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Amanda Miotto




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Career Objectives



I am a versatile and forward-thinking professional, with over a decade of experience in research, software engineering and eResearch within the university sector. I am a natural communicator and collaborator, which has seen me succeed in research, teaching, project delivery and acting leadership roles. I am led by my curiosity, with proven ability to problem solve and drive strategic change through innovation, both within data and tech roles, as well as more broadly across organisations and communities.



Education

Formal Qualifications


Degree Institute Year Completed
Bachelor of Science (Bioinformatics) UniSQ 2007

Certifications and Short Courses

Course Institute Year Completed
Instructor Certification The Carpentries 2015
High Performance Computing (HPC) training for Researchers Pawsey Institute 2017
Agile Business Analysis (AgileBA®) Foundation Course DDLS (now Lumify) 2018
Top Rope Rock Climbing Professional Association of Climbing Instructors 2018
Managing at Griffith Griffith University 2019
Introduction to Artificial Intelligence TAFE NSW 2024



Employment History


Role Institute Year
Manager of eResearch Advisory - Consulting (Acting)

Due to the onset of COVID lockdowns soon after starting this role, a large part of this role was leading the team in adapting to this new environment. This included working through challenges around a sudden shift to WFH, onboarding new staff remotely, ensuring skills and knowledge was shared in preparation of high staff unavailability due to sickness, as well as advocating for my team to ensure new working conditions were safe and suitable for our needs.

Griffith University March-Nov 2020
Software Engineer

For multiple projects across a number of disciplines, I largely worked on back end technologies such as Linux (Redhat, Centos and Ubuntu) Virtual Machines, High Performance Compute (HPC) Platforms, various SQL platforms, Python, R, PHP and Javascript to meet client needs. Further information is found in the Project section.

Griffith University 2010-2016
Bioinformatician

This role included using R, SQL and Linux systems to code analysis tools for DNA research on Parkinson and Stem Cells. From writing scripts to implementing test versions of open source software, building databases and data cleaning, I worked across the whole data analysis pipeline.

Griffith University 2008-2010



Technical Skills


Languages


Platforms and Technologies



Projects


Research Data Management Culture Scan

Griffith Uni - 2022

Project Description:
As part of a National Research Data Management Framework project by ARDC, we conducted an university-wide scan of all academics and the culture around research data management.

Project Outcome:
Report on our current state of Research Data Management Culture, highlighting trends and evidence based potential actions to lead to improvements

My Role in Project:
- Took part in national committee to build the framework draft in the space of Culture
- Coordinating with all research support groups for interactive input, feedback and findings throughout the project
- Building a framework to cover aims, values and experiences of both the researchers individually and the institution as a whole to highlight requirements and gaps
- Creating survey and interview questions, conducting and analysing results
- Authoring the final report and recommendations for publication for actions



Research Education and Development Recording portal

Griffith Uni - 2022

Project Description:
Our Research Education team were manually sending recordings upon request, and were losing a lot of time to this work. I saw the opportunity to support them using a low-tech solution.

Project Outcome:
I set up a Sharepoint site with appropriate permissions and structure, so that staff at any technical level could upload using a folder on their desktop. This recording site is now used heavily, and saves the team in man hours.

My Role in Project:
- Gathered updated requirements
- Applied Critical and Creative Thinking models
- Established a solution
- Built training models aimed for all tech levels



Microscopy Replacement Project

Griffith Uni - 2018-2020

Project Description:
A replacement was needed for our Microscopy archival service as the previous system was out of date and no longer met requirements.

Project Outcome:
An archival system for microscopy images was replaced, and an analytical suite was included, leveraging internal compute hardware.

My Role in Project:
- Gathered updated requirements
- Conducted Market Scan
- Facilitated procurement
- Wrote Solution Architecture and underwent SA board approval
- Worked with Cybersecurity to ensure system met with standards
- Facilitated vendor access for installation and upgrades
- Wrote beginner level documentation
- Worked with research groups to onboard and clear roadbumps for individual labs
- Programmatically exported cherrypicked images from previous system using Python, SQL and Bash



Compounds Australia - CASMaP Project

Compounds Australia (CA), Griffith Institute for Drug Discovery (GRIDD) - 2017-2020

Project Description:
CA needed to aquire a full automated system to run their laboratory equipment and manage physical samples of compounds from clients. While they had a system in place, the system was outdated and no longer met requirements. Additionally, CA were buying new lab equipment that needed installation and integration into these systems.

Project Outcome:
A vendor solution was sourced. Hardware was installed into lab.

My Role in Project:
- Mapped processes, gathered requirements and conducted market scan
- Applied Critical Thinking Models
- Assisted with Procurement as technical expertise
- Facilitated lab hardware installation and integration into local back up and SQL systems
- Mapped physical network integrations and liased with network team to install



Open Heart Project

Engineering at Griffith University and UQ,
partnered with Innovative Cardiovascular Engineering and Technology Laboratory
at Prince Charles Hospital - 2017-2018

Project Description:
Built a platform to foster international collaboration in the field of mechanical circulatory support by developing open source 3D printable heart pumps with testing data.

Project Outcome:
Platform was built on Atlassian Bitbucket and Confluence systems, with publication of an invited editorial

My Role in Project:
- Collected Requirements and designed a solution using Git and Bitbucket
- Applied Critical and Creative Thinking models
- Facilitated discussions with Intellectual Property Specialist on appropriate licencing for 3D printed objects and associated data
- Worked with client and Atlassian to apply and be approved for their Open Source Cloud subscription
- Organized and taught Intro to Git workshop for users
- Worked with Research Lead to run project in Mozilla 2018 Global Sprint
- Submitted project for HealthHack 2018
- Technical lead for Industry Affiliates Program students for two cohorts



High Performance Cluster (HPC) Portal

Griffith Uni - 2016

Project Description:
Creation of a user-facing web portal to submit jobs to High Performance Computing systems, both internal and leveraging cloud infrastructure.

Project Outcome:
While internal portal worked as intended, project was cancelled due to technical differences between universities. Later, this need was met with Singularity which we opted for.

My Role in Project:
- Software Development of portal, using Python, PHP, HTML on a Linux server
- Engagement with researchers to understand usage scenarios
- Highlighted issues that arose during project and resolution where possible



Casper Portal

Compounds Australia (CA), Griffith Institute for Drug Discovery (GRIDD) - 2016

Project Description:
Search engine for researchers to browse or search the ‘Open’ Compound Collections via a web portal.

Project Outcome:
Successful platform built, used until rebuild in 2023

My Role in Project:
- Coded the scientific workflow that searches a chemical via its 3D structure



The Prosecution Project

Griffith Criminology Institute - 2014-2015

Project Description:
The digitization of historic court cases to assist in discovery and searching. Provided imaging and transcription tools to accentuate details in photos for handwriting analysis.

Project Outcome:
Successful platform built, used until upgrade and rebuild in 2019

My Role in Project:
- Developed PHP and Javascript code for Wordpress customizations



Griffith Agribusiness

Griffith Asia Institute - 2014-2016

Project Description:
A platform to share information and receive data from clients in Asia with varying digital literacy.

Project Outcome:
A platform was built with static information, calendar, a dropbox functionality and blogs.

My Role in Project:
- Gathered requirements
- Applied Critical and Creative Thinking models
- Proposed Architecture
- Developed PHP and Javascript code for Wordpress customizations
- Client liaison for alterations and updates



1000 Voices

Research Centre for Clinical and Community Practice - 2014-2015

Project Description:
The 1000 Voices project aims to collect, display, and analyse 1000+ life stories from people with disabilities from around the world.

Project Outcome:
Platform was built and was used until funded project ended.

My Role in Project:
- Working with PHP and Wordpress, developed a multimedia blog that included a wide range of accessibility customizations to provide ease of use for the audience








Strategic Change Projects

Throughout my career, I have proposed, advocated and lead changes to improve our university, our local community and the eResearch field.


Data Science Upskilling Programs

During my work in Bioinformatics, I found there was no support for researchers to learn how to deal with large amounts of data, or data science coding skills. This was reflected in groups of researchers reaching out when I became a programmer, and sharing the same experiences. I established numerous workshops to meet these needs, and started the "Hacky Hours" to support researchers outside of these workshops. Along with my counterparts at other Qld universities, we also started the Qld Research Bazaar conference, where we could share expertise across all Queensland universities. The model was adapted from a similar program seen at UniMelb, customized to fit our needs. Workshops and Hacky Hours were adopted by QCIF for other partner Universities as the program was shown to be beneficial.

Hacky Hour
2015-ongoing

A meetup/helpdesk for researchers starting in the data science field.

Details:

This initiative was set up to compliment the release of 'Intro to Programming for Researchers' classes. We started as support for the programming workshops but became the place researchers came to ask about machine learning, high performance compute, large data storage, where to start in their data science education and assistance with debugging code.

My Role in Project:
  • Creating initial proposal
  • Implementation from start until 2022
  • Trobleshooting programming/code errors and open source scripts
  • Guiding researchers to the most relevant resources to solve their issues
  • Connecting researchers with other resources across the university
  • Sharing knowledge with other universities
  • Using feedback to lead changes, to suit our growing needs
  • Started a coordinators group to share learnings and support other coordinators
  • Shared my learnings on how to start a Hacky Hour group
  • Published and ongoing curation of Hacky Hour Bookmarks for researchers and colleagues to find useful public resources


Project Outcome:

Hundreds have attended since implementation, with outcomes ranging from better reproducibility through code, being able to exponentially speed up analysis through use of cloud compute and HPC, helping researchers with better data security and storage and generally opening up resources and capabilities for researchers.
We also became a casual meeting place to find others across the university doing similar research, and a referral point/liason for researchers to services such as networking, storage and database teams.
To share my learnings on how to set up similar groups, I authored the "Hacky Hour Handbook" lessons learnt, helpful resources and groups to target. Around this time, I migrated into my QCIF role, where these teachings and meetup models were adapted by all Queensland universities.

Acknowledged Contributions:

The Feeding Ecology of Southern Hemisphere Humpback Whales (Megaptera novaeangliae) in a Changing Antarctic Ecosystem Jasmin Gross
2021- Thesis
Finding New Molecular Targets for Parkinson's Disease through Gene Hunting in Queensland Families with Inherited Parkinsonism Bentley, Steven R
2019 - Thesis
De novo SNP discovery and strong genetic structuring between upstream and downstream populations of Paratya australiensis Kemp, 1917 Sharmeen Rahman, Daniel Schmidt, Jane Hughes
2018 - Journal of Crustacean Biology
Integrated conservation planning for river-wetland mosaics e Souza Reis, Vanessa
2018 Thesis
The Effects of Consumption and Exercise Stereotypes on Evaluations: How do People Shape Up in the Eyes of Their Beholders? Lori Ellen Leach
2014 - Thesis



Research Bazaar Qld Conference
2016-Ongoing

Project Description:
The Qld Research Bazaar Conference is aimed at researchers, research students and interested colleagues who want to improve their data and technical skills. This conference offers educational workshops, talks, activities and networking opportunities with a focus on open data and technologies.


My Role in Project:
  • Part of the initial group to bring the event to Qld
  • Organizing Committee member
  • Primary organizer for 2018 and 2022 (hosted at Griffith Uni)
  • Wrote and succesfully pitching proposals
  • Coordinated workshops, teachers, helpers, speakers and sponsors
  • Organizing financial accounts for 2018 and 2022
  • Reaching out to sponsors and organizing sponsorship funds
  • Teaching and assisting in many workshops
  • Speaker and MC
  • Updating webpages/social media ads

Project Outcome:
This conference attracts 250-350 attendees every year, and is fully run by volunteers and university support staff. We run 15-20 workshops every year, host many speakers including Dr Julia Playford, Executive Director of Science Development at Queensland’s Department of Environment and Science, Professor Hugh Possingham, Queensland’s Chief Scientist.

We are proud to run as a non-profit conference, and keep our conference as low cost as possible. In more recent years, through sponsorship, we have been able to offer accessibility grants, to assist our diverse audiences to attend, as well as free tickets for all volunteers and any attendees who are unable to pay. We pride ourselves in our diversity, reflected in our committee, our speakers, teachers and our ethos.


2023 Resbaz Qld Uni of Qld Webpage
2022 Resbaz Qld Griffith University Webpage and Recap
2021 Resbaz Qld Uni of Qld Webpage
2019 Resbaz Brisbane QUT Webpage
2018 Resbaz Brisbane Griffith Uni Webpage and Recap
2017 Resbaz Brisbane Uni of Qld Recap
2016 Resbaz Brisbane QUT Recap



Data Management Culture and future plans

I have been heavily involved in the evolution of Data Management at my institute, building improvements and finding insights. This was through:
National Data Management Framework
2022

Project Description:
Across Australian Universities, it was clear that many universities were early in their data management journey and there were challenges that were common across institutes. The ARDC lead a project for universities to work together and build a National Data Management Framework.

My Role in Project: Expert Working Group Member

Project Outcome: Full report available here

Research Data Management Culture Scan
2022
As per this project, we conducted a university wide scan of culture towards data management. I wrote a recommendations report (publically available) on changes that could be made to improve data management. My role in 2024 is to progress these suggested changes.



Communication Experience



Committees



In addition to many internal committees, I've been part of the following external committees.


Committee Year Description
Software Carpentry Mentoring Committee 2017-ongoing Mentoring new carpentry instructors, trainers and interested parties
Research Software Engineers Group
(Interim committee member)
2018 Member of the initial organizing committee. Have highlighted areas to assist RSE members and worked on group projects. Also part of the BOF session at eResearch Australasia 2018. https://github.com/rse-aunz/rse-au
eResearch Conference Review Committee 2020-2022 Reviewing conference submissions for eResearch Australasia Conference






Talks and Panels



Title Location Year Topic
Communicating with non-experts: Storytelling, programming metaphors and why you should give me all your minions Data Science Bris Meetup 2019 Communication
Impostor Syndrome Tech Newbies Meetup 2019 Impostor Syndrome
Impostor Syndrome Data Science Bris Meetup 2020 Impostor Syndrome
Help me write this talk - Data Science Pathways Data Science Bris Meetup 2021 Communication
8 Reproducible Research things- Practical workshop to get people along the Reproducibility path eResearch Australasia Conference 2019 Reproducible Research
Impostor Syndrome Research Bazaar Qld 2022 Impostor Syndrome
Hacky Hours – Communities to learn and build data science Winter School in Math and Computational Biology (UQ) 2019 Communities
Data Storytelling- Creating and Highlighting Research Impact THETA Conference 2019 Communication
Collaborative Repository for 3D Printable Designs - The Open Heart Project THETA Conference 2019 Technology
Birds of a Feather for Research Software Engineers: Recognition and Career Development for Researchers who Code eResearch Australasia Conference 2018 Communities
Open Heart Project: Collaborative platform for mechanical hearts eResearch Australasia Conference 2018 Technology
Snapshot of eResearch Life Computational Biology Group (COMBINE) at UQ 2018 Communities
Appreciating the ‘Method to the madness’ in Research- Optimizing the Madness via eResearch Technology eResearch Australasia Conference 2017 Technology
Hacky Hour: Can they strengthen our research community? eResearch Australasia Conference 2016 Communities
Birds of a Feather: Optical Microscopy Image Management eResearch Australasia Conference 2012 Technology
We’re stronger together: Launching an Australasian ResBaz Network eResearch Australasia Conference 2022 Communities
Concept mapping across Reproducible Research, Data Management and Sensitive data eResearch Australasia Conference 2021 Reproducible Research
Reproducible Analysis Re:produce 2019 Reproducible Research
Griffith University Computational Resource Framework eResearch Australasia Conference 2013 Technology
A RESTful Web Service for High Performance Computing based on Nimrod eResearch Australasia Conference 2013 Technology
BoF The Research Bazaar – What is Best Practice? eResearch Australasia Conference 2013 Communities



Workshops



Workshops I've Authored



Workshop Title Content Hosted
Data Storytelling A practical workshop focusing on "How to convey the impact of your research to the world". We talk about building blocks of knowledge and expert bias, using visualisations to highlight points and how to get your audience to "feel" the impact of your project. This workshop has been debuted at the THETA conference, and multiple other universities have since used our workshop material. Taught across Griffith university and all Qld Universities from 2019-2022
9 Reproducible Research Things Reproducible Research focuses on the ability to recreate the result of analysis from the raw data- is there enough details saved to ensure this is possible? Adapting concepts from IT for the research space, this is a practical workshop to walk away with 9 ways to make your research more reproducible. Invited hostings at the Re:Produce conference 2019 and the UQ linguistics group. This workshop has been hosted from 2021 at Griffith university and all Qld universities via QCIF.
Make an Online CV Aimed at researchers who were not IT based, this was a walk through of how you can use Jekyll and Github pages to make a basic online resume. The CV you are reading now may be used at a later date for an update to that workshop. Research Bazaar Conference 2021
Intro to HPC for Griffith University A workshop to teach researchers without an IT background how to use the High Performance Compute system at Griffith University. Since been rewritten by other staff. Griffith Uni in 2018-2019


Workshops I've Taught


As well as teaching all the above workshops, I have experience teaching the following:

Workshop Title Content Hosted
Introduction to Python Focusing on working with data, teaching people who have never coded before Across Griffith University, all Queensland Universities, Research Bazaar Conference and many other locations from 2016, online and in person across 40+ workshops.
Introduction to R Focusing on working with data, teaching people who have never coded before Across Griffith University, all Queensland Universities, Research Bazaar Conference, EcoScience Precient and many other locations from 2016, online and in person across 40+ workshops.
Introduction to the Unix Shell Teaching people who have never coded before or seen a command line Across Griffith University, all Queensland Universities, Research Bazaar Conference and many other locations from 2016, online and in person across 10+ workshops.
Introduction to Git and Version Control Teaching people who have never coded before or used Git Across Griffith University, all Queensland Universities, Research Bazaar Conference, Prince Charles Hospital and many other locations from 2016, online and in person across 10+ workshops.
Data Management A practical guide on how to manage research data at Griffith University. Across Griffith University from 2016.






Academic Work


Academic Publications


OpenHeart Project – An Open-Source Research Community in the Field of Mechanical Circulatory Support Jo P Pauls, Amanda Miotto, Andrew Stephens, Shaun D Gregory, Geoff Tansley
2018 - Artificial Organs Journal
Australian Mirror of the UCSC Genome Browser Michael Pheasant, Matthew Bryant, Cas Simons, Wes Barris, Amanda Miotto, Stuart Stephen, Othmar Korn, Dominique Gorse, Jeremy Barker, Vladimir Brusic, Brian P. Dalrymple, Bernard M. Degnan, Lyn Griffiths, James Hogan, Mark A. Ragan, Paul Roe, Peter Timms , Christine A. Wells, and John S. Mattick
2008




Successful Grants


2022 Health Group Seed Grant Scheme

Role: Chief Investigator
To extend and certify an existing prototype neural network (DeepSlope) which rapidly and accurately makes orthopedic measurements


2022 ARDC Institutional Underpinnings Extension Program

Role: Codeveloper
To build a framework of Research Data Management Training that any university can leverage and customize as they need


2021 Health Group New Researcher Grant Scheme

Role: Associate Investigator
Artificial intelligence to accelerate clinical image-based diagnostics used in treating anterior cruciate ligament rupture






Group Placement


Genomics Institute (Now based at IHBI - QUT)

2012-2014
Combination of Bioinformatics work such as R, support for Microscopes and other hardware, storage and client/technical liaison.

Acknowledged Contributions:

A Phenomic Scan of the Norfolk Island Genetic Isolate Identifies a Major Pleiotropic Effect Locus Associated with Metabolic and Renal Disorder Markers Miles C. Benton,Rodney A. Lea,Donia Macartney-Coxson,Michelle Hanna,David A. Eccles,Melanie A. Carless,Geoffrey K. Chambers,Claire Bellis,Harald H. Goring,Joanne E. Curran,Jacquie L. Harper,Gregory Gibson,John Blangero,Lyn R. Griffiths
2015 - PLOS Genetics
Serum bilirubin concentration is modified by UGT1A1 Haplotypes and influences risk of type-2 diabetes in the Norfolk Island Genetic Isolate. Benton, M.C., Lea, R.A., Macartney, D.P., Bellis, C., Curran, J.E., Hanna, M., Eccles, D., Chambers, G.K., Blangero, J., & Griffiths, L.R.
2015 - BMC Genetics
Mapping eQTLs in the Norfolk Island Genetic Isolate Identifies Candidate Genes for CVD Risk Traits Miles C. Benton, Rod A. Lea, Donia Macartney-Coxson, Melanie A. Carless, Harald H. Goring, Claire Bellis, Michelle Hanna, David Eccles, Geoffrey K. Chambers,Joanne E. Curran, Jacquie L. Harper, John Blangero, and Lyn R. Griffiths
2013 - The American Journal of Human Genetics
Identifying Envirogenomic Signatures for Predicting the Clinical Outcomes of Crohns Disease Nasir, Bushra Farah (Thesis)
2013 -



National Centre for Adult Stem Cell Research- Wells Lab ( Now based at UniMelb )

2008-2011
Bioinformatics focused on genomics, using a variety of technologies such as R, Bash, SQL and Python to analyse, visualize, document data as well as in depth technical support for researchers.

Acknowledged Contributions:

Disease-specific, neurosphere-derived cells as models for brain disorders Nicholas Matigian, Greger Abrahamsen, Ratneswary Sutharsan, Anthony L. Cook, Alejandra M. Vitale, Amanda Nouwens, Bernadette Bellette, Jiyuan An, Matthew Anderson, Anthony G. Beckhouse, Maikel Bennebroek, Rowena Cecil, Alistair M. Chalk, Julie Cochrane, Yongjun Fan, François Féron, Richard McCurdy, John J. McGrath, Wayne Murrell, Chris Perry, Jyothy Raju, Sugandha Ravishankar, Peter A. Silburn, Greg T. Sutherland, Stephen Mahler, George D. Mellick, Stephen A. Wood, Carolyn M. Sue, Christine A. Wells, Alan Mackay-Sim
2010 - Disease Models and Mechanisms
A Cross-Study Transcriptional Analysis of Parkinsons Disease Greg T. Sutherland ,Nicholas A. Matigian ,Alistair M. Chalk,Matthew J. Anderson,Peter A. Silburn,Alan Mackay-Sim,Christine A. Wells,George D. Mellick
2009 - PLOS ONE