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Abstract Background To identify as many different transcripts/genes in the Atlantic salmon genome as possible, it is crucial to acquire good cDNA libraries from different tissues and developmental stages, their relevant sequences (ESTs or full length sequences) and attempt to predict function. Such libraries allow identification of a large number of different transcripts and can provide valuable information on genes expressed in a particular tissue at a specific developmental stage. This data is important in constructing a microarray chip, identifying SNPs in coding regions, and for future identification of genes in the whole genome sequence. An important factor that determines the usefulness of generated data for biologists is efficient data access. Public searchable databases play a crucial role in providing such service. Description Twenty-three Atlantic salmon cDNA libraries were constructed from 15 tissues, yielding nearly 155,000 clones. From these libraries 58,109 ESTs were generated, of which 57,212 were used for contig assembly. Following deletion of mitochondrial sequences 55,118 EST sequences were submitted to GenBank. In all, 20,019 unique sequences, consisting of 6,424 contigs and 13,595 singlets, were generated. The Norwegian Salmon Genome Project Database has been constructed and annotation performed by the annotation transfer approach. Annotation was successful for 50.3% (10,075) of the sequences and 6,113 sequences (30.5%) were annotated with Gene Ontology terms for molecular function, biological process and cellular component. Conclusion We describe the construction of cDNA libraries from juvenile/pre-smolt Atlantic salmon (Salmo salar), EST sequencing, clustering, and annotation by assigning putative function to the transcripts. These sequences represents 97% of all sequences submitted to GenBank from the pre-smoltification stage. The data has been grouped into datasets according to its source and type of annotation. Various data query options are offered including searches on function assignments and Gene Ontology terms. Data delivery options include summaries for the datasets and their annotations, detailed self-explanatory annotations, and access to the original BLAST results and Gene Ontology annotation trees. Potential presence of a relatively high number of immune-related genes in the dataset was shown by annotation searches.

Abstract Background Trace or chromatogram files (raw data) are produced by automatic nucleic acid sequencing equipment or sequencers. Each file contains information which can be interpreted by specialised software to reveal the sequence (base calling). This is done by the sequencer proprietary software or publicly available programs. Depending on the size of a sequencing project the number of trace files can vary from just a few to thousands of files. Sequencing quality assessment on various criteria is important at the stage preceding clustering and contig assembly. Two major publicly available packages – Phred and Staden are used by preAssemble to perform sequence quality processing. Results The preAssemble pre-assembly sequence processing pipeline has been developed for small to large scale automatic processing of DNA sequencer chromatogram (trace) data. The Staden Package Pregap4 module and base-calling program Phred are utilized in the pipeline, which produces detailed and self-explanatory output that can be displayed with a web browser. preAssemble can be used successfully with very little previous experience, however options for parameter tuning are provided for advanced users. preAssemble runs under UNIX and LINUX operating systems. It is available for downloading and will run as stand-alone software. It can also be accessed on the Norwegian Salmon Genome Project web site where preAssemble jobs can be run on the project server. Conclusion preAssemble is a tool allowing to perform quality assessment of sequences generated by automatic sequencing equipment. preAssemble is flexible since both interactive jobs on the preAssemble server and the stand alone downloadable version are available. Virtually no previous experience is necessary to run a default preAssemble job, on the other hand options for parameter tuning are provided. Consequently preAssemble can be used as efficiently for just several trace files as for large scale sequence processing.

This is a conceptual paper that examines the origin and development of universities and their current role in global society. There has been an unprecedented and exponential growth of technology and artificial intelligence capabilities over the past ten years which is challenging current working practices and affecting all areas of society. The paper examines how this role may change to match the new demands placed on them by a digitally enabled society that has greater leisure time. The design of the paper is first to detail some of the changes in work practices that are taking place and how these will impact on society. It then offers several ways in which universities could modify their role to respond to these emerging challenges. This could include new courses, new organisational structures and new pedagogical practices. The paper provides a platform for discussion and debate around the strategic vision and direction of travel for higher education.

Inverted multivariate calibration methods are used for the spectrometric determination of the total concentration (c.sub.[Sigma]) of substances of the same type in environmental samples and food products. They represent Ñ.sub.[Sigma] as a sum of generalized signals (A.sub.j), measured at different wavelengths ([lambda].sub.j) and multiplied by corresponding regression coefficients (k.sub.j). The values of k.sub.j are found using chemometric algorithms based on the absorption spectra of mixtures of the known composition included in the training set. At the additive absorbance of mixtures, this method of group analysis gives rather accurate results. The ability of determining the total concentration of analytes with nonadditive absorbance in this way is unobvious; this case has not been studied. The aim of this study was to test the applicability of inverted calibrations for the nonadditive absorbance of analytes. Mixtures of complex compounds of Cu, Co, Ni, Zn, and Pb with the photometric reagent 4-(2-pyridylazo)resorcinol (PAR) were used as model samples. Aqueous solutions of these complexes at pH 10 have rather similar absorption spectra with maxima at 490-530 nm. In the absorption spectra of many solutions containing ions of these metals and an excess of PAR, we observed statistically significant (up to 30 rel %) positive deviations from additivity. To construct an inverted calibration, 14 mixtures with a known total metal concentration (Ñ.sub.[Sigma] from 8 to 25 [micro]mol/L) were used; their absorbance was measured at six wavelengths. The least-squares estimates of regression coefficients were found using the Microsoft Excel software. Based on the resulting calibration, the c.sub.[Sigma] values were calculated for mixtures of test samples. Relative errors in determining Ñ.sub.[Sigma] did not exceed 8 rel % at RSD < 4%, and the systematic errors were statistically insignificant. A further increase in the number of analytical wavelengths and the size of the training set did not decrease the errors significantly. Thus, inverted calibrations are applicable to the determination of the total concentrations of similar substances with both additive and nonadditive absorbances of the sample., Author(s): I. V. Vlasova [sup.1] , V. I. Vershinin [sup.1] Author Affiliations: (1) grid.77431.36, 0000 0001 1010 7619, Dostoevsky State University, , 644077, Omsk, Russia For the spectrometric determination of [...]

The paper deals with the evaluation of specialists' professional training quality within the framework of intersectoral, transborder, public and private models of social partnership described in theories by foreign and Russian scientists. Special attention is paid to providing methodological grounds for cooperation between the total subjects within the vocational education system. The procedure of studying the Russian employers' ideas about the high-quality training for specialists relies on an innovation spiritual and ontological model of social partnership. The model comprises the following components: representation of the educational content through the lens of business futurology on the part of teachers; selection of the educational content through the lens of spiritual and ontological intentions on the part of students; expert evaluation of the educational through the lens of the competitive business environment on the part of the employers. The effectiveness of social partnership is determined proceeding from justified indices: the extent of variability, flexibility and mobility when performing the tasks of teaching the students possessing social and creative assets that are in demand at the labor market in the sphere of children and youth leisure. The paper presents the quantitative and qualitative analysis of the data of questionnaire survey conducted among the directors of educational organizations of culture (a case study of Rostov region of the Russian Federation). The survey has allowed detecting a slight positive dynamics in their evaluations of the quality of specialists' training and outlining the prospects in the development of social partnership between the employers and the educational organizations.