワークショップ参加レポート4) Summer School
An additional event at this years IBSB was the opportunity to participate in a summer school. The
topics covered at the summer school where quite broad ranging from physical approaches such as
the use of bifurcation diagrams to track the stable solutions of non-linear differential equation
systems and stochastic simulation methods for efficiently solving large systems of coupled
differential equations; to statistical methodology such as using optimization strategies for Hidden
Markov Models and their application to learning complex chemical structure and visualization of
global metabolic networks.

The topics taught in the summer school provided a wide view of thecurrent research areas of interest in the fields of systems biology and bioinformatics.
5) Recreational Activities
The recreational activities of the conference involve a cruise along the Spree highlighting thehistory and architecture of Berlin and a Museum tour focusing on the history of Berlin.

Conference SiteSpree River Cruise

Spree River

View from the Top of the Berliner Dome