Search Results for "the command line" - Page 8

Tools for mass spectrometry, especially for protein mass spectrometry and proteomics: Quantification tools, converters for Applied Biosystems (Q Star and Q Trap), calculation of in-silico fragmentation spectra, converter for Mascot result files

This application was developed by Incentro to satisfy requests by clients for a sentiment analyser for the Dutch language. It is currently in it's alpha stage and we expect to have a beta release by November 2012. If you would like to help with the development or testing of this product please contact us at +31[0]15 76 40 750 - of info {at} incentro.com. Deze applicatie is ontwikkeld door Incentro om te voldoen aan klantaanvragen voor een sentimentanalyse module voor de Nederlandse taal....

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...

Cross-platform data acquisition and visualization software with an embedded HTTP-server, binary protocol parsing library, protocol emulation server, remote secure administration server, embedded Groovy scripting facilities and HMI (SCADA) visualization module.

Modern MATLAB-based modelling software for 13C metabolic flux analysis (MFA). Support available in Google group (https://groups.google.com/d/forum/13cmfa-openflux).

A very simple command line tool to convert OSM files to Shapefiles. Written in Java. Think of it as a self-study project.

JBoost is a simple, robust system for classification. JBoost contains implementations of several boosting algorithms in an alternating decision tree framework. In addition, JBoost provides extensible software for adding more learning algorithms.

A very simple tool to automate benchmarking tests on MySQL DBs. It fills MySQL tables columns; perform customized tests; and outputs the results on CSV format. It uses Xeger, a java package for generating random text from regular expressions (http://code.google.com/p/xeger/). Xeger uses dk.brics.automaton java package developed by Anders Møller (http://cs.au.dk/~amoeller/automaton/index.html).

3-layer neural network for regression and classification with sigmoid activation function and command line interface similar to LibSVM. Quick Start: "java -jar nen.jar"

a simple and effective vehicle routing problem’s solger using metaheuristic algorithms's like Tabu Search and Clark'n Wright. It's specialized in single deposit and singe vehicle's capacity VRP's istances. [mainly for educational purposes]

JSpoor is a utility software for logging and recording of user interface events and actions during working sessions of users with a Java/Swing Software. It captures and records both high level (semantic) actions and low level actions such as mouse moves.

Celeste is a tiny and simple Cellular Automata simulator written in Java. It is a command line application that writes an image of each simulation step. Celeste was designed to run Conway's Game of Life but other rulesets can be implemented as well. It is released under the extremely permissive WTFPL.

A gibbs energy calculator based on the CDK.

Java Micro Benchmark - control tasks required to determine the comparative performance characteristics of the computer system on different platforms. Can be used to determine the effect of different software on the performance of a computer system.

Alignment of the assembled sequences to a reference genome is a common way to obtain a likely order for the contigs, though most of times the final decision is taken by the user. We present the jContigSort, a tool that sorts the genome contigs.

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...

For electronics engineers, when using open source EDA tools, one of big challenge is component schematic symbols and footprints. If you are creating footprints for component with more than 100 pins, it becomes very time consuming and challenging to create error free footprints. Here is a simple program to create footprints for open source EDA kicad. The idea is to describe footprint in .csv format and convert .csv to kicad footprint format. At preset program supports Kicad only, but can be...

.... --- Highlights: --- org.knowceans.util: IndexQuickSort, TableList: apply order of one array/list to others +++ Vectors, ArrayUtils: array convenience +++ RandomSamplers, CokusRandom, ArmSampler, Densities: random sampling and distributions +++ Arguments: command line parser +++ StopWatch, Which, ExternalProcess: runtime stuff +++ ParallelFor: OpenMP workalike +++ PatternString, NamedGroupRegex: regex convenience --- org.knowceans.corpus: CorpusSearcher: full-text search engine +++ LabelNumCorpus: svmlight corpus storage and filtering +++ NIPS corpus with text, authors, labels and citations --- org.knowceans.map: InvertibleHashMultiMap, BijectiveHashMap: implement n:m and 1:1 relations. --- Other libs: knowceans-arms = port of the Adaptive Rejection Metropolis Sampler (ARMS) for arbitrary distributions +++ lda-j = port of lda-c, implementing Latent Dirichlet Allocation (LDA)

Shrec is a bioinformatics tool for error correction of HTS read data.

OpenBioGeoSim it's a open source software that simulates the stochastic origin and spread of species geographic ranges in a heterogeneous landscape. It's a free alternative based on Gary Entsminger's BioGeoSim.

This project has been moved to https://github.com/loomchild/maligna . All further development will be done there.

OrthoInspector is a new software system for orthology/paralogy analysis. Its purpose is to facilitate the installation and the maintenance of a database describing orthology/inparalogy relations and to provide tools to exploit these data.

JEuclid is a complete MathML rendering solution, consisting of: a MathViewer application, command line converters from MathML to other formats, an ant task for autmated conversion, display components for AWT and Swing and a component for Apache Cocoon

HanNanum is a Korean Morphological Analyzer and POS Tagger. A plug-in component-based architecture is adapted to the new Java version for flexible use. You can find the work flow for morphological analysis, POS tagging, noun extraction, etc. Contact: kschoi@kaist.ac.kr hjjeong@world.kaist.ac.kr