openBIS (open Biology Information System) is a framework designed for managing and analyzing biological data. It is an open-source platform developed primarily for the life sciences community to handle large volumes of experimental data generated in fields such as genomics, proteomics, and imaging. Overall, openBIS aims to streamline the management and analysis of biological data, facilitating collaboration and accelerating scientific discovery in the life sciences domain.

FreeBSD is a free and open-source Unix-like operating system known for its reliability and stability. It is optimized for performance, especially in networking and disk storage devices.

The Z File System (ZFS) transcends the conventional definition of a file system, representing a paradigm shift in storage management. Combining the traditionally separate roles of volume manager and file system provides ZFS with unique advantages. By comprehending the underlying disk structure, ZFS facilitates the creation of file systems that draw from a shared pool of storage devices. This awareness of physical disk layout enables automatic expansion of existing file systems upon the addition of new disks to the pool, seamlessly integrating the newfound storage capacity. Moreover, ZFS empowers users to tailor specific properties to each storage pool, fostering the creation of datasets rather than relying on a single, monolithic file system. Such granular control enhances flexibility and efficiency in storage allocation and management.

Introduction

Because of its architecture, openBIS is highly scalable. It is capable of storing and providing access to large volumes of data and is configured for distributed storage. By default, raw data and result data are stored in the data store, which is a managed flat-file system. openBIS utilizes a hybrid data repository, where the flat-file data store is augmented with a relational database management system for indexing information, metadata, and selected results. The basic openBIS deployment consists of two servers, the Application Server (AS) and the Data Store Server (DSS). Generally speaking, the AS manages the metadata and links to the data while the DSS manages the data itself.

Data Store

FreeBSD and ZFS filesystem

zpool

Relational Database Management System

postgres

openBIS Deployments

To provide safe environment, separate from the rest of the system. Processes created in the chrooted environment can not access files or resources outside of it. For that reason, compromising a service running in a containarized environment should not allow the attacker to compromise the entire system.

within FreeBSD native jail

AppJail is a framework to create isolated, portable and easy to deploy environments using FreeBSD jails that behaves like an application.

$ pkg install appjail;
$ sysrc appjail_enable="YES";
$ tzsetup;

within FreeBSD Linux binary compatibility jail

Enable and start the Linux ABI. The Linux service will load necessary kernel modules and mount filesystems expected by Linux applications under /compat/linux.

$ sysrc linux_enable="YES";
$ sysrc linux_mounts_enable="YES";
$ service linux start;

Linux software requires more than just an ABI to work. In order to run Linux software a Linux userland must be installed and local timezone must be set.

$ pkg install debootstrap appjail;
$ tzsetup;

AppJail is a framework to create isolated, portable and easy to deploy environments using FreeBSD jails that behaves like a Linux application.

$ sysrc appjail_enable="YES";
$ printf \
  'exec.start: "/bin/true"\nexec.stop: "/bin/true"\npersist\n' \
  > /etc/linux.conf;
$ appjail fetch debootstrap jammy;
$ appjail quick openbis \
  osversion=jammy type=linux+debootstrap \
  start linuxfs alias ip4_inherit devfs_ruleset=0 template=/etc/linux.conf 
  login;

References

1. openBIS: a flexible framework for managing and analyzing complex data in biology research
   • Bauch A., Adamczyk I., Buczek P., Elmer F.-J., Enimanev K., Glyzewski P., Kohler M., Pylak T., Quandt A., Ramakrishnan C., Beisel C., Malmström L., Aebersold R. and Rinn B.; BMC Bioinformatics 2011 12:468

2. openBIS Documentation - ETH Zurich Scientific IT Services; 2024

3. FreeBSD Jails and Containers - FreeBSD Community; 1994-2024

4. FreeBSD Linux Binary Compatibility - FreeBSD Community; 1994-2024

5. AppJail is a framework to create isolated, portable, and easy-to-deploy environments - Jesús Daniel Colmenares Oviedo; 2022-2023