257 research outputs found
Conveyor - a workflow engine for bioinformatics analyses
No full textLinke B. Conveyor - a workflow engine for bioinformatics analyses. Bielefeld: Universität; 2012
BRIGEP - the BRIDGE-based genome-transcriptome-proteome browser
No full textGoesmann A, Linke B, Bartels D, et al. BRIGEP - the BRIDGE-based genome-transcriptome-proteome browser. Nucleic Acids Research. 2005;33(Web Server):W710-W716.The growing amount of information resulting from the increasing number of publicly available genomes and experimental results thereof necessitates the development of comprehensive systems for data processing and analysis. In this paper, we describe the current state and latest developments of our BRIGEP bioinformatics software system consisting of three web-based applications: GenDB, EMMA and ProDB. These applications facilitate the processing and analysis of bacterial genome, transcriptome and proteome data and are actively used by numerous international groups. We are currently in the process of extensively interconnecting these applications. BRIGEP was developed in the Bioinformatics Resource Facility of the Center for Biotechnology at Bielefeld University and is freely available. A demo project with sample data and access to all three tools is available at https://www.cebitec.uni-bielefeld.de/groups/brf/software/brigep/. Code bundles for these and other tools developed in our group are accessible on our FTP server at ftp.cebitec.uni-bielefeld.de/pub/software/
Author Co-Citation Analysis (ACA): a powerful tool for representing implicit knowledge of scholar knowledge workers
No full textIn the last decade, knowledge has emerged as one of the most important and valuable organizational assets. Gradually this importance caused to emergence of new discipline entitled ―knowledge management‖. However one of the major challenges of knowledge management is conversion implicit or tacit knowledge to explicit knowledge. Thus Making knowledge visible so that it can be better accessed, discussed, valued or generally managed is a long-standing objective in knowledge management. Accordingly in this paper author co- citation analysis (ACA) will be proposed as an efficient technique of knowledge visualization in academia (Scholar knowledge workers)
Performing Enlightenment: Johann Burkhard Mencke and Academic Self-Critique
No full textFor many Enlightenment philosophers, to do philosophy was not only to think and write, but also to live and act in the world. This performative purpose changed the meaning of philosophical texts as well as which texts could be considered as philosophical. The essay illustrates this point through the example of Johann Burkhard Mencke’s famous lectures, De charlataneria eruditorum −on charlatanry of the learned− first delivered at the University of Leipzig in 1713 and 1715. Mencke not only discussed the significance and problems of performance, but also emphasized his points by his own performance as a lecturer and as an author. He was not only critical of the false authority of others, but also of his own authority as well as that of his Enlightenment colleagues and allies. The lectures, I argue, exemplify a genre of Enlightenment philosophy that placed self-critique at the center.For many Enlightenment philosophers, to do philosophy was not only to think and write, but also to live and act in the world. This performative purpose changed the meaning of philosophical texts as well as which texts could be considered as philosophical. The essay illustrates this point through the example of Johann Burkhard Mencke’s famous lectures, De charlataneria eruditorum −on charlatanry of the learned− first delivered at the University of Leipzig in 1713 and 1715. Mencke not only discussed the significance and problems of performance, but also emphasized his points by his own performance as a lecturer and as an author. He was not only critical of the false authority of others, but also of his own authority as well as that of his Enlightenment colleagues and allies. The lectures, I argue, exemplify a genre of Enlightenment philosophy that placed self-critique at the center
A prototype taxonomic microarray targeting the rpsA housekeeping gene permits species identification within the rhizobial genus Ensifer
No full textMartens M, Weidner S, Linke B, de Vos P, Gillis M, Willems A. A prototype taxonomic microarray targeting the rpsA housekeeping gene permits species identification within the rhizobial genus Ensifer. SYSTEMATIC AND APPLIED MICROBIOLOGY. 2007;30(5):390-400
Stadt-Theater Düsseldorf / Der Revisor : Sonntag, den 21. März 1909, nachmittags 2 1/2 Uhr ; Operette in 3 Aufzügen
No full text(frei nach Gogols gleichnamigen Lustspiel) von Karl Weis. Spielleitung: Robert Leffler. Musikalische Leitung: Alfons Lilienfeldt. Personen: Ernst Winter, Marie Sieg, Hermine Förster, Eugen Albert, Ernst Herz, Ernst Bedau, Jahn Hofknecht, Peter Kirschbaum, Hermann Burkhard, Ludwig Feichtinger, Carl Linke, Paul Hermann, Marly Hettwer, Arthur Schetter, Karl Gerike, Hugo Lazak, Walter Lenoir, Moritz Orkin, Wilhelm Buc
Flexible metagenome analysis using the MGX framework
No full textJaenicke S, Albaum S, Blumenkamp P, Linke B, Stoye J, Goesmann A. Flexible metagenome analysis using the MGX framework. Microbiome. 2018;6(1): 76
Conveyor: a workflow engine for bioinformatic analyses
No full textLinke B, Giegerich R, Goesmann A. Conveyor: a workflow engine for bioinformatic analyses. Bioinformatics. 2011;27(7):903-911.Motivation: The rapidly increasing amounts of data available from new high-throughput methods have made data processing without automated pipelines infeasible. As was pointed out in several publications, integration of data and analytic resources into workflow systems provides a solution to this problem, simplifying the task of data analysis. Various applications for defining and running workflows in the field of bioinformatics have been proposed and published, e. g. Galaxy, Mobyle, Taverna, Pegasus or Kepler. One of the main aims of such workflow systems is to enable scientists to focus on analysing their datasets instead of taking care for data management, job management or monitoring the execution of computational tasks. The currently available workflow systems achieve this goal, but fundamentally differ in their way of executing workflows.
Results: We have developed the Conveyor software library, a multitiered generic workflow engine for composition, execution and monitoring of complex workflows. It features an open, extensible system architecture and concurrent program execution to exploit resources available on modern multicore CPU hardware. It offers the ability to build complex workflows with branches, loops and other control structures. Two example use cases illustrate the application of the versatile Conveyor engine to common bioinformatics problems
The REGANOR gene prediction server for prokaryotic genomes and a database of high quality gene predictions for prokaryotes
No full textLinke B, McHardy AC, Neuweger H, Krause L, Meyer F. The REGANOR gene prediction server for prokaryotic genomes and a database of high quality gene predictions for prokaryotes. Applied Bioinformatics. 2006;5(3):193-198
Implementasi Algoritma Not So Naive dan Algoritma Burkhard-Keller Tree pada Aplikasi Kamus Bahasa Indonesia-Hokkian Berbasis Android
No full textBahasa Hokkian umumnya dikenal sebagai bahasa ibu komunitas Tionghoa di Medan. Namun belum ada metode yang digunakan untuk mempelajari bahasa tersebut karena masih dilakukan secara manual. Oleh karena itu diperlukan suatu media yang dapat mempermudah seseorang dalam mempelajari bahasa tersebut yaitu aplikasi smartphone yang praktis. Kemudahan dalam mengakses suatu informasi juga sangat penting. Untuk mempermudah seseorang mempelajari bahasa tersebut penulis membuat aplikasi kamus offline berbasis Android dengan menggunakan algoritma Not So Naive sebagai algoritma exact string matching dan algoritma Burkhard-Keller Tree sebagai algoritma approximate string matching dengan menggunakan sistem manajemen database SQLite sebagai media penyimpanan data. Penelitian ini bertujuan untuk membuktikan kelebihan dan kekurangan masing-masing algoritma dalam mengakses suatu informasi serta menampilkan hasil running time kedua algoritma. Dalam hal proses pencarian, kedua algoritma memiliki cara kerja yang berbeda. Algoritma Not So Naive mengidentifikasi terlebih dahulu dua kasus untuk menentukan nilai pergeseran, yang dapat dilakukan sebanyak 2 posisi ke kanan sedangkan algoritma Burkhard-Keller Tree mencari kata berdasarkan batas atas dan batas bawah serta batas toleransi kesalahan yang telah ditetapkan. Hasil penelitian menunjukkan bahwa waktu pencarian algoritma Burkhard-Keller Tree meningkat sebesar 58,26% dan 74% pada algoritma Not So Naive seiring dengan meningkatnya ukuran database. Algoritma Not So Naive memiliki rata-rata running time 25,45ms dan rata-rata running time sebesar 59,95ms pada algoritma Burkhard-Keller Tree.The Hokkien language is generally known as the mother tongue of the Chinese community in Medan. However, there is no method used to learn the language because it is still done manually. Therefore, we need a form of media that can make it easier for someone to learn the language, namely a practical smartphone application. Ease of accessing information is also very important. To make it easier for someone to learn the language, the author creates an Android-based offline dictionary application using the Not So Naive algorithm as an exact string matching algorithm and the Burkhard-Keller Tree algorithm as an approximate string matching algorithm using the SQLite database management system as a data storage medium. This study aims to prove the advantages and disadvantages of each algorithm in accessing information and display the results of the running time of both algorithms. In regards to the search processes, the two algorithms have a different way of working. The Not So Naive algorithm first identifies two cases to decide the value of the shift, which can be done in 2 positions to the right, while the Burkhard-Keller Tree algorithm looks for words based on predetermined upper and lower limits and fault tolerance limits. The results showed that the search time for the Burkhard-Keller Tree algorithm increased by 58,26% and 74% for the Not So Naive algorithm as the database size increased. The Not So Naive algorithm has a mean running time of 24.85 ms and a mean running time of 60.4 ms on the Burkhard-Keller Tree algorithm.96 HalamanSkripsi Sarjan
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