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)
2012
Timothy Hancock1) Overview
IBSB is a workshop held annually since 2001 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, Freie University Berlin, Max Delbrück Center for Molecular Medicine in Berlin,
Kyoto University, University of Tokyo. The workshop is forum for doctoral and post-doctoral
researchers to present their current research and discuss their objectives with peers at asimilar stage within their academic career. This year was the 11 th IBSB workshop and washeld in Humboldt-Universität Berlin.
2) Conference Summary
The work I presented was an exploratory analysis to the evaluate the extent of the genemRNA transcript and metabolite correlation through a pre-specified metabolic network.
This work, which was presented as a poster, extends upon my previous pathway mining
work, but aims to resolve outstanding issues about the interpretability of the extracted
pathways in a biological context.

In part this work was inspired by work presented atprevious IBSB workshops by researchers from Germany. Specifically,
1. Nils Christian, Thomas Handorf, Oliver Ebenhöh, “Metabolic Synergy: Increasing
Biosynthetic Capabilities by Network Cooperation”, IBSB 2007, Genome Informatics
18: 321-330 (2007)
2. Georg Basler, Zoran Nikoloski, Oliver Ebenhöh, Thomas Handorf, “BiosyntheticPotentials

fromSpecies-Specific

MetabolicNetworks”,

IBSB

2008,

GenomeInformatics 20: 135-148 (2008)
These two pieces of work are inspired by physical models of metabolic networks. The workI presented at this years IBSB tries to produce a similar model, but from a data-driven andpathway mining perspective. As such this work presents a merging of idea's which directly
resulted from attendance of previous IBSB.
3) Response and Feedback
The motivation behind the ideas presented in my work lead to numerous questions form
interested researchers from the Germany. This was also bolstered by my recent stay inProfessor Edda Klipp's laboratory.

The questions centered around the similarity of theideas presented by Christian et al (2007) and Basler et al. (2008) to the work presented.
The key discussion points were on the extent to which the analysis experimental data

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

supports the results of physical models.

It an interesting point as the two researchmethodologies appear very different on first inspection, but the results they yield are oftencomplementary. The limitations of the work presented are the simplifications that must be
made to overlay the data onto metabolic network. Such simplifications are not necessarilyfor

thephysicalmodels,and

therefore

thequestions

eitherremarkedonthecomplementary nature of the results with respect to physical modeling, or on the biologicalinterpretation of the results in the face of the simplifications. Ideally research such as thiswould provide solid ground for collaborative research projects which are a direct result ofthe IBSB conferences.
5) Recreational Activities
The recreational activities of the conference involve a cruise and lobster BBQ on Spectacle
Island, BBQ along the Charles river, and a bus tour introducing the long history of Boston.
Open Air Classical Music Performance
On the Charles River

View Of Boston From
Spectacle Island