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Setting up a web-based neuroscience database has never been easier:
The CoCoMac engine goes open source

Rembrandt Bakker1, 2, 3*, Paul H.E. Tiesinga1, Markus Diesmann2, 4, 5 and Thomas Wachtler3
  • 1 Radboud University Nijmegen, Dept. of Neuroinformatics, Donders Institute for Brain, Cognition and Behaviour, Netherlands
  • 2 Research Center Jülich, Institute of Neuroscience and Medicine 6, Germany
  • 3 Ludwig-Maximilians-Universität München, Department Biology II/G-Node, Germany
  • 4 RWTH Aachen University, Faculty of Medicine, Germany
  • 5 RIKEN Brain Science Institute, Japan

We present a web-based framework to (1) set up a relational data base; (2) search and browse its contents interactively; and (3) edit/add content to it. Central to the framework is a database definition file: a text file that describes the database structure in a compact (JSON-based) format. This file can either be written from scratch to set up a new database, or be extracted from an existing database. Multiple versions of the definition file can provide different views (intranet/world wide web) of the same database. The platform provides an interactive search/browse wizard that (1) allows the user to compose complex queries without needing to know the database structure; and (2) presents the search results in tabular form, with interactive (AJAX-based) links to related child and parent tables. Adding/editing data is currently a privilege of the administrator; we are developing a module that allows users to own and edit specific rows of a table and all of its children.

The system is being developed for the CoCoMac 2.0 database (Bakker et al. 2012), which collects published tracing studies to compose a complete picture of the wiring diagram of the Macaque brain. In CoCoMac, the end product is a connectivity matrix (Fig. 1), which is not contained in the database but needs to be computed from it. This workflow is supported in the form of temporary tables that can be dynamically integrated with the database definition. CoCoMac also provides an example of how additional, non-standard views can be added for tables of a given class.

To get started, one needs a working instance of the MySQL data base engine, and a web/intranet server with PHP support. The database definition file should contain a list of tables and their field types, or, if a field references another table, the name of that table preceded by a caret symbol. This file can be automatically parsed from an existing database. An optional javascript file is used to define how the system should display table rows in different contexts, such as within a table cell or itemized list. The system can be downloaded from http://cocomac.g-node.org/git, and seen in action at the CoCoMac 2.0 website http://cocomac.g-node.org. It is also in use for a lab automation project (Bakker et al. 2012a) and various internal projects.

Figure 1
Image

Acknowledgements

Supported by the German INCF Node (BMBF grant 01GQ0801), Helmholtz Association HASB and portfolio theme SMHB. JUGENE Grant JINB33, and EU Grant 269921 (BrainScaleS).

References

Bakker R, Wachtler T and Diesmann M (2012) CoCoMac 2.0 and the future of tract-tracing databases. Front. Neuroinform. 6:30. doi: 10.3389/fninf.2012.00030

Bakker R, Schubert D and Tiesinga P (2012a) P109 Electrophysiology lab automation: a case study. Neuroinformatics 2012, 5th INCF Congress, p. 215

Keywords: Macaque connectivity, Database engine, CoCoMac, MySQL, lab automation, neuroscience database

Conference: Neuroinformatics 2013, Stockholm, Sweden, 27 Aug - 29 Aug, 2013.

Presentation Type: Demo

Topic: Infrastructural and portal services

Citation: Bakker R, Tiesinga P, Diesmann M and Wachtler T (2013). Setting up a web-based neuroscience database has never been easier:
The CoCoMac engine goes open source. Front. Neuroinform. Conference Abstract: Neuroinformatics 2013. doi: 10.3389/conf.fninf.2013.09.00099

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Received: 08 Apr 2013; Published Online: 11 Jul 2013.

* Correspondence: Dr. Rembrandt Bakker, Radboud University Nijmegen, Dept. of Neuroinformatics, Donders Institute for Brain, Cognition and Behaviour, Nijmegen, Netherlands, r.bakker@donders.ru.nl