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At least 55 records · Page 3

JPype

JPype is a Python module to provide full access to Java from within Python. It allows Python to make use of Java only libraries, exploring and visualization of Java structures, development and testing of Java libraries, scientific computing, and much more. By gaining the best of both worlds using Python for rapid prototyping and Java for strong typed production code, JPype provides a powerful environment for engineering and code development. This is achieved not through re-implementing Python, as Jython has done, but rather through interfacing at the native level in both virtual machines. This shared memory based approach achieves decent computing performance, while providing the access to the entirety of CPython and Java libraries.

Nelson, KarlE.↗

Omics Tools

The Omics Tools package provides several small trivial tools for work in genomics. This single portable package, the “omics.jar” file, is a toolbox that works in any Java-based environment, including PCs, Macs, and supercomputers. The number of tools is expected to grow. One tool (called cmsearch.hadoop or cmsearch.local), calls the external cmsearch program to predict non-coding RNA in a genome. The cmsearch program is part of the third-party Infernal package. Omics Tools does not contain Infernal. Infernal may be installed separately. The cmsearch.hadoop subtool requires Apache Hadoop and runs on a supercomputer, though cmsearch.local does not and runs on a server. Omics Tools does not contain Hadoop. Hadoop mat be installed separartely The other tools (cmgbk, cmgff, fastats, pal, randgrp, randgrpr, randsub) do not interface with third-party tools. Omics Tools is written in Java and Scala programming languages. Invoking the “help” command shows currently available tools, as shown below: schaumbe@gpint06:~/proj/omics$ java -jar omics.jar help Known commands are: cmgbk : compare cmsearch and GenBank Infernal hits cmgff : compare hits among two GFF (version 3) files cmsearch.hadoop : find Infernal hits in a genome, on your supercomputer cmsearch.local : find Infernal hits in a genome, on your workstation fastats : FASTA stats, e.g. # bases, GC content pal : stem-loop motif detection by palindromic sequence search (code stub) randgrp : random subsample without replacement, of groups randgrpr : random subsample with replacement, of groups (fast) randsub : random subsample without replacement, of file lines For more help regarding a particular command, use: java -jar omics.jar command help Usage: java -jar omics.jar command args

Schaumberg, Andrew↗

Development of earthquake early warning system using real time signal of broadband seismogram

Earthquake pose serious threat of live and properties for urban area near subduction zone offshore and active fault on land. Jakarta and Bandung is an example of big city that no system of Earthquake early warning (EEW) event very high urbanization, and has many important infra structure in the area. The capital city is potentially high risk ground shaking. EEW can be usefull tool for reducing earthquake hazard, if spatial relation between cities and earthquake source is favorable for such warning and their citizens are properly trained to response early warning message. An EEW and rapid response system can provide the critical information needed to minimized lost of live and property and direct rescue. Earthquake ground shaking with magnitude M>6.0 from zone of Megathrust, southern of West Java should potentially damage in the area of west java especially Bandung and Jakarta City. This research development of EEW parameter such as amplitude displacement (Pd), rapid magnitude determination (M) and Peak ground Velocity (PGV). We explore the practical approach to EEW with the use of Broadband seismogram signal. Time effective EEW which epicenter from megathrust zone has potential to provide EEW in the area of west java such as Jakarta first ground shaking more or less 60 second later and strong shaking 118 second after EEW Alarm on CISI Station. EEW notification at potentially damage in the area of west java can be predicted from the characteristic of Pd > 0.5 cm, M> 6 and PGV > 10 cm/sec. GIS as a tool for presentation of hazard mapping in the affected area.

58 GEOSCIENCES↗

Jas4pp — A data-analysis framework for physics and detector studies

This paper describes the Jas4pp framework for exploring physics cases and for detector-performance studies of future particle collision experiments. Jas4pp is a multi-platform Java program for numeric calculations, scientific visualization in 2D and 3D, storing data in various file formats and displaying collision events and detector geometries. It also includes complex data-analysis algorithms for function minimization, regression analysis, event reconstruction (such as jet reconstruction), limit settings and other libraries widely used in particle physics. The framework can be used with several scripting languages, such as Python/Jython, Groovy and JShell. Several benchmark tests discussed in the paper illustrate significant improvements in the performance of the Groovy and JShell scripting languages compared to the standard Python implementation in C. Furthermore, the improvements for numeric computations in Java are attributed to recent enhancements in the Java Virtual Machine.

97 MATHEMATICS AND COMPUTING↗