ImageJ 2.0.0 rc71 – Image Processing & Analysis in Java

ImageJ 2.0.0 rc71

:: 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.

JTreeView 0.8 – Java based Phylogenetic Tree Viewer

JTreeView 0.8

:: DESCRIPTION

JTreeView is a basic tree viewer that lets you view, reroot, rotate nodes and edit further aspects of New Hampshire bracket format trees.

::DEVELOPER

JTreView team

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java

:: DOWNLOAD

 JTreeView

:: MORE INFORMATION

JABAWS 2.2 – JAva Bioinformatics Analysis Web Services

JABAWS 2.2

:: DESCRIPTION

JABAWS is a collection of web services for bioinformatics, and currently provides services that make it easy to access well-known multiple sequence alignment and protein disorder prediction programs from Jalview. JABAWS is free software which provides web services conveniently packaged to run on your local computer, server, cluster or Amazon EC2 instance. Services for multiple sequence alignment include Clustal Omega, Clustal W, MAFFT, MUSCLE, TCOFFEE and PROBCONS. Analysis services allow prediction of protein disorder with DisEMBL, IUPred, Ronn and GlobPlot; and calculation of amino acid alignment conservation with AACon.

::DEVELOPER

The Barton Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX/ Amazon EC2
  • Java

:: DOWNLOAD

 JABAWS

:: MORE INFORMATION

Citation

Bioinformatics. 2011 Jul 15;27(14):2001-2. doi: 10.1093/bioinformatics/btr304. Epub 2011 May 18.
Java bioinformatics analysis web services for multiple sequence alignment–JABAWS:MSA.
Troshin PV, Procter JB, Barton GJ.

BioJava 4.1.0 – Java Framework for Processing Biological Data

BioJava 4.1.0

:: DESCRIPTION

BioJava is a mature open-source project that provides a framework for processing of biological data. BioJava contains powerful analysis and statistical routines, tools for parsing common file formats and packages for manipulating sequences and 3D structures. It enables rapid bioinformatics application development in the Java programming language.

::DEVELOPER

BioJava Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

BioJava

:: MORE INFORMATION

Citation:

BioJava: an open-source framework for bioinformatics in 2012.
Prlić A, Yates A, Bliven SE, Rose PW, Jacobsen J, Troshin PV, Chapman M, Gao J, Koh CH, Foisy S, Holland R, Rimsa G, Heuer ML, Brandstätter-Müller H, Bourne PE, Willis S.
Bioinformatics. 2012 Oct 15;28(20):2693-5. doi: 10.1093/bioinformatics/bts494.

BioJava: an Open-Source Framework for Bioinformatics ,
Holland RC, Down TA, Pocock M, Prlić A, Huen D, James K, Foisy S, Dräger A, Yates A, Heuer M, Schreiber MJ.
Bioinformatics. 2008 Sep 15;24(18):2096-7. doi: 10.1093/bioinformatics/btn397.

Jmol 14.4.0 – Java Viewer for Chemical Structures in 3D

Jmol 14.4.0

:: 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

jmolforand

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

Jmol

:: MORE INFORMATION

ImgLib2 2.4.1 – Image Processing JAVA Library

ImgLib2 2.4.1

:: 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.

XTandem Parser 1.8.0 – Java based parser for X!Tandem output xml files

XTandem Parser 1.8.0

:: 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 3.4.1 – Java Front End to the Ontology Lookup service

OLS Dialog 3.4.1

:: 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.

JME 2010.02 / JSME 20150614 – Java Molecular Editor

JME 2010.02 / JSME 20150614

:: DESCRIPTION

JME Molecular Editor is a Java applet which allows to draw / edit molecules and reactions (including generation of substructure queries) and to depict molecules directly within an HTML page. Editor can generate Dayligh SMILES or MDL mol file of created structures.

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

::DEVELOPER

Peter Ertl

:: SCREENSHOTS

JSME

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

JME / JSME

:: MORE INFORMATION

Citation

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

EvA 2.2.0-rc1 – Java based framework for Evolutionary Algorithms

EvA 2.2.0-rc1

:: DESCRIPTION

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

::DEVELOPER

the Center for Bioinformatics Tübingen (Zentrum für Bioinformatik Tübingen, ZBIT).

:: SCREENSHOTS

EvA

:: 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)