JEnsembl is a lightweight Java API especially designed for the Ensembl data systems, enabling you to develop integrated applications much easier.
JEnsembl provides access to all the Ensembl and EnsemblGenomes database types and implements various data access functions.
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JEnsembl (Java API to Ensembl) is a lightweight Java API especially designed for the Ensembl data systems, enabling you to develop integrated applications much easier.
JEnsembl provides access to all the Ensembl and EnsemblGenomes database types and implements various data access functions. It is based on JDO and can handle millions of objects per session. It is 100x faster than the old Ensembl API on very large datasets.
The JEnsembl API:
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JEnsembl [Mac/Win]
JEnsembl is a java API especially designed for the Ensembl data systems, enabling you to develop integrated applications much easier. JEnsembl provides access to all the Ensembl and EnsemblGenomes database types and implements various data access functions.
JEnsembl API (hereafter referred to as JEnsembl) is inspired by the OA API. It consists of JEnsembl-Static and JEnsembl-Dynamic parts. JEnsembl-Static is a fast binding static linking API with the Ensembl API call interface while JEnsembl-Dynamic is dynamically linked JEnsembl-Static, and it’s a thin interface layer between JEnsembl-Static and Java API.
JEnsembl-Static implements API functions that are strictly and specifically used by JEnsembl-Dynamic.
JEnsembl-Dynamic implements API functions that are not used by JEnsembl-Static
JEnsembl-Static is used directly by JEnsembl-Dynamic.
JEnsembl-Dynamic is used directly by application developers.
Both the Static and Dynamic APIs can be used in combination with JET or other bindings.
If your goal is to integrate the Ensembl API into an existing application, then the right choice is JET. If you don’t need interaction with the server, then JEnsembl-Static is more appropriate.
Also a lot of convenient utilities for Ensembl data systems are available in JEnsembl package. For example the ‘EnsemblUtils’ package contains lot of useful classes for manipulation Ensembl data.
For example the ‘GenomicChartUtils’ class offers convenient graphical representations of sequences, genes, transcripts, cDNAs, etc.
For example given the ENSG00000131000, ENSG00000171459 and ENSG00000131000 genes and transcripts
Java code:
/*
GenomicChartUtils.plot(String geneId, String transcriptId, String color)
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JEnsembl
An API for fast and robust access to biological annotations from
Ensembl
An API for fast and robust access to Ensembl/EnsemblGenomes data
An API for fast and robust access to Ensembl data
An API for fast and robust access to EnsemblGenomes data
An API for full text searching and an API for accessing Ensembl data for any species
Description:
In 2002, Ensembl started the development of a robust platform for data
analysis, and about a year later released the first version of a
production quality Java API. The API was based on EMBOSS/Egg, has
been
extensively
tested in
production and has enabled the creation of many
other
applications.
The API has then been further developed to also include databases that
are not related to Ensembl, such as Entrez Gene, RefSeq, UniGene.
JEnsembl is an API in the Ensembl/Ensembl Genomes family. As part of
Ensembl,
JEnsembl is
licensed under the
GNU Lesser General Public
License (LGPL) version 2.1.
Latest Version
* Ensembl: version 52
* JEnsembl: version 0.4.0
JEnsembl Source:
* JEnsembl git repository:
* JEnsembl on Maven Repository:
Repository:
Release:
JEnsembl 0.4.0 sources:
License
JEnsembl is licensed under the GNU Lesser General Public License (LGPL)
version 2.1.
Users of JEnsembl can choose their licence for using JEnsembl either
under the GNU General Public License (GPL) version 2 or version 3.
License Summary:
What’s New In JEnsembl?
A lightweight Java API for
access to the Ensembl/EnsemblGenomes databases.
It provides access to all the ensembl(or other ensembl
output formats) database types, and implement various data
access functions.
Sample application:
import JEnsembl.*;
public class foo extends JEnsembl {
public static void main(String[] args) {
foo et= new foo();
et.init();
et.checkEuGeneInfo();
}
}
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The My Emu Mark II is a compact car introduced by the Australian company My Emu in August 2008. The Mark II can seat four adults and has a maximum speed of. My Emu claims the car can climb a hill of 10%.
Development
The Mark II followed on from a previous model, the My Emu Mark II Special Edition, which became the standard model and which was later, in August 2008, replaced by the revised range of My Emu cars. The new car comes with the same engine as the Special Edition but offers double the power of the original model. The 2011 Mark II, which was unveiled at the Internationale Automobile Show Frankfurt, was officially launched in Germany in May 2011. The Mark II has garnered strong sales.
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