There’s good news for MorphoBank users. Twenty years after its initial release, the tried-and-tested phylogenetic research tool has new and improved application architecture, new functionality, and an intuitive modern interface.
Why did MorphoBank need an update?
MorphoBank is an essential and trusted tool for phylogenetics researchers, including those working in comparative biology, paleontology, anthropology, and tree-of-life research. It doubles as a powerful tool used to create morphological matrices and a long-term repository of open access morphological data.
“MorphoBank is a valuable community-led platform that is integral to ensuring that paleontological research data are published in a fashion that facilitates reproducibility and reusability.” Dr. Bryan Gee, Burke Museum at the University of Washington
“MorphoBank is a valuable community-led platform that is integral to ensuring that paleontological research data are published in a fashion that facilitates reproducibility and reusability,” said Dr. Bryan Gee of the Burke Museum at the University of Washington. Gee routinely publishes data on MorphoBank and reuses the information that other researchers have shared in the database. He added that attempting to reuse data published elsewhere, in less optimal platforms and formats, can be a struggle.
But more than 20 years after its initial founding, MorphoBank was due for a refresh. Including improvements both to application architecture and user interface design.
“The old MorphoBank platform was built on a monolithic PHP architecture meant for much smaller datasets,” explained Xingguo Chen, Phoenix Bioinformatics staff software engineer and technical lead for the project. Phoenix Bioinformatics is the nonprofit organization that hosts MorphoBank, along with several other digital tools for scholarly research.
Over time, as researchers added tens of thousands of images, matrices, and taxa, to MorphoBank it became harder to maintain and slower under heavy use.
“We wanted to modernize the system for better performance, security, and scalability. And to make it easier to evolve with new research workflows and larger data volumes,” Chen said.
The new MorphoBank is a complete rebuild using modern open-source technologies like Vue 3, Node.js/Express, MySQL/Aurora, and Docker. Some of the biggest improvements include:
- Faster performance through an API-driven design, database optimization, and CDN caching.
- Modern UI/UX with a clean, mobile-friendly interface for projects, matrices, and images.
- Scalable backend using containerized services and AWS Aurora for reliability.
“The platform is much faster for all tasks such as browsing and loading any projects. New tools were added for analysis as well,” said Kartik Khosa, a fullstack software engineer with Phoenix.
The role of the MorphoBank community
The team identified these specific areas for improvement based on user feedback, which focused on slow page loads and workflow bottlenecks, Chen said.
MorphoBank community members including frequent contributors and curators were active in the re-platforming process, influencing both design and functionality of the new site. Early on, user focus groups helped identify and prioritize needs. Later, a public beta test invited feedback from the broader community, who were helpful in flagging use cases the team hadn’t considered or fully tested.
“The team running MorphoBank has been very responsive to user feedback. I very much look forward to using what I expect will be a faster and improved interface,” said Dr. Robert Asher, a researcher at Cambridge University. Asher has contributed 10 projects to MorphoBank over 18 years.
“I routinely benefit from the platform features, data and metadata standards, and partnership with society journals, as well as the responsiveness of the MorphoBank team to suggestions and questions,” said Gee. Gee has contributed 12 projects to date, beginning in 2019.
Technological hurdles
One major challenge was relocating the data to Amazon S3, Khosa said. The old platform held all user data on disk. Given the amount of data being added each month, that was quickly becoming unsustainable. The migration was complex, but well worth the effort, Khosa said. The improved efficiency and cost savings all help to keep MorphoBank fully open access and free to use.
“The biggest surprise was how complex the matrix system really is,” Chen said. While it may look like a simple table, the MorphoBank matrix editor supports polymorphic states, dependencies, annotations, linked images, and real-time collaboration.
“Rebuilding all that in a modern web stack meant rethinking the data model and workflows from scratch. It gave us a new appreciation for how much scientific and technical detail the original system had, and how deeply researchers rely on those nuances.”
Help drive future progress at MorphoBank
MorphoBank is an open-source project supported by members and a grant from the National Science Foundation. All our tools are free to use, and everything in MorphoBank is fully Open Access. That’s only possible because of the support of our member libraries and museums. Contact us to learn more about membership.
Going forward, the Phoenix Bioinformatics technical team has big plans, if funding permits. We aim to continue expanding matrix creation editing options, including adding support for more data formats and improving scoring efficiency.
