Search Results for "simple java code" - Page 2
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Showing 80 open source projects for "simple java code"
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GNomEx
A Genomic LIMS and Data Repository
Our source code is now on GitHub: https://github.com/hci-gnomex/gnomex. Please refer to GitHub for the latest code. GNomEx is Genomic LIMS and Data Repository. It holds annotated experiments and downstream analysis and serves data tracks to popular genome browsers such as IGB, IGV, and UCSC genome browser. The LIMS handles all aspects of the experiment from order through results delivery. -
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bioNerDS
Bioinformatics Named Entity Recogniser for Databases and Software
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PromKappa 2.0 (DNA patterns in Java)
PromKappa 2.0 (Java source code and bin)
A Java adaptation of DNA patterns based on the article "Eukaryotic genomes may exhibit up to 10 generic classes of gene promoters". by Ilie Guta (Java source code for DNA patterns) -
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GeneticAlgorithms
Framework for using the Genetic Algorithms optimization heuristic.
GeneticAlgorithms is a simple and lightweight framework to implement an optimization heuristic following the Genetic Algorithms model. A genetic algorithm mimics the natural processes of evolution, selection and "survival of the fittest". This framework is intuitive and good integrated with Java 1.5 SDK and later. -
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Gene Studio is a free tool for modelling of DNA manipulation. It will allow to work with vectors, to design primers, to clone molecules and provide user friendly intewrface.
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The target system of this project is to develop mathematically efficient program code generator from cellml like biological models described by mathematical markup languages.
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GenoCAD is a CAD software for synthetic biology. This application provides a web-based tool to design plasmids, artificial gene networks, and other synthetic genetic systems composed of standard genetic parts. It includes a parts management system, a rule-based design tool, and a simulation engine. This project has morphed into a SaaS model. The open source code is no longer maintained.
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Deem
Analyze time-course data with significance tests, clustering, modeling
Use statistical methods to analyze time-course data (gene expression microarray and RNA-seq data in particular, but not limited to). Apply significance tests to filter out only significant genes or time series. Cluster time series into similar groups. Generate network models, including linear or non-linear models. Variable selection and optimization routines included. Written in Scala and R. The application is a cross-platform desktop app with a simple GUI and is fully functional... -
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CIG-P
CIG-P is a simple yet flexible data visualization tool
CIG-P is a higher order visualization tool for AP-MS which generates intuitive circular diagrams for visually appealing final representation of AP-MS data. CIG-P can be used to compare a) different AP-MS datasets of various baits or b) a particular bait under various perturbations (lenticular section CIG-P). The output of CIG-P is a simple and intuitively easy to grasp visualization of a complex dataset. Publication: CIG-P: Cicular Interaction Graph for... -
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SSWAP
Simple Semantic Web Architecture and Protocol
SSWAP (Simple Semantic Web Architecture and Protocol; pronounced "swap") is an architecture, protocol, and platform that uses reasoning to semantically integrate disparate data and services on the web. Running live at http://sswap.info. -
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This package contains code for use with Short Read DNA Sequencing technologies, and includes packages for ChIP-Seq, Whole Transcriptome Shotgun Sequencing, Whole Genome Shotgun Sequencing, SNP Detection, Transcript expression and file conversion.
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BioDare
BioDare is Biological Data Repository focused on timeseries data
BioDare (Biological Data Repository) was developed under the multi-site ROBuST project (http://hallidaylab.bio.ed.ac.uk/ROBuST.html) to support data exchange inside the project. It is a web application which allows data-sharing (including public dissemination), data-processing and analysis, with the main focus on time-series data produced in circadian experiments. The main features of BioDare are: - an online repository for experimental data accompanied by extensive... -
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PIVOT
PIVOT is a simple yet flexible visualization data tool
PIVOT is a simple yet flexible visualization tool based on Circos (Krzywinski et al., 2009), which offers a fast and aesthetical visualization of data and information. The Protein Interaction Visualization and Observation Tool (PIVOT) was developed specifically for the visualization of protein interaction. It is difficult to spot the proteins that have an interaction when given a large list of proteins but with PIVOT, it is easy to identify the them at a glance. PIVOT displays an image... -
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Javamony
A Student's Approach to the Phylogenetic Problem
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 fundamental problems in phylogenetics. Therefore, for my own educational benefit, all code is original. ... -
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Face Detect (JavaCV)
Face Detection and Facial Feature Extraction using JavaCV
A simple Face detection program using JavaCV and OpenCV . Implementing facial feature extraction and face recognition. -
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ScreeningAssistant 2 is a modular software dedicated to perform various simple and advanced chemoinformatics analysis around chemical libraries.
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samsn
A tool to handle multi-stage mass spectrometry data
The source code for SAMSN can be found in github at https://github.com/miquelrojascherto/samsn -
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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.
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A Generalized Combinatorial Approach for Detecting Gene-by-Gene and Gene-by-Environment Interactions
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The code here is a parser for CALBC corpus into Java object.
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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.
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A simple tool to import the diff, gtf and tracking files from cufflinks, cuffcompare, cuffdiff into a new sqlite database for data mining.
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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.
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Adjusting PKL-Files derived from MS-experiments. The development of the project has been MOVED TO https://github.com/binfalse/adjustpkl
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JHeatChart is a simple Java library for generating heat map charts.
