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jPHYDIT: a JAVA-based integrated environment for molecular phylogeny of ribosomal RNA sequences

Bioinformatics, 2005-07, Vol.21 (14), p.3171-3173

2005

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MpTheory Java library: a multi-platform Java library for systems biology based on the Metabolic P theory

Bioinformatics, 2015-04, Vol.31 (8), p.1328-1330

2015

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JED: a Java Essential Dynamics Program for comparative analysis of protein trajectories

BMC bioinformatics, 2017-05, Vol.18 (1), p.271-9, Article 271

2017

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HALO—a Java framework for precise transcript half-life determination

Bioinformatics, 2010-05, Vol.26 (9), p.1264-1266

2010

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JS-MS: a cross-platform, modular javascript viewer for mass spectrometry signals

BMC bioinformatics, 2017-11, Vol.18 (1), p.469-469, Article 469

2017

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FERN - a Java framework for stochastic simulation and evaluation of reaction networks

BMC bioinformatics, 2008-08, Vol.9 (1), p.356-356, Article 356

2008

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jSquid: a Java applet for graphical on-line network exploration

Bioinformatics, 2008-06, Vol.24 (12), p.1467-1468

2008

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C.U.R.R.F. (Codon Usage regarding Restriction Finder): A Free Java®-Based Tool to Detect Potential Restriction Sites in Both Coding and Non-Coding DNA Sequences

Molecular biotechnology, 2012-10, Vol.52 (2), p.123-128

2012

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Genoviz Software Development Kit: Java tool kit for building genomics visualization applications

BMC bioinformatics, 2009-08, Vol.10 (1), p.266-266, Article 266

2009

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A web-based system for creating, viewing, and editing precursor mass spectrometry ground truth data

BMC bioinformatics, 2020-09, Vol.21 (1), p.1-418, Article 418

2020

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SpinSPJ: a novel NMR scripting system to implement artificial intelligence and advanced applications

BMC bioinformatics, 2021-12, Vol.22 (1), p.581-581, Article 581

2021

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GraphDNA: a Java program for graphical display of DNA composition analyses

BMC bioinformatics, 2007-01, Vol.8 (1), p.21-21, Article 21

2007

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NGS-FC: A Next-Generation Sequencing Data Format Converter

IEEE/ACM transactions on computational biology and bioinformatics, 2018-09, Vol.15 (5), p.1683-1691

2018

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JUST (Java User Segmentation Tool) for semi-automatic segmentation of tomographic maps

Journal of structural biology, 2008-03, Vol.161 (3), p.287-297

2008

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A comparison of three programming languages for a full-fledged next-generation sequencing tool

BMC bioinformatics, 2019-06, Vol.20 (1), p.301-301, Article 301

2019

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In silico fragmentation for computer assisted identification of metabolite mass spectra

BMC bioinformatics, 2010-03, Vol.11 (1), p.148-148, Article 148

2010

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simBio: A Java package for the development of detailed cell models

Progress in biophysics and molecular biology, 2006, Vol.90 (1), p.360-377

2006

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Hybrid Automata Library: A flexible platform for hybrid modeling with real-time visualization

PLoS computational biology, 2020-03, Vol.16 (3), p.e1007635-e1007635

2020

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clusterMaker2: a major update to clusterMaker, a multi-algorithm clustering app for Cytoscape

BMC bioinformatics, 2023-04, Vol.24 (1), p.134-134, Article 134

2023

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BioJava 5: A community driven open-source bioinformatics library

PLoS computational biology, 2019-02, Vol.15 (2), p.e1006791-e1006791

2019

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Aird: a computation-oriented mass spectrometry data format enables a higher compression ratio and less decoding time

BMC bioinformatics, 2022-01, Vol.23 (1), p.35-35, Article 35

2022

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A Java chemical structure editor supporting the Modular Chemical Descriptor Language (MCDL)

Molecules (Basel, Switzerland), 2006-03, Vol.11 (4), p.219-231

2006

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123VCF: an intuitive and efficient tool for filtering VCF files

BMC bioinformatics, 2024-02, Vol.25 (1), p.68-68, Article 68

2024

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JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison

BMC bioinformatics, 2013-01, Vol.14 (1), p.18-18, Article 18

2013

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Using biological pathway data with paxtools

PLoS computational biology, 2013-09, Vol.9 (9), p.e1003194-e1003194

2013

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jPHYDIT: a JAVA-based integrated environment for molecular phylogeny of ribosomal RNA sequences

MpTheory Java library: a multi-platform Java library for systems biology based on the Metabolic P theory

JED: a Java Essential Dynamics Program for comparative analysis of protein trajectories

HALO—a Java framework for precise transcript half-life determination

JS-MS: a cross-platform, modular javascript viewer for mass spectrometry signals

FERN - a Java framework for stochastic simulation and evaluation of reaction networks

jSquid: a Java applet for graphical on-line network exploration

C.U.R.R.F. (Codon Usage regarding Restriction Finder): A Free Java®-Based Tool to Detect Potential Restriction Sites in Both Coding and Non-Coding DNA Sequences

Genoviz Software Development Kit: Java tool kit for building genomics visualization applications

A web-based system for creating, viewing, and editing precursor mass spectrometry ground truth data

SpinSPJ: a novel NMR scripting system to implement artificial intelligence and advanced applications

GraphDNA: a Java program for graphical display of DNA composition analyses

NGS-FC: A Next-Generation Sequencing Data Format Converter

JUST (Java User Segmentation Tool) for semi-automatic segmentation of tomographic maps

A comparison of three programming languages for a full-fledged next-generation sequencing tool

In silico fragmentation for computer assisted identification of metabolite mass spectra

simBio: A Java package for the development of detailed cell models

Hybrid Automata Library: A flexible platform for hybrid modeling with real-time visualization

clusterMaker2: a major update to clusterMaker, a multi-algorithm clustering app for Cytoscape

BioJava 5: A community driven open-source bioinformatics library

Aird: a computation-oriented mass spectrometry data format enables a higher compression ratio and less decoding time

A Java chemical structure editor supporting the Modular Chemical Descriptor Language (MCDL)

123VCF: an intuitive and efficient tool for filtering VCF files

JContextExplorer: a tree-based approach to facilitate cross-species genomic context comparison

Using biological pathway data with paxtools

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