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Based on the not-so-successful Pysimony (https://sourceforge.net/projects/pysimony/), the same determined student takes another go at the phylogenetic problem.
Javamony is invoked as follows:
java -jar Javamony.jar [input.fasta] [random / stepwise (starting tree)] [# of bootstraps] [outgroup taxon #1] [outgroup taxon #2] ...
Not meant as a competitive phylogenetic inference program, Javamony is an opportunity for me to acquire the Java language while learning to address and solve...
Zephyr is a script-driven experiment automation program that works various measurement instruments and actuators. It supports instruments from Agilent, Eco Physics, ICS Electronics, Keithley, Omega, Teledyne and other manufacturers. The script language is XML-based. Syntax highlighting is available. The source code is included in the distribution. Contact the project admin to get SVN access.
The goal of this project is to provide a couple of Fortran code to those students who selected the course of "Climate Modeling" in the department of atmospheric and oceanic sciences at Peking University.
这个项目的目标是给选择“气候模拟”课程(北京大学大气与海洋科学系)的同学提供与课程学习有关的源代码程序。
We are subject to GNU/GPL license and happy to open the code to the public.
我们遵守GNU/GPL协议,并乐于开放代码给所有需要的人。
PetriNetExec a library for embedding Petri Nets into Java applications
Briefly said, PetriNetExec is an open-sourceJava library which allows you to embed Petri Nets into your Java application.
Using PetriNetExec you can define places and transitions, connect them using arcs and inhibitors, define the initial marking and then fire events and see how tokens flow into the network.
* PetriNetExec does not provide a GUI for editing the network nor will it provide in the near future.
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OmniHelp is a cross-platform, browser-independent, tri-pane help viewer built in pure JavaScript and CSS with HTML 4. Some functions (such as help embedding) may in the future be in Java, C, or C++; CSH is fully supported. All code is under the LGPL.
Composer for OWL-S-based Semantic Web Services that can load SWRL-based Semantic Bridges to mediate between heterogeneous ontology concepts. Exports semantic. enh. BPEL code. Dependency to BerliOS-project: "sembpelext". Also see QualiPSo.org for details.
A cross platform GUI for several code formatter, beautifier and indenter like AStyle, GNU Indent, GreatCode, HTML Tidy, Uncrustify and many more. Main feature is a live preview to directly see how the selected formatting option affects the source code.
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A program for exploring complex functions, much like the now out-dated f(z). Domain colored plots of complex functions. Click evaluate. Uses reflection so you can code almost anything for your formula. All java. Please help.
current build is now 12_8_11:
Code reformulation, not only to improve/repair, but also to take into account libraries that I don't release (e.g., the applet one). The Jars are compiled under Sun Windows JVM 1.7.0_1.
This is a Java-based project for complex event extraction from text and co-reference resolution. Currently the code can read BioNLP shared task format (http://2011.bionlp-st.org/) and i2b2 Natural Language Processing for Clinical Data shared task format (https://www.i2b2.org/NLP/DataSets/Main.php). Event extraction includes finding events and the parameters for an event in a text.
The method is based on SVM but other ML algorithms can be adopted. The method details are explained in the...
A fast, simple Java library for calculating Voronoi lines given an array of input coordinates. It does not feature code to display the results graphically.
Its an Eclipse 3.5 Plugin.
It can be used to find linear paths for unit testing of any method.
The linear path covers all the child methods and till leaf level of the hierarchy.
The packages which should be covered in the path can be controlled.
This program allows you to create a transmission hologram using just a computer, a laser-printer, and an overhead transparency. This hologram will behave like one created using a laser and can be projected or viewed with a point source.
Atomic Transformation Code is an EPL-licensed low-level model transformation language implemented upon the Eclipse EMF project. It is an intermediate layer created with the goal of executing any model transformation language, such as QVT, or RubyTL.
Parsers for biological data based on scanner generators like Flex (C), Re2c(C), Jflex (Java) and Ifickle (Tcl). This scanner generators are providing easier maintainance, development and higher speed than hand written scanners. Scanner output is SQL.
The Java Code Clone Detection API (JCCD) allows to implement individual code clone detectors. These code clone detectors can be easily integrated into other Java applications. JCCD is based on a pipeline architecture which allows to replace whole par
haggies is an optimizing code generator. It can read in expressions in common notation and generate output for many programming languages including C/C++, Java, Fortran, Python and many others.
RoboBeans is an interface to the "Robocup 2D Soccer Simulation Server" that allows developers to write Robocup teams\agents concentrating on behaviour and AI without having to worry about syntax of communication or network issues.
The Xholon project explores: software as systems of linked nodes, organized hierarchically. The Xholon toolkit supports this back-to-basics approach, and demonstrates practical benefits through examples from numerous domains.