Search Results for "java framework"
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Showing 55 open source projects for "java framework"
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ProbeMaker is a framework for design of sets of oligonucleotide probes. It allows the design of different types of probes made up of separate sequence elements. A Plug-in mechanism allows extension of the framework with new functionalities.
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NGSEP
NGSEP (Next Generation Sequencing Experience Platform)
NGSEP is an integrated framework for analysis of short and long DNA high throughput sequencing reads. The current version provides functionalities for both de-novo and reference guided analysis of sequencing data, including genome assembly, read mapping, variants detection and genotyping and de-novo analysis of data generated from reduced representation protocols. NGSEP also provides modules for analysis of genomic variation databases (VCF files), including functional annotation, filtering,... -
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The Systems Biology Format Converter (SBFC) is a Java generic framework aiming to translate any systems biology model format into another. The SBFC Web Site providing detailed feature description and instructions for installing, using and developing new modules is: http://sbfc.sourceforge.net/ . Currently, SBFC allows the user to convert SBML models into the formats: BioPax, Matlab, Octave, XPP, DOT, and SBGN.
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This project moved to GitHub in 2021 and is available at: https://cbrinkrolf.github.io/VANESA/ This tool is a platform-independent software to create individual pathways and to examine biological networks of distributed, heterogeneous data sources, e.g. KEGG, BRENDA. VANESA also offers Petri net modeling of extended hybrid Petri nets which can be also simulated using the OpenModelica framework.
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SBW (Systems Biology Workbench)
Framework for Systems Biology
The Systems Biology Workbench(SBW) is a framework for application intercommunications. It uses a broker-based, distributed, message-passing architecture, supports many languages including Java, C++, Perl & Python, and runs under Linux,OSX & Win32. It comes with a large number of modules, encompassing the whole modeling cycle: creating computational models, simulating and analyzing them, visualizing the information, in order to improve the models. -
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Toxtree: Toxic Hazard Estimation
Toxicity prediction for chemical compounds
...The latest version includes the following toxicity prediction modules: -Cramer rules (oral toxicity) -Toxicity mode of action via Verhaar scheme -Skin irritation and Eye irritation prediction -Benigni / Bossa rulebase for mutagenicity and carcinogenicity prediction -START biodegradation and persistence prediction -Skin sensitisation reactivity domain -Kroes TTC Decision tree -SMARTCyp - Cytochrome P450-Mediated Drug Metabolism and metabolites prediction -Structure Alerts for the in vivo micronucleus assay in rodents (ISSMIC) -Structural Alerts for Functional Group Identification (ISSFUNC) -Structural alerts associated with covalent protein binding and DNA binding. - Ames mutagenicity Toxtree provides a plugin framework to incorporate different approaches to the estimation. Platform independent (written in Java), with the use of The Chemistry Development Kit. -
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Niche Analyst (NicheA) was developed based on the BAM framework which allows users to create virtual spaces and virtual species, and to analyze ecological niches in both multivariate environmental and geographic spaces, linking views of the niche in the two spaces. The unique functionality in NicheA, not available in other software programs, is estimating Grinnellian niches of species based on environmental variables and occurrence records, but with a clear focus on fundamental ecological...
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scFvMiner
Scripts for analysing NGS data
These scripts written in java can be used for deep sequencing analysis of the scFv antibodies from a synthetic antibody library and yields complete sequence information on the randomized areas of antibodies enriched from the library by phage display. The methods are descriped in Lövgen, J., Pursiheimo, J.P., Pyykkö, M., Salmi, J. & Lamminmäki, U. (2016) Next generation sequencing of all variable loops of synthetic single framework scFv – application in anti-HDL antibody selections. ... -
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This ohnlp project has released "pipelines" that were contributed by members of the OHNLP Consortium. The pipelines are based on the Apache UIMA framework. medKAT/P, MedCoref, MedTagger, MedXN, and cTAKES are licensed under Apache License V2.0. MedTime is licensed under GNU General Public License version 3.0 (GPLv3). cTAKES development has moved to apache.org. See http://ctakes.apache.org/
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JMGF
Java implementation for the Mascot Generic File Format (MGF).
JMGF is a lightweight framework for handling MGF files. It supports reading, writing and parsing of MGF files. Files may be read/ written at once, or stream-based (memory efficient). It's stable, very intuitive and good integrated with Java 1.5 SDK and later. -
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JFASTA
Java implementation for the FASTA file format.
JFASTA is a lightweight framework for handling FASTA files. It supports reading, writing and parsing of single- or multi-FASTA files. Files may be read/ written at once, or stream-based (memory efficient). It's stable, very intuitive and good integrated with Java 1.5 SDK and later. -
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openModeller is a complete C++ framework for species potential distribution modelling. The project also includes a graphical user interface, a web service interface and an API for Python.
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BioUtils - Proteomics
Lightweight framework for handling biological and bioinformatical data
The BioUtils - Proteomics package is a lightweight Java framework for handling commonly used data produced and needed in the field of Mass spectrometry in general and especially in the field of Proteomics. It's stable, intuitive to use and good integrated with Java 6 SDK and later. -
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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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Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework with the Picard SAM JDK, and command line tools similar to SAMtools. The file formats currently supported are BAM, SAM, FASTQ, FASTA, QSEQ, BCF, and VCF. For a longer high-level description of Hadoop-BAM, refer to the article "Hadoop-BAM: directly manipulating next generation sequencing data in the cloud" in Bioinformatics Volume 28 Issue 6 pp. 876-877, available online at: http://dx.doi.org/10.1093/bioinformatics/bts054 Note that the library part of Hadoop-BAM is mainly for developers with experience in using Hadoop. ...
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MZmine 2
A framework for differential analysis of mass spectrometry data
MZmine 2 is a framework written in Java for differential analysis of mass spectrometry data. -
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HRDAG
Framework for Hierarchical Graph Decomposition
This is a framework used to decompose hierarchical graphs, i.e.,graphs which were created from or contain a hierarchy of modules. Each module is reused several times in the hierarchy. This may be useful to reverse-engineer human constructs like electronic equipment, manufactured machines, or bureaucratic hierarchies; but also to decompose natural constructs like gene-relation or protein-relation nets. -
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xAffect
Sensor Middleware
xAffect is a software framework for online recording, processing and storage of multi sensor data. It was developed at FZI Research Center for Information Technology, Karlsruhe, Germany. xAffect can be used as a flexible, customizable middleware between physiological sensors and applications which require online feature computation (e.g. biofeedback or affective computing). Moreover, it can also be used as a standalone application for data acquisition and visualization. -
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Framework for text mining, data integration and data analysis. Keywords: ontology and graph alignment, relation mining, warehouse, semantic database integration, bioinformatics, systems biology, microarray, Java.
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A software framework to build maps for Neurospora crassa genome based on probabilistic models of meiotic recombination. A netbeans platform application is built to incorporate the computations. Project issues are mainatined at https://freecode4susant.atlassian.net/browse/GENOMEMAP
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Darwin 2: Java Framework for Evolutionary Computation (genetic algorithm, GA). A true framework with out-of-the-box functionality and extensibility of all classes. Interface-based pattern with dependency-injection to configure components.
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A comparative map and trait visualization framework enabling visual integration of genomic data from disparate data sources and allowing rich client-side interactivity and manipulation. Extensible through plugins for new datasources and algorithms.
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Anna is lightweight Java framework to build pipeline systems of any kind. It will take care of recurrent needs such as dependency management, data serialisation and synchronization as well as parallelization of execution.
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The Edinburgh Pathway Editor (EPE) is a tool and framework that allows the drawing and manipulation of Biological Networks, such as signalling or matabolic pathways. The editor supports several notations including SBGN and Cytoscape notations.
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A collection of tools for working with the comparative data analysis ontology including import/export facilities for common phylogenetic file formats, and also a triple-store framework.
