Open Source Java Scientific/Engineering Software - Page 68

NOTE: Since 2022 this hosting of PLEXIL is deprecated. PLEXIL has moved to GitHub at https://github.com/plexil-group/plexil. Documentation is found at https://plexil-group.github.io/plexil_docs. Please use these new locations. PLEXIL is a plan execution language and technology developed by NASA and used in automation and autonomy applications at NASA and in the public sector. This software includes compilers for the language, the executive (runtime environment), and related tools. It runs on Unix-based computers, including macOS and Linux.

PPICompare detects statistically significant rewiring events in protein-protein interaction networks - even if they are caused by alternative splicing - and reports plenty of information to that. The input data needs to be constructed with PPIXpress (see https://sourceforge.net/projects/ppixpress/). The original publication can be found on https://bmcsystbiol.biomedcentral.com/articles/10.1186/s12918-017-0400-x.

PSI stands for Prototype-Simulate-Interact. Its aim is to provide a complete, modular, flexible and easy-to-use framework to prototype dashboards and cockpits.

PSIMAP is the Protein Structural Interactome MAP, a map of all the domain level protein-protein interactions in the Protein Data Bank (PDB). PSIsoft is an archive of the software used to generate and analyse PSIMAP.

PTESFinder is a computational pipeline for identifying Post-transcriptional Exon Shuffling events from high-throughput RNAseq data. PTESFinder leverages the power of established RNASeq tools and systematically excludes all known classes of false positive structures by applying stringent filters designed to specifically target these false positives. PTESFinder compares alignment qualities of reads mapping to putative PTES structures with qualities of the same reads when mapped to genomic regions and canonically spliced transcripts. This approach increases the confidence in PTES supporting reads. Reads emanating from template-switching events are often characterised by large indels when aligned to the transcriptome. PTESFinder uses additional filters to exclude reads with ambiguous alignments around PTES exon-exon junctions, further increasing confidence in these supporting reads. PTESFinder identifies more PTES structures than other published methods whilst maintaining high specificity.

Platform for Annotated Corpora in XML Integrated tool for corpus linguists built on Eclipse, Vex, Subversive, etc. for creating and editing transcriptions and annotations, querying, managing version controlled data, and building a shippable corpus.

ParallelSim is a parallel processor simulator written in Java which shows the effect of increasing the workload keeping the number of processing elements constant in one simulation. The number of processors is scalable and can be increased in subsequent iterations of simulation. The parameters like initial load, load offset, number of processors are declared as constants and can be changed directly in the source code to emulate different scenarios. It is also capable of plotting a graph at the end of each simulation to give an overview of how the simulation went. The output of simulation will vary from machine to machine depending upon the underlying hardware, for e.g., the timings will be different on a dual core and a quad core processor. Feel free to reach out to me if you have any suggestions or queries.

parsing simulator can be used to determine first ,follow , nullable and can be used to calculate LR items.

PedGMDR is GMDR's twin project.

Given a simple net-list describing the high level power architecture of your system Penthode: - simulates the voltage and current from device turn on to the steady state. - highlights components working out of specification - draws a nice power tree diagram showing the currents/powers balance - plots node transient voltage and gate current waveforms It is possible to change component parameters interactively to improve the design

PepSir checks and filters for peptide proteotypicity.

PerMoTo is a Performance Modelling Tool suite for decision support in the capacity and performance management of distributed transaction processing systems based on Queueing Theory and Discrete Event Simulation.

Labyrinth is a small gui application which, provides a random and recursive generated perfect labyrinth. Each generated labyrinth has a start and an exit point deep in it. Some robot can search for the exit of the labyrinth by using different algorithms.

Periodic table of the chemical elements for Java (J2ME) enabled devices. http://kenai.com/projects/periodic/pages/Home

Peruser is a open-source lightweight knowledge application framework. Peruser speaks XML and RDF and is implemented in Java. Peruser code runs within Cocoon, as a standalone webapp, as console programs invoked through ant, or as embeddable java code.

Petri-LLD is a graphical development environment for real-time automation control and is written in Java. It is based on a form of Petri net, and compiles to a number of programmable logic controller (PLC) languages as well as Java and Visual Basic.

A Creatinine Clearance Calculator which Will Calculate and dose Drug for renal insufficiency and automate a progress note for the Patient Chart

PhyloPattern is a Java/Prolog API, helpful to simulate human reading of phylogenetic trees. Bioinformatician can: annotate trees, apply complex patterns to a tree to search specific architectures or extract information, compare trees with dynamically gen

Alife research platform to study the evolvability of different assembly-like computer languages. It's similar to Tierra and Avida but it's designed to be more general.

Main source code is moved at https://github.com/jpahullo/planetsim. We recommend authors of contributions sections to move your code to github. Since then, contributions remain here for your use at will. PlanetSim is an object oriented simulation framework for overlay networks and services. This framework presents a layered and modular architecture with well defined hotspots documented using classical design patterns.

The Campaign Simulator is an attempt to statistically model and predict the outcome of an American presidential election; several users assume the roles of competitive candidates and inflict the repercussions of certain decisions on a GSS based dataset.

PolityBuilder is a collection of java libraries and applications for exploring the relationship between individual psychology and political phenomena. It is based on research conducted by Andrew Reilly at the Australian National University.

PolyJen: Polymerization in a digital laboratory

Fits and scores vertices from models onto reference vertices to find its polyhedral identity and symmetry quantitatively. Java based with GUI

Port Access 1.0 This is a Win32 programming platform indipendent Microsoft Windows 98/NT/2000/XP compatible hardware port access driver and API for Visual Basic,Java and Visual C++ . This project still under development.