SciDB, Java and Matlab

Hello SciDB community,
I’m a super new to SciDB, so please forgive me for my not-existing knowledge.
We are looking for a database where to store our data (as in vectors, matrices) and SciDB looks pretty promising.

I’ve looked around and I have not found too much documentation regarding the java library for SciDB and using SciDB from Matlab.
Here are my questions:

  • can SciDB be accessed from Matlab? if so, how are the performances?
  • is the SciDB java library available as a stand alone installation? …and does it work with the latest version 19.3?
  • can we use a SciDB instance both from Matlab and Python, meaning is there any known issues saving data from one environment and retrieving them from the other and/or viceversa?

Thank you so much for any help in advance.
I do really hope that SciDB can be the tool that we have been looking for in the past year or so.


Happy to hear that your search has led you to us. Hope our solutions can suffice your matrix / vector storage needs.

Let me provide a few links / pull in a few more people that might be able to help:

  • I use scidbR (install using devtools::install_github("Paradigm4/SciDBR")) for storing matrix and vector data at the REVEAL/Genomics R API for managing multi-omics data.
  • Others have used scidb-py for similar work.

Now to answer your questions:

Yes, that is one of the important features of scidb – one can program it from multiple languages, thus allowing data storage in a common language agnostic location.

In one recent project, we first used scidb-R / scidb-py for regular interactive analysis with the data. Then once a set of internal database queries were finalized (e.g. a series of AFL calls to constitute a workflow), we passed those AFL calls directly from MATLAB to scidb via our web-client shim. Note that scidb-R and scidb-py also invoke shim under the hood.

  • See this post about JDBC connector usage in 18.1. The binaries for 19.3 are available at the downloads page for 19.3. Will check internally to see if we have any updates to the JDBC docs for scidb.