749 research outputs found
Reflections on experimental science: Martin Perl
No full textThis is a collection of important lecture and original articles and commentaries by Martin Perl, discoverer of the tau lepton and the third generation of elementary particles, and this year's Nobel Prize winner. This book contains a fascinating and realistic picture of experimental science based on the high energy physics research work carried out by him. Using reprints of his articles with his commentaries, the author presents the various aspects of experimental research in science: the pleasures and risks of experimental work; the pain and frustration with experiments that are useless or fa
Perl one-liners
No full text130 Time-Saving, Problem-Solving Perl Scripts That Get Things DonePart of the fun of programming in Perl lies in tackling tedious tasks with short, efficient, and reusable code. Often, the perfect tool is the one-liner, a small but powerful program that fits in one line of code and does one thing really well.In Perl One-Liners, author and impatient hacker Peteris Krumins takes you through more than 100 compelling one-liners that do all sorts of handy things, such as manipulate line spacing, tally column values in a table, and get a list of users on a system. This cookbook of useful, customiza
Bioinformatic pipeline and perl scripts
No full textContains the commands process paired end Illumina reads generated by our strategy, and the perl scripts that process some of the data.</div
Perl script 2
No full textPerl script written by Kanchon Dasmahapatra (University of York; [email protected]). This script uses the output from "filter_multiple_sample_gatk1.5_vcf_mtDNA_indels.pl" and writes the base calls to a fasta file
A suite of Perl modules for handling microarray data
No full textWe describe PerlMAT, a Perl microarray toolkit providing easy to use object-oriented methods for the simplified manipulation, management and analysis of microarray data. The toolkit provides objects for the encapsulation of microarray spots and reporters, several common microarray data file formats and GAL files. In addition, an analysis object provides methods for data processing, and an image object enables the visualisation of microarray data. This important addition to the Perl developer's library will facilitate more widespread use of Perl for microarray application development within the bioinformatics community. The coherent interface and well-documented code enables rapid analysis by even inexperienced Perl developers. © The Author 2008. Published by Oxford University Press. All rights reserved
Modifying a kidney injury score by including perioperative data Comparison of three predictive scores
No full textAt present, several scores have been developed to assess the risk of acute kidney injury (AKI) after cardiac surgery, and every score represents a compromise between the completeness of the factors and the early evaluation of the AKI risk. This study examined whether the predictive reliability of an AKI risk score can be significantly improved by applying not only preoperative risk factors but also intraoperative and postoperative parameters for the calculation of the score. Three scores were deduced from the data of 662 patients undergoing cardiac surgery; these were based on preoperative (score 1), pre- and intraoperative (score 2) or on pre-, intra- and postoperative parameters (score 3). Sensitivity and specificity for the prediction of an AKI were determined from a validation population comprising 529 additional patients. AKI occurred in 455 patients (38.2%). Sensitivity and specificity of the scores were 60.9% and 67.6% (score 1), 60.4% and 68.2% (score 2) and 66.8% and 64.8% (score 3). The inclusion of intra- and postoperative parameters into a predictive model does not significantly improve the ability to identify patients at risk of AKI. As scores based on preoperative parameters allow for the earliest possible risk stratification, they should be preferred in clinical practice
Introduction to The Canvas and Other Stories by Salamea Perl
No full textThe Canvas and Other Stories by Salomea Perl is a bilingual Yiddish-English text featuring the only known stories Perl wrote and published in the various Yiddish newspapers of her time. Uncovered after two years of research and translated by Ruth Murphy, the book presents the original Yiddish text and English translation in a side-by-side format. Murphy\u27s translations present Perl\u27s voice to English readers, while Perl\u27s rich, authentic Yiddish brings readers back to the Jewish, Yiddish-speaking streets of turn-of-the-century Poland. The insightful introduction by Dr. Justin Cammy gives the historical background of both the text and its author. The work of Salomea Perl, an author completely unknown until these translations, is an important addition to ongoing discovery of female Yiddish writers.
Salomea Perl (1869-1916) was born in the town of Lomża (now Poland) and raised in the larger city of Lublin. After completing studies at the University of Geneva, she settled in Warsaw. Her Yiddish first stories were published n Yontev Bletlekh, the self-proclaimed radical magazine published by Y. L. Peretz, starting in 1895. Her seventh and final known Yiddish work was published in 1910.
The publication here of all seven known stories by Salomea Perl is not only important because it marks the rediscovery of a forgotten Yiddish writer. It also allows us to consider her unsentimental portraits of a Jewish world in transition. Her stories reveal deep class divisions and the prevalence of Jewish poverty. She investigates how the religious values that guided everyday life often lacked compassion for lived experience. Perl explores the social and cultural ruptures caused by internal migration from small towns to big cities, and new manifestations of secular Jewish identity associated with modern life.
At the same time, for every frayed relationship between a husband and wife or a daughter shunning her father, Perl\u27s fiction also reveals unassuming acts of self-sacrifice and modesty. For every abandonment of religious obligation in favor of the seductions of the secular-modern world there remain those who are content to carry on lives of relative simplicity.
From the Introduction by Justin Cammy, Associate Professor of Jewish Studies and Comparative Literature at Smith College in Northampton, Massachusetts
Source: Publisherhttps://scholarworks.smith.edu/jud_books/1005/thumbnail.jp
FacetOntology: Expressive Descriptions of Facets in the Semantic Web
No full textThe formal structure of the information on the Semantic Web lends itself to faceted browsing, an information retrieval method where users can filter results based on the values of properties ("facets"). Numerous faceted browsers have been created to browse RDF and Linked Data, but these systems use their own ontologies for defining how data is queried to populate their facets. Since the source data is the same format across these systems (specifically, RDF), we can unify the different methods of describing how to query the underlying data, to enable compatibility across systems, and provide an extensible base ontology for future systems.To this end, we present FacetOntology, an ontology that defines how to query data to form a faceted browser, and a number of transformations and filters that can be applied to data before it is shown to users. FacetOntology overcomes limitations in the expressivity of existing work, by enabling the full expressivity of SPARQL when selecting data for facets. By applying a FacetOntology definition to data, a set of facets are specified, each with queries and filters to source RDF data, which enables faceted browsing systems to be created using that RDF data
Perl script 1
No full textPerl script written by Kanchon Dasmahapatra (University of York; [email protected]). This script uses a variant file (VCF) generated by GATK to call the individual bases per position for a haploid genome. After this script, run "convert_callsfile_to_one_line_fasta.pl" script to covert the base calls to a fasta file
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