O'Really?

Genomes to Systems is a biannual conference held in Manchester covering the latest post-genome developments. Here are some brief and incomplete notes on some of the speakers and topics from day two of the 2008 conference.

1. Plenary lecture by Luis Serrano, Barcelona on Evolvability and hierarchy in rewired bacterial gene networks.

Session one: Systems Biology – Computational Environments

2. Mike Hucka, Caltech, California: The Systems Biology Markup Language (SBML): present status and ongoing efforts for extensions
3. Nicolas Le Novère: European Bioinformatics Institute (EBI): Principled annotation of quantitative models in Systems Biology including ELIXIR and The Systems Biology Ontology (SBO)
4. Ursula Kummer, Heidelberg: COPASI: a modelling environment for simulation and identification of biochemical processes
5. Hiroaki Kitano, SBI, Tokyo: SBGN: the Systems Biology Graphical Notation. There was no electronics industry without circuit diagrams, likewise systems biology requires a standard visual notation for network diagrams. see also PAYAO

Lunch, followed by EBI workshops:

• Browsing Genomes with Ensembl: Bert Overduin, see Ensembl.org genome browser and The new ensembl weblog
• ArrayExpress: a public repository for microarray data: Gabriella Rustici

Afternoon session: Facts from the flood: text mining for biomedicine, organised and chaired by Sophia Ananiadou, NaCTeM

1. Alfonso Valencia, CNB, Madrid: Text-mining in in the context of genome annotation covering ENFIN, BioCreative challenge and metaserver. See upcoming biocreative special issue of Genome Biology, Linking entries in protein interaction database to structured text: The FEBS Letters experiment and A text-mining perspective on the requirements for electronically annotated abstracts. New bioinformatics methods easy to develop, much more challenging to validate!
2. Lynette Hirschman, MITRE Corporation, Building Biological Databases: Where Text Mining can help see Evaluation of text data mining for database curation: lessons learned from the KDD Challenge Cup and Text mining: Powering the Database revolution
3. Jun’Ichi Tsujii, University of Tokyo and Manchester: Information extraction: linking text to pathways including a description of PathText.
4. Andrey Rzhetsky, Columbia, New York: Text-mining: a tool for understanding human disease, see Network properties of genes harboring inherited disease mutations and Probing genetic overlap among complex human phenotypes

Two hour poster session, best poster prize sponsored by eposters: the online journal of scientific posters, followed by last two lectures of the day:

1. Plenary lecture by Ron Breaker, Yale University on Gene control by metabolite-sensing riboswitches
2. Informal talk by Larry DeLucas Space Travel and Genomics in Space describing Larry’s trip on board the 12th mission of the columbia orbiter (wow, an excellent and inspiring talk!)