[Linux-aus] Grant Application from Guoyi Zhang for Willi26: An Open-Source Phylogenetic Interpreter in Rust for Research and Education

Sun Sep 13 02:55:16 AEST 2026

Hi M0les

Thank you very much for your support. Yes, your summary is correct. Regarding the amount, AUD 1,100 should be sufficient if the manuscript is published in PeerJ, but it would not fully cover the publication fee for PLOS ONE.

I am also conscious that I do not want this application to place an unnecessary financial burden on LA. However, I would be very happy to follow your suggestion: having a higher amount available if LA allows, drawing only what is actually required for publication, and returning any unused remainder to LA.

For acknowledgement, I currently plan to acknowledge Linux Australia’s financial support in the resulting publication, at the beginning of the Willi26 Git repository, and in the footer of the Willi26 website, as I have routinely done for previous support. I would also be happy to report the progress and eventual outcome back to LA.

Thanks again for your interest and support!

Best regards,
Guoyi

________________________________
From: Miles Goodhew <linux at m0les.com>
Sent: Saturday, September 12, 2026 7:16 PM
To: Guoyi Zhang <Guoyi.Zhang at australian.museum>; committee at lists.linux.org.au <committee at lists.linux.org.au>; Linux-Aus <linux-aus at lists.linux.org.au>
Cc: Linux Australia Website <grant-applications at linux.org.au>
Subject: Re: [Linux-aus] Grant Application from Guoyi Zhang for Willi26: An Open-Source Phylogenetic Interpreter in Rust for Research and Education

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Hi All,
  I'll stress that I'm not really an academic and thus not deeply familiar with the whole academic publishing scene (and I'm particularly unfamiliar with phylogenetics and associated areas of research).
  To summarise my understanding of the application:
  Guoyi Zhang is seeking Linux Australia (LA) financial sponsorship for publishing the open source Willi26 tool into open-access research journals.
  To the best of my determination Guoyi is accomplished in her field, the Willi26 tool seems a useful piece of open source software, the 3 cited journals (PeerJ, Plos One and Royal Society Open Access) are all open-access.
  Unless I'm missing something outside my scope of experience, I'm in favour of LA approving this application. Obviously we'd expect the usual acknowledgement for the support from LA in the publication and progress/result reporting back.
  The only qualification I'd add is that the requested sum ($1100) is on the low side for some of the cited journals. It might be safer to have a higher amount that can be drawn from as-needed and any unused remainder returned to LA.

Thanks for the application!

M0les.

On Fri, 11 Sep 2026, at 14:48, Linux Australia Website via linux-aus wrote:
Your Email Address: starsareintherose at outlook.com<mailto:starsareintherose at outlook.com>
Project name: Willi26: An Open-Source Phylogenetic Interpreter in Rust for Research and Education
Grant Type: Project Grant
Aim of the project: Understanding how organisms are related through evolution is fundamental to biology. Evolutionary trees are used not only in modern genomic research but also by palaeontologists and taxonomists documenting biodiversity from fossils and morphological characteristics. For many of these researchers, maximum parsimony (MP), a conceptually simple approach that compares alternative evolutionary trees and seeks those requiring the fewest character changes, remains an important method of phylogenetic analysis.
Despite this continuing use, researchers working with morphological data still depend heavily on closed-source software. Several open-source implementations of fast MP tree searching exist, including MPBoot and oblong, but these are primarily command-line analysis programs rather than interactive phylogenetic environments. This makes complicated analytical procedures involving successive tree searches, character manipulation, tree manipulation and exploration considerably more difficult to implement. In practice, much morphology-based phylogenetic research continues to depend on closed-source programs, including TNT, PAUP*, NONA and Hennig86. There is currently no widely adopted open-source MP interpreter providing a comparable interactive workflow.
Willi26 aims to begin filling this gap by developing a modern, open-source maximum-parsimony phylogenetic interpreter in Rust.
The first stage of development takes Hennig86 as its starting point. Hennig86 is one of the most historically influential implementations of computational cladistics and was an important predecessor to TNT, which is now widely used for morphology-based phylogenetic analysis. Its relatively compact functionality also provides a realistic and clearly defined starting point for building a new interpreter. Willi26 will first reproduce and validate this established MP environment and then use it as a foundation for developing a modern open-source alternative capable of increasingly sophisticated contemporary phylogenetic workflows and, in the longer term, competing with established closed-source software.
Opening this computational framework also has value beyond professional phylogenetic research. The basic logic of maximum parsimony is comparatively easy to demonstrate: given observations about a set of organisms, different evolutionary trees can be compared by counting the changes required to explain those observations. The same open-source algorithms developed for Willi26 can therefore provide a reusable foundation for future educational tools that allow school students, university students and biologists without specialist computational training to interactively explore evolutionary trees and understand how biologists reconstruct evolutionary history.
An important final stage will be bringing Willi26 to the scientific communities that could actually use it. Simply publishing source code in a repository is unlikely, by itself, to reach the palaeontologists and taxonomists who currently rely on established closed-source software. We therefore plan to accompany the open-source release with a peer-reviewed, open-access publication in an established scientific journal, documenting and validating the software and introducing it directly to its intended research community. An open-access publication is particularly consistent with the project's objective: both the software itself and the scholarly documentation explaining and validating it should be freely accessible.
Estimated cost breakdown of the project: - Rust software development and testing — A$0 requested (applicant in-kind contribution)
- Computing resources and software — A$0 requested (existing resources and open-source tools)
- Source-code hosting and distribution — A$0 requested
- Documentation — A$0 requested (applicant in-kind contribution)
- Open-access publication and dissemination (e.g., PeerJ, Plos one, Royal Society Open Science) — approximately A$1,100
- Total requested from Linux Australia — approximately A$1,100
Project team details: Willi26 is currently a single-developer open-source project led by Guoyi Zhang, a PhD researcher at the Australian Museum working in evolutionary biology, systematics, and computational phylogenetics.
Zhang's research focuses on phylogenetics, evolutionary biology, and the development of computational approaches for analysing biological data. This combination of domain expertise and software development is directly relevant to Willi26, which requires both an understanding of maximum-parsimony methodology and the ability to translate established phylogenetic algorithms into tested, maintainable software.
Zhang has extensive experience in developing and maintaining open scientific software. She is the developer of guoyi.run<http://guoyi.run/> (https://github.com/starsareintherose/TNT_Script), an openly available tool providing a reproducible, one-step workflow for maximum-parsimony phylogenetic analyses using TNT. The associated peer-reviewed publication receives more than ten citations annually. This work has provided direct experience with the practical use, scripting, and reproducibility limitations of contemporary maximum-parsimony software and helped motivate the development of a fully open-source alternative.
She also leads the development of BioArchLinux (bioarchlinux.org<http://bioarchlinux.org/>), a Linux-based open-source software repository dedicated to bioinformatics and computational biology. BioArchLinux is a collaborative project with contributions from more than ten developers, giving Zhang direct experience in coordinating development and maintaining scientific software within an open-source community. It has grown into one of the largest independently maintained Linux distribution repositories dedicated to bioinformatics software. The project and its underlying approach have been described in Bioinformatics, the flagship journal of the International Society for Computational Biology.
Zhang is also the developer of GBEPP (https://github.com/starsareintherose/RGBEPP), an open-source phylogenomics pipeline built with Nextflow and D that provides reproducible processing of phylogenomic datasets. Together, these projects demonstrate experience spanning open-source software development, Linux software packaging and distribution, reproducible scientific workflows, and phylogenetic computation.
Willi26 (https://crates.io/crates/willi26) extends this existing work from reproducible workflows and software distribution to the underlying phylogenetic software itself. It is being written in Rust, combining memory safety and modern software-engineering practices with efficient native execution and cross-platform portability.
All Willi26 source code will be maintained in a publicly accessible repository under an open-source licence. Its development history, documentation, examples, issue tracking, and releases will also remain public, enabling users and other developers to inspect, test, reuse, and contribute to the project.
The longer-term objective is to establish a maintainable open-source alternative for maximum-parsimony phylogenetics that can be extended by both the scientific and open-source communities.
First Name: Guoyi
Last Name: Zhang
Email Address: guoyi.zhang at austmus.gov.au<mailto:guoyi.zhang at austmus.gov.au>
A statement including a willingness to provide regular project updates on the project: I am willing to provide regular updates to Linux Australia and the wider community throughout the development of Willi26.
Project progress will be publicly visible through the open-source repository, including source-code development, issues, documentation, testing, and software releases. I will also provide periodic project updates describing major milestones, including implementation of core Hennig86 or even TNT functionality, validation against existing maximum-parsimony software, public releases, documentation and progress towards the open-access software publication.
At the completion of the funded project, I will provide a final update summarising the work completed, the outcomes of the project, links to the source code and documentation, validation results, software releases, and any resulting scholarly publication.
I am also willing to share the outcomes with the Linux Australia community and to acknowledge Linux Australia's support in the project repository, documentation, and resulting publication.

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