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<p>Adding my support to this grant application, and some additional
background information. </p>
<p>Publishing in open access research journals is not free. </p>
<p>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. </p>
<p>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. </p>
<p>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. </p>
<p>PhDs, as Guoyi is, often have limited funds to spend on APCs,
even though *getting* a PhD is usually dependent on being
published. </p>
<p>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. </p>
<p><br>
</p>
<p>Kind regards, </p>
<p>Kathy Reid</p>
<p><br>
</p>
<br>
<p><br>
</p>
<div class="moz-cite-prefix">On 12/9/26 19:16, Miles Goodhew via
linux-aus wrote:<br>
</div>
<blockquote type="cite"
cite="mid:50ecfbf0-0c43-45d2-8926-533ef030cd57@app.fastmail.com">
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<div>Hi All,</div>
<div> 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).</div>
<div> To summarise my understanding of the application:</div>
<div> Guoyi Zhang is seeking Linux Australia (LA) financial
sponsorship for publishing the open source Willi26 tool into
open-access research journals.</div>
<div> 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.</div>
<div> 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.</div>
<div> 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.</div>
<div><br>
</div>
<div>Thanks for the application!</div>
<div><br>
</div>
<div>M0les.</div>
<div><br>
</div>
<div>On Fri, 11 Sep 2026, at 14:48, Linux Australia Website via
linux-aus wrote:</div>
<blockquote type="cite" id="qt" style="">
<div>Your Email Address: <a
href="mailto:starsareintherose@outlook.com"
moz-do-not-send="true" class="moz-txt-link-freetext">starsareintherose@outlook.com</a></div>
<div>Project name: Willi26: An Open-Source Phylogenetic
Interpreter in Rust for Research and Education</div>
<div>Grant Type: Project Grant</div>
<div>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.</div>
<div>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.</div>
<div>Willi26 aims to begin filling this gap by developing a
modern, open-source maximum-parsimony phylogenetic interpreter
in Rust.</div>
<div>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.</div>
<div>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.</div>
<div>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.</div>
<div>Estimated cost breakdown of the project: - Rust software
development and testing — A$0 requested (applicant in-kind
contribution)</div>
<div>- Computing resources and software — A$0 requested
(existing resources and open-source tools)</div>
<div>- Source-code hosting and distribution — A$0 requested</div>
<div>- Documentation — A$0 requested (applicant in-kind
contribution)</div>
<div>- Open-access publication and dissemination (e.g., PeerJ,
Plos one, Royal Society Open Science) — approximately A$1,100</div>
<div>- Total requested from Linux Australia — approximately
A$1,100</div>
<div>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.</div>
<div>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.</div>
<div>Zhang has extensive experience in developing and
maintaining open scientific software. She is the developer of <a
href="http://guoyi.run" moz-do-not-send="true">guoyi.run</a>
(<a href="https://github.com/starsareintherose/TNT_Script"
moz-do-not-send="true" class="moz-txt-link-freetext">https://github.com/starsareintherose/TNT_Script</a>),
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.</div>
<div>She also leads the development of BioArchLinux (<a
href="http://bioarchlinux.org" moz-do-not-send="true">bioarchlinux.org</a>),
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.</div>
<div>Zhang is also the developer of GBEPP (<a
href="https://github.com/starsareintherose/RGBEPP"
moz-do-not-send="true" class="moz-txt-link-freetext">https://github.com/starsareintherose/RGBEPP</a>),
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.</div>
<div>Willi26 (<a href="https://crates.io/crates/willi26"
moz-do-not-send="true" class="moz-txt-link-freetext">https://crates.io/crates/willi26</a>)
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.</div>
<div>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.</div>
<div>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.</div>
<div>First Name: Guoyi</div>
<div>Last Name: Zhang</div>
<div>Email Address: <a href="mailto:guoyi.zhang@austmus.gov.au"
moz-do-not-send="true" class="moz-txt-link-freetext">guoyi.zhang@austmus.gov.au</a></div>
<div>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.</div>
<div>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.</div>
<div>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.</div>
<div>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.</div>
<div><br>
</div>
<div>_______________________________________________</div>
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<div><b>Attachments:</b></div>
<ul>
<li>6aa3880502cd1.csv</li>
</ul>
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