Mass Spectrometry Informatics in Systems Biology

Mass spectrometry (MS) became a standard tool for identifying metabolites in biological tissues, and metabolomics is slowly acknowledged as a legitimate research discipline for characterizing biological conditions. The computational analyses of metabolomics, however, lag behind compared with the rapid advances in analytical aspects for two reasons. First is the lack of standardized data repository for mass spectra: each research institution is flooded with gigabytes of mass-spectral data from its own analytical groups and cannot host a world-class repository for mass spectra. The second reason is the lack of informatics experts that are fully experienced with spectral analyses. The two barriers must be overcome to establish a publicly free data server for MS analysis in metabolomics as does GenBank in genomics and UniProt in proteomics. The workshop brought together bioinformaticians working on mass spectral analyses in Finland and Japan with the goal to establish a consortium to freely exchange and publicize mass spectra of metabolites measured on various platforms computational tools to analyze spectra spectral knowledge that are computationally predicted from standardized data. This book contains the abstracts of the presentations given in the workshop. The programme of the workshop consisted of oral presentations from Japan and Finland, invited lectures from Steffen Neumann (Leibniz Institute of Plant Biochemistry), Matej Oresic (VTT), Merja Penttila (VTT) and Nicola Zamboni (ETH Zurich) as well as free form discussion among the participants. The event was funded by Academy of Finland (grants 139203 and 118653), Japan Society for the Promotion of Science (JSPS Japan-Finland Bilateral Semi- nar Program 2010) and Department of Computer Science University of Helsinki. We would like to thank all the people contributing to the technical pro- gramme and the sponsors for making the workshop possible. Helsinki, October 2010 Masanori Arita, Markus Heinonen and Juho Rousu

Professional non-neutrality: criticising the third party in psychotherapy

Using audio-recorded data from cognitive-constructivist psychotherapy, the article shows a particular institutional context in which successful professional action does not adhere to the pattern of affective neutrality which Parsons saw as an inherent component of medicine and psychotherapy. In our data, the professional’s non-neutrality functions as a tool for achieving institutional goals. The analysis focuses on the psychotherapist’s actions that convey a critical stance towards a third party with whom the patient has experienced problems. The data analysis revealed two practices of this kind of critique: (1) the therapist can confirm the critique that the patient has expressed or (2) return to the critique from which the patient has focused away. These actions are shown to build grounds for the therapist’s further actions that challenge the patient’s dysfunctional beliefs. The article suggests that in the case of psychotherapy, actions that as such might be seen as apparent lapses from the neutral professional role can in their specific context perform the task of the institution at hand.