pClust – A Sprinkle of Java Over Hardcore SIMD C

Created by researchers at the Bioinformatics and Computational Biology lab at the Washington State University, pClust is an open source (BSD) software package that enables fast and efficient clustering of protein and DNA sequences. The speedup is achieved by using the highly efficient, parallelized software Parasail for sequence alignment and Grappolo for clustering.

Sequence alignment algorithms are implemented in SIMD C (C99) for efficiency. Parasail library contains vectorized implementations of the three most popular sequence alignment algorithms guaranteed to find optimal alignments. As its output, Parasail returns a graph and three alignment statistics for each edge computed. Aligned protein sequences can then be clustered with Grappolo based on their similarity measure. And, because of its multi-threaded implementation using OpenMP, Grappolo is very fast. For a graph with approximately 2M edges high-homogeneity protein clusters are identified by Grappolo in less than 1 minute.

Finally, pClust graphical user interface, implemented in Java, provides convenient control of many sequence alignment parameters including gap opening and extend penalties, computation bit precision, choice of scoring matrix (PAM and BLOSUM), and many others:

pClust screenshot

Case Study: pClust Use for Construction of Phylogenomic Network of 102 Organisms

Using the pipeline of pClust = Parasail + Grappolo, the researchers at BCB lab constructed a complete genome phylogenomic network of 102 microorganisms. The 120K protein sequences were aligned and clustered with pClust and the pairwise distances between the genomes were computed. The total computation time was under 10 minutes.

Use of Excelsior JET

BCB lab uses Excelsior JET to create Mac‑ and Windows‑compatible installers for pClust. Here is what they had to say about our product:

We were really pleased to discover Excelsior JET. It provides a painless deployment toolkit for use in creating installers that contain all necessary files, including the application executable file, runtime files, data files, documentation, licenses, and so on.

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Simulin And UMHDL: Free Tools for Teaching And Learning Hardware Design

The early adopters of the OS X version of Excelsior JET are starting to publish their natively compiled Java apps.

Professor Pedro Pablo Garrido Abenza teaches Advanced Programming and Computer Technology at Miguel Hernandez University in Spain. Over the years, he created and refined two educational tools that are used by students taking the CT course:

SimulĂ­n, a digital circuit simulator,

and UMHDL, an open-source IDE for learning VHDL.

Both applications are written in Java, and Prof. Garrido has been using Excelsior JET since 2008 to compile and package them as native binaries for Windows and Linux. Now he has OS X versions available too.

Simulin and UMHDL binaries are freely available for download. If you teach, or want to learn, hardware design, check them out! (UMHDL is open source, so you can modify and extend it as you please.)

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Sponsored Project: SimuLab Flight Simulator

We have donated free Excelsior JET licenses to the SimuLab project, aimed at creating an open source flight simulator. They were apparently impressed by the performance of the native build:

  1. CPU peaks (highest cycle consumption): JRE 62%, JET 53%
  2. Memory: JRE 227MB, JET 133MB (highlighting mine – DL)
  3. Startup: not measured but JET outperformed the JRE BY FAR as expected.

If you are passionate about flight simulators and Java, check out SimuLab and consider contributing some of your spare time or money (does anyone in today’s world still have any of these?)

If you are already working on an interesting non-commercial Java app and feel that the use of Excelsior JET might benefit its end users, feel free to apply for a free license.

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TuxGuitar Goes Native, Appears In Excelsior JET Gallery

TuxGuilar

TuxGuitar, an open source project aimed at creating a multitrack tablature editor and player in Java, has released version 1.0-rc1. TuxGuitar users may now choose between two native, JRE-independent downloads, one optimized and packaged using Excelsior JET and the other with GCJ, and the conventional bytecode package that requires a JRE to run.

TuxGuitar now appears in the Excelsior JET Application Gallery.

If you want us to add your product to the Gallery, please contact us.

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JaLingo available as a native Windows app

JaLingo is a free OS independent dictionary application, which we are sponsoring by providing the author with a free copy of Excelsior JET, Professional Edition. JaLingo 0.6.0, released on December 11th, is available as both platform-independent jar and as a native Windows application. The author reports that the natively compiled version works faster, and of course it works on any Windows PC regardless of whether it has Java installed.

The sponsorship program is open to authors of non-commercial Java software interested in optimizing and packaging their applications for Windows and/or Linux using Excelsior JET. Please email us if you are interested. Note that your application does not have to be open-source.

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