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neurobank
neurobank is the Meliza lab’s data management system. It’s designed for neural and behavioral data, but could be used for other kinds of experiments. The software helps generate unique identifiers for data resources, including stimuli, protocols, and recording units. No more guessing what version of a stimulus you presented in an experiment, where you stored an important recording, and whether you’ve backed it up or archived it.
You can think of neurobank like git for your data. Every resource gets a unique identifier and doesn’t get changed once the identifier is assigned. This provides you with the confidence that some stimulus “xyzzy” that you used in an experiment in 2005 is the same as the one you used last week.
What are resources? Resources include sources, which are used to control an experiment, and data, which result from running the experiment. Resources do not include things that evolve, like code, figures, or manuscripts. These should be managed in a standard version control system.
There are two components to the neurobank system. One part is the registry, a service that stores identifiers, ensures they’re unique, and resolves identifiers to the location where the resource is stored. django-neurobank is an implementation of this service that uses a postgres backend and the django REST framework. This package provides a simple python and commandline interface for interacting with the registry.
The second component is an archive, a storage and retrieval mechanism, which is also provided by this package. We keep our archives on a filesystem shared over NFS to our local compute cluster for fast, filesystem-based access. These archives have a simple directory structure with a little nesting so that you don’t have single directories filling up with hundreds of thousands of files. This package also provides some mechanisms for moving older data to and from cold storage on tape.
The full documentation, with guides to each task and references for the command line and the Python interface, is at https://neurobank.readthedocs.io/.
Installation
For the neurobank CLI, it’s recommended to install using pipx or uv tool. To use the Python interface, pip install neurobank>=1.0,<2 or add it to your pyproject.toml.
neurobank runs on Linux, macOS and Windows, but archive management requires a POSIX filesystem, so the Windows client only supports read operations.
A quick tour
Most commands need a registry, given with -r or the NBANK_REGISTRY environment variable, and the registry may need credentials, given with -a username:password or in your .netrc file. Check that you can reach it and who you’re authenticating as with
export NBANK_REGISTRY=https://myregistry.org/neurobank/
nbank registry infoCreate an archive, which registers it and sets up its directory (see Setting up archives):
nbank archive init /home/data/my-projectDeposit files. Each one is registered under its filename unless you ask for an automatic identifier (-A), and moved into the archive. Use -d to specify the datatype (use nbank dtype list to query the available options on your registry), --experimenter to specify who generated the resource, and --animal to specify the experimental subject. Use -k to add additional free-form, key-value metadata (see Depositing resources):
nbank deposit -d vocalization-wav --experimenter dmeliza -k condition=awake /home/data/my-project st32_1_2_1.wavFind resources, look at their records, and change their metadata (see Searching the registry):
nbank search -d vocalization-wav --experimenter dmeliza
nbank info st32_1_2_1
nbank modify -k condition=anesthetized st32_1_2_1Get the paths of the files, link them into a working directory, or copy them to a machine that can’t read the archive (see Accessing resources):
nbank locate st32_1_2_1
nbank locate -L analysis/ st32_1_2_1
nbank fetch -d stimuli/ st32_1_2_1Check archives against the registry, and copy resources between archives or to tape (see Managing archives):
nbank check archive /home/data/my-projectIn Python, nbank.core has the same operations: deposit, search, describe, update, and find_resources, which gives the path of a file for each resource, from an archive on this host or a cached download.
License
neurobank is licensed under the GNU General Public License, version 2. You still own your data files and any associated metadata. See COPYING for more details.
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Release files for neurobank 1.0.0rc1
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