Tag: Java

GC4S v1.6.0 – Bioinformatics-oriented collection of GUI Components for (Java) Swing

GC4S v1.6.0

:: DESCRIPTION

GC4S is an open-source library that provides a bioinformatics-oriented collection of GUI Components for (Java) Swing.

::DEVELOPER

SING Group.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows
  • Java

:: DOWNLOAD

GC4S

:: MORE INFORMATION

Citation

López-Fernández H, Reboiro-Jato M, Glez-Peña D, Laza R, Pavón R, Fdez-Riverola F.
GC4S: A bioinformatics-oriented Java software library of reusable graphical user interface components.
PLoS One. 2018 Sep 20;13(9):e0204474. doi: 10.1371/journal.pone.0204474. PMID: 30235322; PMCID: PMC6147514.

ImageJ 2.2.0 – Image Processing & Analysis in Java

ImageJ 2.2.0

:: DESCRIPTION

ImageJ is a public domain Java image processing program.ImageJ was designed with an open architecture that provides extensibility via Java plugins and recordable macros. Custom acquisition, analysis and processing plugins can be developed using ImageJ’s built-in editor and a Java compiler. User-written plugins make it possible to solve many image processing and analysis problems, from three-dimensional live-cell imaging, to radiological image processing, multiple imaging system data comparisons to automated hematology systems.

::DEVELOPER

ImageJ team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

ImageJ

:: MORE INFORMATION

Citation:

Abramoff, M.D., Magelhaes, P.J., Ram, S.J. “Image Processing with ImageJ“.
Biophotonics International, volume 11, issue 7, pp. 36-42, 2004.

J-Circos – A Java Graphic User Interface for Circos Plot

J-Circos

:: DESCRIPTION

J-Circos is a Circos plot tool that is an interactive visualization tool that can plot Circos figures, as well as being able to dynamically add data to the figure, and providing information for specific data points using mouse hover display and zoom in/out functions.

::DEVELOPER

Australian Prostate Cancer Research Centre – Queensland

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 J-Circos

:: MORE INFORMATION

Citation

J-Circos: An Interactive Circos plotter.
An J, Lai J, Sajjanhar A, Batra J, Wang C, Nelson CC.
Bioinformatics. 2014 Dec 24. pii: btu842.

EvA 2.2.0 – Java based framework for Evolutionary Algorithms

EvA 2.2.0

:: DESCRIPTION

EvA2 (an Evolutionary Algorithms framework, revised version 2) is a comprehensive heuristic optimization framework with emphasis on Evolutionary Algorithms implemented in Java.

::DEVELOPER

EvA team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/ WIndows / MacOSX
  • Java

:: DOWNLOAD

  EvA

:: MORE INFORMATION

Citation

Felix Streichert and Holger Ulmer
JavaEvA: A Java based framework for Evolutionary Algorithms
Technical Report (PDF, 2005)

JSME 20210713 – Java Molecular Editor

 JSME 20210713

:: DESCRIPTION

JSME is a free molecule editor written in JavaScript. JSME is a direct successor of the JME Molecule Editor applet.

::DEVELOPER

Peter Ertl

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

JSME

:: MORE INFORMATION

Citation

B. Bienfait and P. Ertl,
JSME: a free molecule editor in JavaScript,
J. Cheminformatics 5:24 (2013)

JACUSA v2.0.2-RC – JAVA framework for accurate SNV Assessment

JACUSA v2.0.2-RC

:: DESCRIPTION

JACUSA2 is a one-stop solution to detect single nucleotide variants (SNVs) and reverse transcriptase induced arrest events in Next-generation sequencing (NGS) data.

::DEVELOPER

Dieterich lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Jav

:: DOWNLOAD

JACUSA2

:: MORE INFORMATION

Citation.

Piechotta M, Wyler E, Ohler U, Landthaler M, Dieterich C.
JACUSA: site-specific identification of RNA editing events from replicate sequencing data.
BMC Bioinformatics. 2017 Jan 3;18(1):7. doi: 10.1186/s12859-016-1432-8. PMID: 28049429; PMCID: PMC5210316.

XTandem Parser 1.13.0 – Java based parser for X!Tandem output xml files

XTandem Parser 1.13.0

:: DESCRIPTION

XTandem Parser is a Java project for extracting information from X!Tandem output xml files.

::DEVELOPER

The Proteomics Unit at the University of Bergen (PROBE)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux
  • Java

:: DOWNLOAD

 XTandem Parser

:: MORE INFORMATION

Citation

Proteomics. 2010 Apr;10(7):1522-4.
XTandem Parser: an open-source library to parse and analyse X!Tandem MS/MS search results.
Muth T, Vaudel M, Barsnes H, Martens L, Sickmann A.

OLS Dialog 3.4.14 – Java Front End to the Ontology Lookup service

OLS Dialog 3.4.14

:: DESCRIPTION

OLS Dialog is a Java front end to the Ontology Lookup Service allowing easy access to an extensive list of biomedical ontologies

::DEVELOPER

The Proteomics Unit at the University of Bergen (PROBE)

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux
  • Java

:: DOWNLOAD

 OLS Dialog

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Jan 17;11:34.
OLS dialog: an open-source front end to the ontology lookup service.
Barsnes H, Côté RG, Eidhammer I, Martens L.

ImgLib2 2-5.12.0 – Image Processing JAVA Library

ImgLib2 2-5.12.0

:: DESCRIPTION

ImgLib2 is a general-purpose, multidimensional image processing library.

::DEVELOPER

ImgLib2 team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

  ImgLib2

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Nov 15;28(22):3009-11. doi: 10.1093/bioinformatics/bts543. Epub 2012 Sep 8.
ImgLib2–generic image processing in Java.
Pietzsch T, Preibisch S, Tomancák P, Saalfeld S.

Jmol 14.31.44 – Java Viewer for Chemical Structures in 3D

Jmol 14.31.44

:: DESCRIPTION

Jmol is a free, open source molecule web browser applet for chemical structures in 3D for students, educators, and researchers in chemistry and biochemistry.

::DEVELOPER

Jmol Team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

Jmol

:: MORE INFORMATION

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