BinBase database system

this is a completely automated analysis tool for the annotations of mass specs. Currently we are only supporting leco chrommmatof based data, but we are working on the support for other platforms

This software is available free of charge in form of it's source code under the LGPL license. Binaeries on the other hand are only available in form of a support contract with the company Coding and More. Please feel free to email us at contact@codingandmore.org to inquire about more details.

Requirements

• rocks linux 5.3, 6.1 cluster or system capable running a VMWare virtual machine
• java6, no java5 support anymore
• chromatof processed txt files leco

Downloads

Currently BinBase can only be build from source and the only available Downloads are of the BinView administration software.

If you need help with the installation, please contact the BinBase support company at contact@codingandmore.org and we are happy to answer your initial questions and tell you how to get started free of charge.

Support

If you need professional support please contact the company Coding and More using this contact@codingandmore.org email address. We offer remote support using a ssh, email, chat or by phone. We also offer training in how to use MiniX and BinBase as well as providing additional documentation.

Building BinBase from source:

BinBase can be easily build from source, but does require a couple of software packages installed on your local system. Please look here about further information how to compile the installer. We do expect that you are having a running PostgresSQL database server, JBoss application server and Rocks Linux cluster up and running. If this is not the case, we highly recommend that you contact us and request a quote for using the VMWare image. Which comes completely configured and ready to use.

https://code.google.com/p/binbase/wiki/building

BinBase - Features

This is just a small overview of features and BinBase currently has several dozen features. Sadly we lost the major part of the documentation during a server crash in 2012 and so still trying to write and add to this documentation whenever time permits.

• unsupervised - BinBase 3.0.0 and newer
• completely automated form of analysis - BinBase 3.0.0 and newer
• retention index calculation and correction - BinBase 3.0.0 and newer
• DSL support for custom and advanced calculations - BinBase 4.0.0 and newer
• posible connect to LIMS system's - BinBase 3.0.0 and newer
• completely accessible and usable over SOAP based webservices - BinBase 3.0.0 and newer
• optimized to run on ROCKS Linux high performance clusters - BinBase 3.0.0 and newer
• centralized configuration - BinBase 3.0.0 and newer
• absolute quantification using DSL's - BinBase 4.2.0 and newer
• Modification of Spectra data during the matching phase - BinBase 4.2.0 and newer
• BinView - the BinBase naming tool - BinBase 4.1.0 and newer
• Automatic scaling function available able to improve retention index correction - BinBase 4.2.0 and newer

MiniX - Features

MiniX is part of the BinBase tool suite and is used to define and generate experimental studies, to be calculated with BinBase. It also manages result files, keeps track of attachments and monitors your instrument.

• Defining study design to generate studies
• Support for multiple Instrument
• Generation of Sequence files for LECO GC-Tofs
• Automatic monitoring of retention index markers for each registered BinBase instance
• Dump and Restore of Experimental metadata

Project Owner/Maintainer

This project s was started in 2001 by Gert Wohlgemuth and maintained and further developed by him. For questions and help feel free to contact him at this address

Gert Wohlgemuth is also maintaining a blog and explain features and daily configuration issues here

This software uses open source licenses from:

Eclipse

JBoss

IntelliJ Idea

JProfiler