Welcome

BinBase

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The BinBase is an enterprise application system to automate the handling and annotation of mass spec data and is based on several open source technologies. Currently we provide two solutions.

• BinBase - standalone
• BinBase + miniX

Basically the approach of the BinBase standalone version is not to be a program you start and it runs. It's more an idea which should be implemented in your work flow using external language access. For example you can install it and run it, but you wont have access to meta informations like species and organs. For this you need to write an implementation of an interface or need to use our miniX system.

Since there was a lot of demand of this software to be used without a setupX/miniX software. We decided to develop a simple program, called the DSLCalculator to simplify the interaction with BinBase. This tool basically allows you to define a so called DSL file and run it against the System. This is the most flexible way possible to use the system and can be also integrated with miniX.

Please read here for more informations about the DSL based system and it's possibilities.

Public Access

The BinBase has a couple of public accessible tools and web services.

BinBase Compound Browser
SetupX

BinBase Public Web service

BinBase Pubchem Web service

BinBase Customer Success stories

1. installation routine of BinBase and SetupX in the UC Davis Bioinformatic core lab
   

General things

1. what can I use it for
2. features
3. binbase vs binbase + SetupX
4. hardware and software requirements
5. installation and updating
6. common problems with running BinBase
7. release notes
8. download BinBase
9. building BinBase from the svn directory
10. how do we make sure BinBase is stable and works
11. getting help and tutorials
12. why do we use a cluster

How does BinBase Work

1. similarity calculation
2. retention index correction
3. first pass annotation
4. second pass annotation
5. third pass annotation
6. detecting isomers

Configuration

1. configuring the import and export directories
   

Data in and output

1. supported input format
2. supported sample name patterns
3. supported output format
4. customizing the generated output file
5. combining data from several gctof in one database

Writing extensions for the system

1. matching extensions
2. changing how the similarity is calculated
3. provide your own meta data provider
4. accessing the web services

BinBase tools

1. BDI - Tools
2. Cluster - Tools
3. General BinBase Tools
4. Bellerophon
5. Runtime Monitor
6. User Management
7. BinBase Compound Browser
8. BinBase Scheduler
9. BinBase SetupX Connection
10. overview of webservices

BinBase references

1. talks/publications
2. sourceforge.net
3. ohloh.net