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. 2024 Jun 1;80(Pt 6):439-450.
doi: 10.1107/S2059798324004881. Epub 2024 Jun 4.

Introduction of the Capsules environment to support further growth of the SBGrid structural biology software collection

Carol Herre  1 , Alex Ho  1 , Ben Eisenbraun  1 , James Vincent  1 , Thomas Nicholson  2 , Giorgos Boutsioukis  2 , Peter A Meyer  1 , Michelle Ottaviano  1 , Kurt L Krause  2 , Jason Key  1 , Piotr Sliz  1
Affiliations

Introduction of the Capsules environment to support further growth of the SBGrid structural biology software collection

Carol Herre et al. Acta Crystallogr D Struct Biol. .

Abstract

The expansive scientific software ecosystem, characterized by millions of titles across various platforms and formats, poses significant challenges in maintaining reproducibility and provenance in scientific research. The diversity of independently developed applications, evolving versions and heterogeneous components highlights the need for rigorous methodologies to navigate these complexities. In response to these challenges, the SBGrid team builds, installs and configures over 530 specialized software applications for use in the on-premises and cloud-based computing environments of SBGrid Consortium members. To address the intricacies of supporting this diverse application collection, the team has developed the Capsule Software Execution Environment, generally referred to as Capsules. Capsules rely on a collection of programmatically generated bash scripts that work together to isolate the runtime environment of one application from all other applications, thereby providing a transparent cross-platform solution without requiring specialized tools or elevated account privileges for researchers. Capsules facilitate modular, secure software distribution while maintaining a centralized, conflict-free environment. The SBGrid platform, which combines Capsules with the SBGrid collection of structural biology applications, aligns with FAIR goals by enhancing the findability, accessibility, interoperability and reusability of scientific software, ensuring seamless functionality across diverse computing environments. Its adaptability enables application beyond structural biology into other scientific fields.

Keywords: Capsule Software Execution Environment; FAIR principles; SBGrid; high-performance computing; scientific software; structural biology; structure determination.

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Figures

Figure 1
Figure 1
SBGrid platform and growth of the SBGrid collection. (a) The SBGrid platform was developed to install and upgrade a growing collection of structural biology software on computers in hundreds of academic and industrial structural biology laboratories, as well as their corresponding cloud computing resources. (b) Cumulative growth of software titles and (c) software versions in the 64-bit Linux and Intel/ARM macOS branches of the SBGrid collection. The 64-bit Linux and Intel/ARM macOS branches were established in 2003 and 2006, respectively, and gradually replaced the earlier 32-bit Linux, PowerPC-based Mac OS X and original SGI IRIX branches. Data for January 2024 were collected in February 2024, showcasing the most recent expansion of the collection.
Figure 2
Figure 2
(a) Distribution of software titles within the SBGrid collection by country of origin and their percentage share within the SBGrid collection. The total number of titles developed within each country is indicated in parentheses. The top ten applications used from March 2023 to March 2024 were developed in the United Kingdom and the United States. The applications are ranked as follows: UCSF Chimera/ChimeraX (Pettersen et al., 2004; Goddard et al., 2018; US), CCP4 (Agirre et al., 2023; UK), Phenix (Liebschner et al., 2019; US), RELION (Scheres, 2012; UK), PyMOL (Schrödinger; US), IMOD (Kremer et al., 1996; US), ProDY (Bakan et al., 2011; US), EMAN2 (Tang et al., 2007; US), Coot (Emsley et al., 2010; UK) and CCP-EM (Wood et al., 2015; Burnley et al., 2017; UK). (b) A choropleth map illustrating the distribution of software title origins within the SBGrid collection, with color intensities reflecting the quantity of software originating or predominantly originating from each country. The map underscores the wide-ranging geographical origins of the software titles compiled in the SBGrid collection.
Figure 3
Figure 3
Two actively developed branches of the SBGrid collection support 64-bit Linux and Intel/ARM macOS OS. Within each branch, software is organized through application- and version-specific subdirectories.
Figure 4
Figure 4
Modular packaging of the SBGrid collection. Each of the approximately 500 software titles is independently packaged into Capsules, isolating them from the broader system to prevent increasing complexity. The runtime environments are programmatically generated using ED files, ensuring a streamlined setup tailored to the specific needs of each software title, with exceptions noted for non-executable content.
Figure 5
Figure 5
Comprehensive illustration of the Capsules initiation and application execution process on computers in SBGrid Consortium laboratories (assuming that SBGrid has been already pre-installed with the SBGrid installation manager). This figure showcases the streamlined, single-step initiation method where users begin by executing an OS-agnostic SBGrid Startup Configuration file, compatible with bash/zsh and tcsh for various UNIX shell environments. Users can then incorporate a user-specific configuration file (.sbgrid.conf) to fine-tune software versions and preferences. Once the environment has been activated, users gain immediate, zero-configuration access to an extensive collection of executables, facilitated by the SBGrid Capsules Executable Mapper (CEM), which efficiently resolves naming conflicts between executables with identical names, ensuring smooth execution of the desired executable. This process underscores the ease-of-use approach of the SBGrid system to managing distributed computing resources.
Figure 6
Figure 6
Capsules logging of local and global application usage. The composite figure of two pie charts illustrates the distribution of host operating systems running SBGrid jobs in January 2024 on on-premises and cloud-based computers supporting the SBGrid Consortium laboratories. It shows operating systems with shares over 1% and an aggregate ‘Others’ category that accounts for operating systems each under 1%. (a) The pie chart illustrates the percentage of user-hosting operating systems, filtered by unique hosts, running approximately four million SBGrid jobs in January 2024. (b) The pie chart shows OS usage by jobs running a molecular-visualization application in January 2024. The log analytics reveal that more users run the molecular-visualization application on Mac than on Linux. Notably, CentOS-7 maintains the second-largest share in both (a) and (b) despite its declining usage following the announcement that it will reach end of life (EOL) in June 2024, reflecting its prior prominence in high-performance computing and scientific computing environments due to its long-term stability.
Figure 7
Figure 7
Monthly usage metrics for the same molecular-visualization title as reported in Fig. 6 ▸(b). This figure charts the usage of a molecular-visualization application from January 2023 to January 2024. It shows the number of application versions used, including minor releases, and the number of unique host OSs on which the application runs. These data points are plotted on the left y axis as solid lines. On the right y axis, the figure displays the monthly count of sites and users engaging with the application, indicated by dashed lines.
Figure 8
Figure 8
The SBGrid installation manager provides an intuitive and user-friendly interface that serves as the primary platform for both individual users and system administrators to manage SBGrid software. An efficient, secure and scalable tool for installation and maintenance tasks, it supports a variety of functions, including the activation of new installations with provided credentials, diagnostics and installing and updating, as well as removing, software.
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