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project.html
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<!DOCTYPE html>
<html lang="en" dir="ltr">
<head>
<!--site description-->
<meta charset="utf-8" />
<meta name="viewport" content="width=device-width, initial-scale=1.0" />
<title>Heru Handika | I Study Non-Charismatic Mammals</title>
<meta
name="description"
content="I study small mammals in Southeast Asia. My research focus on documenting species diversity, understanding patterns of species distribution
across space and time, and species adaptation to novel environment."
/>
<meta
name="keywords"
content="species, biodiversity, evolution, adaptation, novel environment, biology, Southeast Asia"
/>
<meta name="author" content="Heru Handika" />
<!-- CSS and other external libraries -->
<link
href="https://fonts.googleapis.com/css?family=Lora&display=swap"
rel="stylesheet"
/>
<link
href="https://fonts.googleapis.com/css?family=Montserrat&display=swap"
rel="stylesheet"
/>
<link
href="https://cdn.jsdelivr.net/npm/[email protected]/dist/css/bootstrap.min.css"
rel="stylesheet"
integrity="sha384-Zenh87qX5JnK2Jl0vWa8Ck2rdkQ2Bzep5IDxbcnCeuOxjzrPF/et3URy9Bv1WTRi"
crossorigin="anonymous"
/>
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rel="apple-touch-icon"
sizes="180x180"
href="icons/apple-touch-icon.png"
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type="image/png"
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<body>
<div class="top" id="top-proj">
<!-- Navigation Menu -->
<nav class="navbar fixed-top navbar-expand-lg navbar-dark">
<button
class="navbar-toggler"
type="button"
data-bs-toggle="collapse"
data-bs-target="#navbarTogglerDemo03"
aria-controls="navbarTogglerDemo03"
aria-expanded="false"
aria-label="Toggle navigation"
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<span class="navbar-toggler-icon"></span>
</button>
<div class="collapse navbar-collapse" id="navbarTogglerDemo03">
<ul class="navbar-nav mx-auto">
<li class="nav-item">
<a class="nav-link" href="index.html">About</a>
</li>
<li class="nav-item">
<a class="nav-link active" href="project.html">Projects</a>
</li>
<li class="nav-item">
<a class="nav-link" href="pub.html">Publications</a>
</li>
<li class="nav-item">
<a class="nav-link" href="teaching.html">Teaching & Outreach</a>
</li>
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<a class="nav-link" href="fieldwork.html">Fieldwork</a>
</li>
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<a class="nav-link" href="code.html">Code</a>
</li>
<li class="nav-item">
<a class="nav-link" href="contact.html">Contact</a>
</li>
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</nav>
</div>
<!-- Navigation Menu ends -->
<!-- Body Contents -->
<div class="content">
<div class="row align-items-center">
<div class="col-md-6 col-sm-12">
<h2 class="project">Small Mammal Diversity & Evolution</h2>
<h3 class="project">
Understanding patterns that generate species diversity within a
complex island system
</h3>
<!-- columns for each section. Sum 12 for all columns for large and 12 for each for small to turn columns into rows -->
<p class="project">
Indo-Australian Archipelago is among the most complex island system
on earth. Some islands, such as Sumatra, Java, and Borneo, were
continuous landmass during the Pleistocene low see level, called
Sunda Shelf. Sulawesi was separate islands. Other islands never been
connected to other landmasses, such as the Moluccas and Lesser Sunda
islands. Within the islands, isolated mountains present more
opportunities for speciation. We work on deciphering small mammal
diversity and evolution in this complex island system, with
particular focus on Sulawesi and the Sunda Shelf.
</p>
</div>
<div class="col-md-6 col-sm-12">
<div class="img-padded">
<img
src="img/b_coelestis.webp"
alt="A photo of Bunomys coelestis"
class="img-fluid rounded"
/>
</div>
</div>
</div>
<div class="row align-items-center">
<div class="col-md-6 col-sm-12">
<img
src="img/l_meyeri.webp"
alt="A photo of Lenomys meyeri"
class="img-fluid rounded"
width="400px"
/>
</div>
<div class="col-md-6 col-sm-12">
<h4 class="project">Project 1</h4>
<h3 class="project">
In situ diversification of Hill Rats (<i>Bunomys</i>) on Sulawesi
</h3>
<p class="project">
The hill-rat species group, also referred as the
<i>Bunomys</i> Clade, is the most diverse endemic rodent group on
Sulawesi. From a single known colonizing ancestor, the group has
diversified into 18+ species. Some species occur throughout the
island. The other species are restricted to a single area of
endemism or only known from a single mountain. This project is the
main focus of my PhD. We hope to understand how complex geological
history of Sulawesi shaped the diversity of the group. Our
understanding of this process will help us to understand the
evolution of small mammals in complex island systems. It will also
provide an improved understanding of species distribution to inform
conservation efforts on Sulawesi.
</p>
<p class="project">
Publications:<br />
Handika et. al. (In prep)<br />
<a href="https://doi.org/10.1111/zsc.12460" target="_blank"
>Handika et. al. (2021)</a
>
</p>
</div>
<hr />
</div>
<div class="row align-items-center">
<div class="col-md-6 col-sm-12">
<h2 class="project">Inclusive Open Source Software</h2>
<h3 class="project">Accessible software empowering new learners</h3>
<p class="project">
From fieldwork to laboratory work, field-based evolutionary studies
have become increasingly complex. For museum scientists, collecting
specimens with dozens of accompanying parts are common practices
nowadays. Genomic sequencing from thousands of loci to a whole
genome have become the norm. I am working on developing open and
accessible software to minimize the complexity, targeting the most
neglected aspect of the workflow.
</p>
<h3 class="project">
A language agnostic approach, cross-platforms, and extensive
documentation
</h3>
<p class="project">
I utilize language agnostic approaches to produce efficient,
reproducible, and inclusive software for field-based evolutionary
studies. We take away the complexity from the users by simplifying
installation process, reducing app dependencies, mobile and GUI
support, and extensive documentation to aid new learners. We target
wide-range of operating systems to ensure that our software is
accessible to as many people as possible.
</p>
</div>
<div class="col-md-6 col-sm-12">
<div class="img-padded">
<img
src="img/coding.webp"
alt="coding"
class="img-fluid rounded"
width="400px"
/>
</div>
</div>
</div>
<div class="row align-items-center">
<div class="col-md-6 col-sm-12">
<img
src="img/segui.webp"
alt="coding"
class="img-fluid rounded"
width="400px"
/>
</div>
<div class="col-md-6 col-sm-12">
<h4 class="project">Project 1</h4>
<h3 class="project">
SEGUL/SEGUI, phylogenomic data manipulation and summary Statistics
</h3>
<p class="project">
The journey of my PhD has thought me that we are too reliant on High
Performance Computers (HPC) to solve the complexity of phylogenomic
studies. It includes the less computational intensive aspect, such
as alignment manipulation and summary statistics. We rethink the
approach to instead bringing phylogenomic to computers available for
most people. SEGUL/SEGUI, is phylogenomic data manipulation and
summary statistics software developed with the goal of being
accessible to everyone. Of course, everyone means those who are
interested in phylogenomics. 😊
</p>
<p class="project">
<em> SEGUL/SEGUI runs on everything. Almost literally</em>. Starting
from a single code base command line application written using Rust,
we are able to scale SEGUL to support GUI interaction. It supports
major platforms, from smartphone to HPC. We include extensive
documentation to help beginners studying phylogenomics.
</p>
<p class="project">
Publications:<br />
<a
href="https://doi.org/10.22541/au.165167823.30911834/v1"
target="_blank"
>Handika & Esselstyn (In review)</a
>
</p>
</div>
</div>
<div class="row align-items-center">
<div class="col-md-6 col-sm-12">
<h4 class="project">Project 2</h4>
<h3 class="project">
NAHPU, a field cataloging app for efficient data acquisition and
improved collaboration
</h3>
<p class="project">
Nahpu is a collaborative effort to develop a field cataloging app to
improve data acquisition efficiency and cross-institutional
collaboration. Nahpu aims to minimize transcription errors, improved
fieldwork reproducibility and data sharing, and provide a tool for
everyone to conduct responsible field collecting.
</p>
<p class="project">
Publications:<br />
Handika et. al. (In Prep)
</p>
</div>
<div class="col-md-6 col-sm-12">
<img
src="img/nahpu.webp"
alt="coding"
class="img-fluid rounded"
width="400px"
/>
</div>
<hr />
</div>
<div class="row align-items-center">
<div class="col-md-6 col-sm-12">
<h2 class="project">Other Projects</h2>
<h3 class="project">Specimen Digitization</h3>
<p class="project">
This project is led by Dr. Nurainas at the Herbarium Universitas
Andalas (ANDA) funded through the collection and data mobilization
grant provided by the Global Biodiversity Information Facility
(GBIF). Project progress is available
<a
href="https://www.gbif.org/publisher/43f4255c-f218-4a17-857a-ba3ac8456191"
>here</a
>.
</p>
</div>
<div class="col-md-6 col-sm-12">
<img
src="img/plant-specimen.webp"
alt="digitization"
class="img-fluid rounded"
/>
</div>
</div>
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