Experimental Divertor Similarity Database Parameters

A set of experimentally-determined dimensionless parameters is proposed for characterizing the regime of divertor operation. The objective is to be able to compare as unambiguously as possible the operation of different divertors and to understand what physical similarities and differences they represent. Examples from Alcator C-Mod are given.Comment: Plain Tex (8 pages) plus 5 postscipt figure

Models wagging the dog: are circuits constructed with disparate parameters?

In a recent article, Prinz, Bucher, and Marder (2004) addressed the fundamental question of whether neural systems are built with a fixed blueprint of tightly controlled parameters or in a way in which properties can vary largely from one individual to another, using a database modeling approach. Here, we examine the main conclusion that neural circuits indeed are built with largely varying parameters in the light of our own experimental and modeling observations. We critically discuss the experimental and theoretical evidence, including the general adequacy of database approaches for questions of this kind, and come to the conclusion that the last word for this fundamental question has not yet been spoken

The Relationship between the UniProt Knowledgebase (UniProtKB) and the IntAct Molecular Interaction Databases

IntAct provides a freely available, open source database system and analysis tools for protein interaction data. All interactions are derived from literature curation or direct user submission and all experimental information relating to binary protein-protein
interactions is entered into the IntAct database by curators, via a web-based editor. Interaction information is added to the SUBUNIT comment and the RP line of the relevant publication within the UniProtKB entry. There may be a single INTERACTION comment present within a UniProtKB entry, which conveys information relevant to binary protein-protein interactions. This is automatically derived from the IntAct database and is updated on a triweekly basis. Interactions can be derived by any appropriate experimental method but must be confirmed by a second interaction if resulting from a single yeast2hybrid experiment. For large-scale experiments, interactions are considered if a high confidence score is assigned by the authors. The INTERACTION line contains a direct link to IntAct that provides detailed information for the experimental support. These lines are not changed manually and any discrepancy is reported to IntAct for updates. There is also a database crossreference line within the UniProtKB entry i.e.: DR IntAct _UniProtKB AC, which directs the user to additional interaction data for that molecule. 
UniProt is supported by grants from the National Institutes of Health, European Commission, Swiss Federal Government and PATRIC BRC.
IntAct is funded by the European Commission under FELICS, contract number 021902 (RII3) within the Research Infrastructure Action of the FP6 "Structuring the European Research Area" Programme

ChlamyCyc - a comprehensive database and web-portal centered on _Chlamydomonas reinhardtii_

*Background* - The unicellular green alga _Chlamydomonas reinhardtii_ is an important eukaryotic model organism for the study of photosynthesis and growth, as well as flagella development and other cellular processes. In the era of high-throughput technologies there is an imperative need to integrate large-scale data sets from high-throughput experimental techniques using computational methods and database resources to provide comprehensive information about the whole cellular system of a single organism.
*Results* - In the framework of the German Systems Biology initiative GoFORSYS a pathway/genome database and web-portal for _Chlamydomonas reinhardtii_ (ChlamyCyc) was established, which currently features about 270 metabolic pathways with related genes, enzymes, and compound information. ChlamyCyc was assembled using an integrative approach combining the recently published genome sequence, bioinformatics methods, and experimental data from metabolomics and proteomics experiments. We analyzed and integrated a combination of primary and secondary database resources, such as existing genome annotations from JGI, EST collections, orthology information, and MapMan classification.
*Conclusion* - Chlamycyc provides a curated and integrated systems biology repository that will enable and assist in systematic studies of fundamental cellular processes in _Chlamydomonas reinhardtii_. The ChlamyCyc database and web-portal is freely available under http://chlamycyc.mpimp-golm.mpg.de

Determination of Low-Energy Parameters of Neutron--Proton Scattering on the Basis of Modern Experimental Data from Partial-Wave Analyses

The triplet and singlet low-energy parameters in the effective-range expansion for neutron--proton scattering are determined by using the latest experimental data on respective phase shifts from the SAID nucleon--nucleon database. The results differ markedly from the analogous parameters obtained on the basis of the phase shifts of the Nijmegen group and contradict the parameter values that are presently used as experimental ones. The values found with the aid of the phase shifts from the SAID nucleon--nucleon database for the total cross section for the scattering of zero-energy neutrons by protons, $\sigma_{0}=20.426$b, and the neutron--proton coherent scattering length, $f=-3.755$fm, agree perfectly with the experimental cross-section values obtained by Houk, $\sigma_{0}=20.436\pm 0.023$b, and experimental scattering-length values obtained by Houk and Wilson, $f=-3.756\pm 0.009$fm, but they contradict cross-section values of $\sigma_{0}=20.491\pm 0.014$b according to Dilg and coherent-scattering-length values of $f=-3.7409\pm 0.0011$fm according to Koester and Nistler.Comment: 17 pages, to be published in Physics of Atomic Nucle