A software enabling to query, browse, fetch and retrieve sequences from NCBI and EBI public servers.
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README.md

BioDocumentViewer

License AGPL Build Status

Introduction

BioDocumentViewer is a software enabling to query, browse, view and retrieve sequences from NCBI and EBI public servers.

The software has been made to facilitate the use of public web services, NCBI Entrez eUtils services (NCBI, Bethesda, USA) and EB-eye Search services (EBI, Hinxton, UK), so that it is easy to query databanks and retrieve set of sequences in batch mode.

Main features

The following screenshot illustrates BioDocumentViewer main features:

  • The QueryBuilder on the top left side; here, we use NCBI as data provider;
  • the DocumentNavigator on the left side; a batch sequence retrieval job is running to get more than 100K sequences, respecting NCBI recommendations;
  • the 3D Strucrure Viewer on the right side, showing a glycosidase PDB structure;
  • the Sequence Viewer, displaying a fully annotated Refseq gene

BioDocumentViewer

Requirements

Use a Java Virtual Machine 1.7 (or above) from Oracle.

As a result of using Java, BioDocumentViewer is available for Linux, Mac OSX and Windows systems.

Not tested with any other JVM providers but Oracle... so there is no guarantee that the software will work as expected if not using Oracle's JVM.

Working with the binary release

The most easy way to use BioDocViewer Tool consists in downloading an official release. It is made of a single Java binary archive file:

biodocviewer-x.y.z.jar

It is available from this Github page: check [Releases] tab and download the latest release.

We invite all users to start working with that "jar" file, as explained in the next section.

Notice for developers: this unique JAR file is absolutely not intended to be embedded within any other applications since it contains all the dependencies (third-party libraries) into a single large file. So, if you want to include BioDocViewer into some other softwares, start from its source code (git clone).

User manual

A user manual is available here.

License and dependencies

BioDocViewer itself is released under the GNU Affero General Public License, Version 3.0. AGPL

BioDocViewer depends on several thrid-party libraries as stated in the NOTICE.txt file provided with this project.

-- (c) 2006-2017 - Patrick G. Durand