MorphDepot and its points of interaction for new software developments in the field of single cell research.
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1
Ludwig-Maximilians-Universität, Department Biology II, Germany
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2
Fukuoka University, Department of Earth System Science, Japan
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3
University of Hyogo, School of Human Science and Environment, Japan
Does “being a neuroscientist” imply “being a computer scientist” (or “being a programmer”)? Reasonable evidence for that statement provides the fact that neuroscientific progress increasingly depends on data management efforts that involve storing and structuring data, querying and analyzing data, exchange of data, and re-analysis of previously recorded data – all within the digital world. In order to avoid this statement coming true and to enable the neuroscientist to keep focused on neuroscientific questions, we need an ecosystem of scientific software tools that can integrate modern developments fast and that is capable of being integrated into the scientists workbench without deep knowledge of computer science.
We present “MorphDepot” [1], a Python package for managing morphological data together with corresponding single cell recordings, that was designed with focus on two aspects: (1) software implementation was as tightly as possible aligned to neuroscientific use cases in order to minimize developmental overhead; (2) we designed various software interfaces in order to maximize impact and usability of the tool. In particular, three levels of interaction for MorphDepot with other software or with the scientist are provided: (1) a file-system level, (2) an application programming interface (API) level, (3) and a graphical user interface (GUI) level. Each level supports specific use cases: (1) the file-system level provides the possibility to use a diversity of software that operates on files and directories, such as file manager, image viewer, specific analysis software, version control systems, or synchronization software; (2) the API level provides the possibility of communication between different software, applications, or scripts, including web services. This allows integration of analysis tools and automation of scientific workflow processes; (3) the GUI-level provides a direct interface of a specific service for a scientist, for example by a web application.
As a reference system, MorphDepot supports the GinJang project [2] in managing morphological data successfully between two INCF-nodes, J-Node [3] and G-Node [4].
With this software architecture, we add a tool to the ecosystem of neuroscientific software that integrates smoothly with established tools and allows the scientist to focus on neuroscience instead of computer science.
[1] https://github.com/G-Node/MorphDepot
[2] http://projects.g-node.org/ginjang/
[3] http://www.neuroinf.jp
[4] http://www.g-node.org/
Acknowledgements
Supported by the Federal Ministry of Education and Research (BMBF, grant 01GQ0801 and grant 01GQ1116) and Strategic International Research Cooperative Program, Japan Science and Technology Agency JST.
Keywords:
neuroinformatics,
Databases as Topic,
morphological computation,
Electrophysiology,
Data Collection
Conference:
Neuroinformatics 2013, Stockholm, Sweden, 27 Aug - 29 Aug, 2013.
Presentation Type:
Poster
Topic:
Infrastructural and portal services
Citation:
Rautenberg
PL,
Sobolev
A,
Stoewer
A,
Kazuki
K,
Ai
H,
Ikeno
H and
Wachtler
T
(2013). MorphDepot and its points of interaction for new software developments in the field of single cell research..
Front. Neuroinform.
Conference Abstract:
Neuroinformatics 2013.
doi: 10.3389/conf.fninf.2013.09.00049
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Received:
26 Apr 2013;
Published Online:
11 Jul 2013.
*
Correspondence:
Dr. Philipp L Rautenberg, Ludwig-Maximilians-Universität, Department Biology II, Planegg-Martinsried, Germany, philipp.rautenberg@gmail.com