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

[Kathy Reid]

Adding my support to this grant application, and some additional 
background information.

Publishing in open access research journals is not free.

The journals - most of whom are owned by a small handful of academic 
publishers - Elsevier, Wiley, Springer, Taylor and Francis and SAGE - 
charge academics an "Article Processing Charge" for each article they 
submit to a journal, even though it might be open access. This ranges by 
journal for the fee, which for prestigious journals can be upwards of 
$AUD 3000.

Academics provide peer review for these journals, usually for free. Yes, 
if you're wondering if academics provide the content and labour for the 
journal, and have to pay for the privilege, you're absolutely right - 
it's a huge bone of contention in academia.

Some institutions will enter into arrangements via subscription where 
the APC is waived as part of the subscription, but it's usually only 
larger institutions that can afford to do this, and I suspect the 
Australian Museum is not one of them.

PhDs, as Guoyi is, often have limited funds to spend on APCs, even 
though *getting* a PhD is usually dependent on being published.

At a broader level, Open Access in academia is a huge issue of inequity 
and academic labour providing huge profits for publishers. At a grant 
level, I think we're doing the right thing by being supportive of a 
single researcher's efforts.


Kind regards,

Kathy Reid




On 12/9/26 19:16, Miles Goodhew via linux-aus wrote:
> 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
>> 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
>> 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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>> *Attachments:*
>>
>>   * 6aa3880502cd1.csv
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