HCO-db database


We stored our simulation files into an archive and the characteristics of the simulated instances into a database (HCO-db). This page describes the contents of the HCO-db database of 10.5 million HCO model instances. The construction and analysis of the database are described in detail in


Doloc-Mihu A, Calabrese RL (2011). A database of computational models of a half-center oscillator for analyzing how neuronal parameters influence network activity. J Biol Phys, Springer, 37(3): 263-283 [PubMed].


·         HCO archive

·         HCO-db database


HCO archive

We stored our simulation data (files) into an archive. For fast access to these files, we organized the archive into folders and sub-folders. There are 100 folders called sim1 to sim100. Each of them (except the last one) contains 100 subfolders named sim_1 to sim_100. Each subfolder contains all the files corresponding to 1,050 simulated instances.


Each simulated instance has generated between 4 to 6 files, depending on the activity type. The names of these files start with the name of the respective instance, followed by file content information. On average, the files of a simulated instance occupied about 6MB space on disk.


To save storage space, for each simulated instance we recorded its voltage traces and the conductances of ISynS, Ih, and ICaS of both neurons in a binary file (a binary files has a smaller size than an ASCII file); further, we used a disk_out format to be able to compress it. For compressing the binary (voltage) files, we used Flac (Free Lossless Audio Codec). The total size of the entire archive of the files of our 10,485,760 simulated instances was 2.4TB.


The archive is freely available for interested researchers. Because of its size, it is not practicable to download the archive over the internet. Instead, we are happy to send a set of DVDs that include a copy of the archive to anybody who is interested upon e-mail request to Anca Doloc-Mihu (adolocm at


HCO-db database

We built an efficient relational MySQL database table (HCO-db) with the resulting HCO instances characteristics. To build the database and to record the characteristics and the parameters of each simulated model instance into this database, we used our own Java 1.5 scripts.


For each simulated instance, the script read the characteristics of the instance from its ASCII file and recorded them into a row of the database. Each model in the database has its own unique identifier (unique number which also is a primary key in the database), which makes it easier to query. In addition for efficient querying, we used another 13 indexes: for each parameter, for each neuron type, and for the system type (group label).


We chose the optimal data type for each field in the database to minimize the storage space required and to speed up the querying process. For example, the parameter values weren't recorded as floating point values, but as small integers which gave the percents of the parameter values with respect to their canonical values. Also, we did not record the spike files and the voltage files into the database; we just recorded a pointer to the place in the archive where they reside (the name of the folder/subfolder for each model). The recorded data occupied approximately 2 GB and the indexes occupied 1 GB; our database has a total size of approximately 3.06 GB. Click here to see the structure of HCO-db.


The HCO-db is freely available for interested researchers. Download the HCO-db files here. (coming soon!)

Last updated July 15, 2012. Please send comments to