AMSI BioInfoSummer is Australia’s leading bioinformatics and mathematical and computational biology training event. The 2018 edition was held at UWA from 3-7 December, jointly hosted by the University of Western Australia (UWA), Murdoch University and Edith Cowan University. It was the first time the event has been held in WA.
138 students, researchers, academics and professionals attended the five-day program, including representatives from all the WA universities, main medical research institutes and several state government departments as well as interstate participants.
The five-day program gave attendees the opportunity to be involved at every level; from hands-on introductory levels for beginners through to specialist lectures from International speakers together with some of Australia’s top scientists and academics. There was plenty of opportunity for the networking at the program extra events which included:
Opening Session
The event was officially opened by Professor Peter Klinken AC, Chief Scientist of Western Australia after a traditional welcome to Nyoongar country by Walter McGuire. UWA Deputy Vice Chancellor of Research Professor Robyn Owens also welcomed participants to the UWA campus before the opening address was delivered by Professor Susan Wilson.
Poster Session and Diversity in STEM lunch
A poster session was held on Tuesday 4 December chaired by Dr Saskia Freytag from the Walter & Eliza Hall Institute of Medical Research. Twelve delegates submitted abstracts and took up the challenge of spruiking their poster and research in under two minutes as part of the Fast Forward Presentations. A catered networking lunch celebrating Diversity in STEM followed on from the poster session and gave attendees the opportunity to view each of the posters and participate in a Q&A session with the poster presenters.
Public Lecture
Professor Rebecca Johnson, Director of the Australian Museum Research Institute (AMRI) gave a public lecture on Wildlife Detectives: The Story of Genome Research, Discovery and Exploration at Australia’s first museum to over 70 attendees. Rebecca presented case studies from her work to demonstrate how important museum research is to engage, educate and inspire custodianship in the next generation of researchers.
COMBINE Careers Session
Organised in partnership with the University of Western Australia COMBINE (the student-run Australian organisation for students in computational biology, bioinformatics, and related fields) representative, the Careers Session showcased bioinformatics career opportunities and provided a forum for discussion around the different career pathways. The panel line up consisted of
- Professor Matthew Hahn, Indiana University
- Dr Monica Kehoe, WA Department of Primary Industries and Regional Development
- Dr Ashley Waardenberg, James Cook University
- Professor Sue Wilson, The University of New South Wales
- PLUS a presentation on the APR.Intern program from Rachel Geddes
AMSI BioInfoSummer 2018 was jointly funded by the Australian Mathematical Sciences Institute and the Australian Government’s Department of Education and Training, with support from The University of Western Australia, Murdoch University, Edith Cowan University, Pawsey Supercomputing Centre, EMBL Australian Bioinformatics Resource (EMBL-ABR), Decode Science, the Harry Butler Institute, the Australian Bioinformatics and Computational Biology Society (ABACBS) and the BHP Foundation through the AMSI CHOOSEMATHS program.
“The program was a blend of scientific seminars and practical workshops with plenty of time for networking in-between.”
Associate Professor
Nicola Armstrong
AMSI BioInfoSummer 2018 Event Director
Murdoch University
THEMES
DAY 1: Introduction to bioinformatics
Guest speaker: Professor Peter Klinken AC, Chief Scientist of Western Australia
DAY 2: Single Cell ’omics
International guest speakers: Assistant Professor Stephanie Hicks, Johns Hopkins Bloomberg School of Public health and Mr Jason Williams, Cold Spring Harbor Laboratory, DNA Learning Center
DAY 3: Plants and Animals
International guest speaker: Professor Zhiping Weng, University of Massachusetts Medical School
DAY 4: Epigenetics
International guest speakers: Assistant Professor Simon van Herringen, Radboud University and Professor Matthew Hahn, Indiana University
DAY 5: Metabolimics and Proteomics
SPONSORS
Georgie Samaha
The University of Sydney
Georgina is currently a PhD candidate at The University of Sydney. Using next generation sequencing technologies and genomics, she is creating tools for the conservation of threatened species and management of inherited genetic diseases within domestic and wild felid populations. In her research, she has applied genome-based strategies to two scenarios affecting feline health. The first of which is revealing the genetic mechanisms underlying feline diabetes mellitus in domestic cats, which serve as a novel disease model for type 2 diabetes in humans. The second scenario is directed toward the conservation and genetic disorder management of four species of wild felids that are listed as either threatened or endangered.
Can you give me a quick overview of the type of mathematics you are studying and its potential impacts for the broader community
I am applying genome-based strategies to two scenarios affecting feline health. I’m using statistical genetics to expose the inherited factors that underlie diabetes, a complex disease, in domestic cats. The domestic cat serves as a useful animal model for type 2 diabetes in humans. I’m also applying mathematical genetics and computational biology to the development of a conservation management tool for threatened and endangered wild felid species. We’re using statistical modelling to identify single nucleotide polymorphisms in four species of felids and develop a variant database and genotyping assay.
How important was receiving a CHOOSEMATHS grant in terms of your ability to attend and fully participate in the AMSI BioInfoSummer 2017 sessions throughout the week?
I’m very grateful for being a recipient of the CHOOSEMATHS Grant in attending AMSI BioInfoSummer 2017. Being reimbursed for the costs of my registration, flights from Sydney to Melbourne and my accommodation for the week will be helpful to me as a PhD student. As a PhD student on a fixed scholarship, living week to week, I don’t always have access to the money required for the costs associated attending events such as this.
How important are initiatives such as the CHOOSEMATHS Grants in terms of fostering the participation and achievement of women in mathematics, particularly in terms of access to networking opportunities and further training opportunities?
I welcome the opportunity to benefit from the effort to overcome the cultural and organisational factors that discourage women from engaging in pursuing STEM careers. I believe in valuable roles played by specialist women’s services, such as this Grant. Again, I am grateful for the funding. Being given choice is important to me and essential to my participation, as a woman, in my industry.
The conference was a great opportunity to network with and learn from women who’s careers I admire and I’m glad to have been able to participate in it.
In what ways has the experience impacted your maths studies? Has it influenced the direction of your research?
I am new to the field of bioinformatics, and the AMSI conference introduced me to areas of computational mathematics that I have not yet encountered in my studies so far. I also learned a lot about bioinformatics tools that are publicly available and how to access them. Some of the tools I came across during the conference, I intend to access in my own work.
What was the most valuable part of AMSI BioInfoSummer 2017 for you in terms of furthering your career in mathematical sciences?
I found many of the talks to be very useful, I am new to the industry and the talks provided me with a useful introduction to many areas of research I was not aware of. I think I can apply a lot of what I learned over the week to my own research and collaborative efforts with others.
A presentation on the AMSI Intern program was included as part of the Careers Session. One of the aims of the AMSI Intern program is to maximise employability and help prepare research graduates to drive industry/private sector research. Are you hoping to work with industry? How important is this experience for researchers? Particularly in terms of offering career flexibility for women?
Whether I continue a career in academia or hold a public or private sector position I will be working with industry partners.
The CHOOSEMATHS Grants are part of a broader program being delivered by AMSI Schools with support from BHP Billiton to turn the tide on Australia’s maths deficit and strengthen maths education and participation of women across the discipline. What do you see as the big challenges facing maths in Australia, particularly for women?
So far, I have been fortunate enough to have studied in an immediate environment that is dominated by women. The research group I am a part of and my academic supervisors are all women and as such I have not experienced much sexism or discrimination in my immediate workplace or learning environment. I am a white woman, who is surrounded by supportive women who have established careers and take me very seriously as a student. My experience probably isn’t a very good reflection of the broader experience of women in STEM, as I come from such a privileged position.
Did you always want to pursue a career in maths? Were you encouraged to study these subjects at school? Do any particular mentors come to mind? Any outstanding teachers?
No, this has been something I have fallen into.
Where do you see yourself in five or ten years time?
I would like to continue working in the broader area of medical genetics research, if possible but am very open to whatever comes my way over the next few years and where my PhD takes me.
Ahead of his presentations at AMSI BioInfoSummer 2018, Jason Williams from Cold Spring Harbor Laboratory, USA shares with us what drives his work in the bioinformatics education and training field as well as current challenges and the important skills required of researchers.
Tell me about your work. What drives your interest in this field?
Connecting students and researchers with data skills are what drive my day-to-day work. At Cold Spring Harbor I started in the research arena, then made the move to the Learning Center – a unit within the lab with the mission of preparing people to live in the “gene age”. Discoveries in the life sciences won’t just affect the choices we make about healthcare, but literally our ability to live on a planet facing a growing population and a changing climate. My contribution to these efforts ranges from reaching high school students directly – developing opportunities to learn biology in a hands-on way, to working with researchers who are by nature life-long students. Increasingly for both groups, one of the best ways to foster progress is through building bioinformatics and data science skills. Although computers and the Internet are parts of our everyday lives, leveraging computing to learn and do science is still not an integral part of most biologist’s formal preparation. I work to improve the undergraduate curriculum in biology – infusing it with more computational skills – in ways that will have national and international impact. Through communities like The Carpentries, I’m also working to accelerate science by improving how research professionals learn on a global scale.
What are the most interesting “big questions” or challenges facing researchers in your area?
I have worked with groups in the US to study both the bioinformatics competencies that the undergraduate curriculum should include, as well as the barriers educators face in delivering this education. We know that training for a variety of data skills is the biggest unmet need for researchers who now need this training to keep pace with our ability to produce data exponentially faster and at lower cost. We don’t have a full understanding of the best ways to satisfy these needs. Recent studies suggest that many of our informal training methods are inadequate. Since faculty won’t be going back to college we need to better understand how to bridge the gap between these expert researchers and educators and the skills they need to apply new and increasingly complex methods – from high-performance computing, to machine learning.
What are some key industry applications of your work?
Industry is an exciting topic but with the exception of pharma it may be removed from what biologist frequently think about. A commonality between industry, my work, and biology is data science. Data Science is a product of the tech sector – although many in academia are undergoing a rebrand to signal that they have ‘always’ been doing data science. Companies small-and-large are creating tools and computational resources that far surpass the scales we are used to working with in academia. This is why a small startup with no staff can take software (built by others) and an idea and build it into a successful product. Previously, academia’s large software/computing applications have been very focused HPC applications (e.g. simulations in chemistry in physics). Now, I think biologists are the startups. They can take their idea (which may be a small area of biology, a genome, a metabolic process) and leverage commercial computing and software infrastructure to solve novel problems. The human resources – people trained with data science skills, can operate in overlapping spaces, with students having career opportunities in the tech sector and with tech sector solutions finding reuse in genomics and healthcare.
What advice do you have for future researchers?
While Moore’s law is a well-known rule describing how often our computing capacity doubles, I’m not aware of an equally simple metric for capturing how quickly our knowledge and approaches to research are changing in science; clearly, we are on an exponential trend. We need to move away from thinking our schooling at any given point will allow us to comfortably understand the tools we will be using 5 years from now. While in some ways this confronts us with a potentially unwinnable battle, I hope that folks see two opportunities. I’ve heard it said that the most important skill of the 21st century will be the ability to learn, unlearn, and relearn. That said, one thing we should take time to do is learn about how to learn (and teach) effectively – metacognition. The second opportunity is to move as far away as possible from science as product of a individuals, and towards science as an effort of communities where people have learned to work in teams and value diversity of abilities, perspectives, and ideas.
Jason is Assistant Director – External Collaborations of Cold Spring Harbor Laboratory’s DNA Learning Center, and is the Education, Outreach, and Training lead for CyVerse (A U.S. national life science cyberinfrastructure project funded by NSF). Jason organizes, instructs, and speaks at a variety of bioinformatics-related workshops, conferences, and meetings annually. He also serves in an advisory capacity on a variety of bioinformatics and open science projects including his service as Chair of the International Science Advisory Board for EMBL-Australian Bioinformatics Resource. He also serves on the External Panel of Consultants to the National Institutes of Health (NIH) Data Commons Initiative and the NIH’s National Heart Lung and Blood Institute’s Data STAGE (Storage, Toolspace, Access and analytics for biG data Empowerment). He is an active Software and Data Carpentry instructor, and a former Chair of the Software Carpentry foundation. Jason also teaches at the Yeshiva University High School for Girls.
Mr Jason Williams
Assistant Director, External Collaborations, Cold Spring Harbor Laboratory, DNA Learning Center
Jason will present on ‘Improving the Bioinformatics Curriculum‘ and run an ‘Introduction to RNA-Seq with the Kallisto and Sleuth workflows‘ workshop at AMSI BioInfoSummer 2018 which will be held at The University of Western Australia, Perth from 3-7 December.
AMSI BioInfoSummer 2017 was held at Monash University from 4-8 December and hosted by the Monash Bioinfomatics Platform. Over 170 students, researchers, academics and professionals gathered for the five-day event to increase their knowledge and skills in this truly interdisciplinary field.
The symposium was opened by BioInfoSummer founder, Professor Susan Wilson (The University of New South Wales) who was introduced by Professor Geoff Prince (AMSI). Following the opening, Associate Professor David Powell (Monash University and AMSI BioInfoSummer 2017 Event Director) introduced Professor Melanie Bahlo (Walter & Eliza Hall Institute of Medical Research) who gave the keynote presentation titled “Bioinformatics: just pipelines, isn’t it?”
The program commenced with an introduction to bioinformatics on day one followed by four days of specialised content focused on:
- visualisation, modelling and analysis
- RNA-seq
- proteomics and metabolomics and
- single-cell genomics.
Over the course of the week, attendees got to hear from 24 national speakers and 3 international speakers including Professor Steve Rozen (Duke-NUS Medical School Singapore), Dr Michael Lawrence (Genentech, USA) and Dr Tallulah Andrews (The Wellcome Trust Sanger Institute, UK) as well as 5 workshop presenters. To compliment the scientific program, the following additional program extras and networking events were incorporated into the symposium for delegates to maximise their AMSI BioInfoSummer experience:
- Welcome lunch and reception
- Celebrating Diversity in STEM networking lunch
- Poster competition
- Public lecture by Professor John Mattick AO from the Garvin Institute of Medical Research on “Genomics, Big Data and the Future of Medical Research and Healthcare”
- COMBINE Careers Session where attendees had the opportunity to ask questions of the diverse panel about the different career pathways in bioinformatics
The gender balance of attendees at BioInfoSummer was essentially even, and the organising committee also ensured the program was balanced.
Associate Professor David Powell
AMSI BioInfoSummer 2017
Event Director
Melbourne Bioinformatics Platform
Monash University
AMSI BioInfoSummer 2017 was jointly funded by the Department of Education and Training and the Australian Mathematical Sciences Institute, with support from Monash University, the Australian Bioinformatics and Computational Biology Society (ABACBS), MAXIMA and the BHP Billiton Foundation (part of the Choose Maths Initiative).
AMSI BioInfoSummer 2016 was held in November at the University of Adelaide, hosted by the School of Mathematical Sciences, with a collaborative effort in organisation from the University of Adelaide, University of South Australia, Flinders University and the South Australian Health and Medical Research Institute (SAHMRI).
The symposium was opened by Professor Warren Bebbington (Vice‐Chancellor and President, The University of Adelaide), Leanne Harvey (A/g Chief Executive Officer, Australian Research Council) and Professor Terry Speed (Laboratory Head, Walter & Eliza Hall Institute of Medical Research and Chair of the AMSI Scientific Advisory Committee) in the Flentje Lecture Theatre, each addressing the delegation of over 200 with an inviting welcome to the University of Adelaide, AMSI BioInfoSummer and the comprehensive bioinformatics program ahead.
The five‐day program, designed for mathematicians, statisticians and biologists, started with an introductory overview on day one followed by four days of specialised content focused on;
- high‐dimensional data and multivariate analysis
- experimental design and analysis for RNA sequencing
- programming for bioinformatics and
- analysis of long‐read (third‐generation) data.
Each day included a mix of keynote speakers, lectures and hands‐on workshop practical sessions, in addition to a variety of program extras.
“The program comprised a blend of presentations by leading national and international researchers, and hands‐on workshops on bioinformatics programming, providing unique exposure to the field of bioinformatics for delegates from a range of cognate disciplines.”
Associate Professor Gary Glonek
AMSI BioInfoSummer 2016 Event Director
The University of Adelaide
Featuring 15 national and international keynote speakers including Professor Orly Alter (University of Utah), Professor Simon Anders (Institute for Molecular Medicine, Finland), Dr Jason Chin (Pacific Biosciences), Professor Mingyao Li (University of Pennsylvania) and Professor Xia Yang (University of California, Los Angeles), the organising committee was committed to working towards gender balance throughout the event, and was delighted to have assembled a program of equal gender balance, which attracted a delegation that was similarly equal.
Additional program extras and outreach events were incorporated into the timetable to offer a number of networking and social activities for delegates to maximise their AMSI BioInfoSummer experience. A highlight and extremely popular event was the Poster Talks and Poster Session, which gave presenters the opportunity to spruik their research and share their work in the bioinformatics space with the delegation, in addition to a Women in STEM panel event, COMBINE careers session, public lecture and coding competition.
AMSI BioInfoSummer 2016 was jointly funded by the Department of Education and Training and the Australian Mathematical Sciences Institute, with support from The University of Adelaide, the Australian Bioinformatics and Computational Biology Society (ABACBS), EMBL Australia, Illumina, Flinders University, The University of South Australia and the BHP Billiton Foundation (part of the Choose Maths Initiative).
Georgie Samaha
The University of Sydney
Georgina is currently a PhD candidate at The University of Sydney. Using next generation sequencing technologies and genomics, she is creating tools for the conservation of threatened species and management of inherited genetic diseases within domestic and wild felid populations. In her research, she has applied genome-based strategies to two scenarios affecting feline health. The first of which is revealing the genetic mechanisms underlying feline diabetes mellitus in domestic cats, which serve as a novel disease model for type 2 diabetes in humans. The second scenario is directed toward the conservation and genetic disorder management of four species of wild felids that are listed as either threatened or endangered.
Can you give me a quick overview of the type of mathematics you are studying and its potential impacts for the broader community
I am applying genome-based strategies to two scenarios affecting feline health. I’m using statistical genetics to expose the inherited factors that underlie diabetes, a complex disease, in domestic cats. The domestic cat serves as a useful animal model for type 2 diabetes in humans. I’m also applying mathematical genetics and computational biology to the development of a conservation management tool for threatened and endangered wild felid species. We’re using statistical modelling to identify single nucleotide polymorphisms in four species of felids and develop a variant database and genotyping assay.
How important was receiving a CHOOSEMATHS grant in terms of your ability to attend and fully participate in the AMSI BioInfoSummer 2017 sessions throughout the week?
I’m very grateful for being a recipient of the CHOOSEMATHS Grant in attending AMSI BioInfoSummer 2017. Being reimbursed for the costs of my registration, flights from Sydney to Melbourne and my accommodation for the week will be helpful to me as a PhD student. As a PhD student on a fixed scholarship, living week to week, I don’t always have access to the money required for the costs associated attending events such as this.
How important are initiatives such as the CHOOSEMATHS Grants in terms of fostering the participation and achievement of women in mathematics, particularly in terms of access to networking opportunities and further training opportunities?
I welcome the opportunity to benefit from the effort to overcome the cultural and organisational factors that discourage women from engaging in pursuing STEM careers. I believe in valuable roles played by specialist women’s services, such as this Grant. Again, I am grateful for the funding. Being given choice is important to me and essential to my participation, as a woman, in my industry.
The conference was a great opportunity to network with and learn from women who’s careers I admire and I’m glad to have been able to participate in it.
In what ways has the experience impacted your maths studies? Has it influenced the direction of your research?
I am new to the field of bioinformatics, and the AMSI conference introduced me to areas of computational mathematics that I have not yet encountered in my studies so far. I also learned a lot about bioinformatics tools that are publicly available and how to access them. Some of the tools I came across during the conference, I intend to access in my own work.
What was the most valuable part of AMSI BioInfoSummer 2017 for you in terms of furthering your career in mathematical sciences?
I found many of the talks to be very useful, I am new to the industry and the talks provided me with a useful introduction to many areas of research I was not aware of. I think I can apply a lot of what I learned over the week to my own research and collaborative efforts with others.
A presentation on the AMSI Intern program was included as part of the Careers Session. One of the aims of the AMSI Intern program is to maximise employability and help prepare research graduates to drive industry/private sector research. Are you hoping to work with industry? How important is this experience for researchers? Particularly in terms of offering career flexibility for women?
Whether I continue a career in academia or hold a public or private sector position I will be working with industry partners.
The CHOOSEMATHS Grants are part of a broader program being delivered by AMSI Schools with support from BHP Billiton to turn the tide on Australia’s maths deficit and strengthen maths education and participation of women across the discipline. What do you see as the big challenges facing maths in Australia, particularly for women?
So far, I have been fortunate enough to have studied in an immediate environment that is dominated by women. The research group I am a part of and my academic supervisors are all women and as such I have not experienced much sexism or discrimination in my immediate workplace or learning environment. I am a white woman, who is surrounded by supportive women who have established careers and take me very seriously as a student. My experience probably isn’t a very good reflection of the broader experience of women in STEM, as I come from such a privileged position.
Did you always want to pursue a career in maths? Were you encouraged to study these subjects at school? Do any particular mentors come to mind? Any outstanding teachers?
No, this has been something I have fallen into.
Where do you see yourself in five or ten years time?
I would like to continue working in the broader area of medical genetics research, if possible but am very open to whatever comes my way over the next few years and where my PhD takes me.
Brooke Whitelaw
James Cook University
Brooke Whitelaw is originally from Melbourne where she completed a Bachelor of Wildlife Conservation Biology with First class honours at La Trobe University in 2015. Her Research Project focused on the proteins within the posterior salivary glands (the venom producing gland of octopods) of the southern blue-ringed octopus (Hapalochlaena maculosa) and the southern sand octopus (Octopus kaurna). Following graduation she worked as a Research Assistant in Jan Strugnell’s lab at La Trobe University working on the population genetics of Victorian yellow tailed kingfish.
At the end of February 2017 Brooke moved to Townsville where she is currently a PhD Candidate at James Cook University. Her PhD project follows on from her previous work investigating octopus venom and toxicity and focuses on the Blue-ringed octopus genus (Hapalochlaena). Her current interests include the delineation of the Hapalochlaena genus, understanding octopod venom evolution through comparative genomics and genetic linkage mapping techniques and the origin of tetrodotoxin in Hapalochlaena and its distribution within and between species.
Can you give me a quick overview of the type of mathematics you are studying and its potential impacts for the broader community
My research relies on predictive models for genome annotation.
How important was receiving a CHOOSEMATHS grant in terms of your ability to attend and fully participate in the AMSI BioInfoSummer 2017 sessions throughout the week?
The grant provided was integral for attaining flights to attend the conference.
How important are initiatives such as the CHOOSEMATHS Grants in terms of fostering the participation and achievement of women in mathematics, particularly in terms of access to networking opportunities and further training opportunities?
The networking lunch provided a relaxed environment for women throughout different fields of mathematical research and different stages within their careers to freely communicate and form connections.
In what ways has the experience impacted your maths studies? Has it influenced the direction of your research?
This experience has motivated me to seek more education regarding my bioinformatics skills.
What was the most valuable part of AMSI BioInfoSummer 2017 for you in terms of furthering your career in mathematical sciences?
I found the CHOOSEMATHS lunch and careers panel to be the most influential and has motivated me to bolster my skills and maintain more connections within mathematical science fields.
A presentation on the AMSI Intern program was included as part of the Careers Session. One of the aims of the AMSI Intern program is to maximise employability and help prepare research graduates to drive industry/private sector research. Are you hoping to work with industry? How important is this experience for researchers? Particularly in terms of offering career flexibility for women?
I was particularly interested in the AMSI intern program and appreciated the opportunity to understand the program better both through the presentation and by asking question after.
The CHOOSEMATHS Grants are part of a broader program being delivered by AMSI Schools with support from BHP Billiton to turn the tide on Australia’s maths deficit and strengthen maths education and participation of women across the discipline. What do you see as the big challenges facing maths in Australia, particularly for women?
One of the major challenges is the encouragement of women in secondary education to pursue maths with their studies.
Did you always want to pursue a career in maths? Were you encouraged to study these subjects at school? Do any particular mentors come to mind? Any outstanding teachers?
I was never encouraged to pursue maths and found it to be a weaker subject of mine, only through my higher education (bachelors, honours and PhD) have I realised the importance of mathematics in my career.
Where do you see yourself in five or ten years time?
Still in some form of research or industry working with large datasets and improving my bioinformatics skills.
Emily Plant
University of Southern Queensland
Emily Plant has spent the last three years studying a Bachelor of Science (majoring in Mathematics and Statistics) at the University of Southern Queensland in Toowoomba. She is also involved in USQ’s peer assisted learning support program, Meet-Up, where she leads course specific sessions independently in which students learn collaboratively. As Emily is particularly interested in the bioinformatics and biostatistics fields, she is considering a future career in them. Emily is continuing her studies by commencing her Honours degree in 2018, also at the University of Southern Queensland.
Can you give me a quick overview of the type of mathematics you are studying and its potential impacts for the broader community
My Bachelor degree has provided me with the necessary foundation in a broad range of topics to pursue further studies in mathematics and statistics, such as my upcoming honours. These further studies will be where my work will impact the broader community.
How important was receiving a CHOOSEMATHS grant in terms of your ability to attend and fully participate in the AMSI BioInfoSummer 2017 sessions throughout the week?
If I had not been received the grant, I would not have been able to fund my attendance of BioInfoSummer myself.
How important are initiatives such as the CHOOSEMATHS Grants in terms of fostering the participation and achievement of women in mathematics, particularly in terms of access to networking opportunities and further training opportunities?
These initiatives are hugely important. The grants especially allow students to attend these events when they otherwise couldn’t, and therefore provide a fantastic opportunity for networking.
In what ways has the experience impacted your maths studies? Has it influenced the direction of your research?
I attended BioInfoSummer to see if a career in bioinformatics or biostatics is something that would interest me. I’ve determined that such a career does seem enticing, so in the future I may pursue more biologically oriented positions and opportunities.
What was the most valuable part of AMSI BioInfoSummer 2017 for you in terms of furthering your career in mathematical sciences?
Learning about all the exciting research the speakers are doing. It was an invaluable opportunity to help give some insight about which direction I would like to take my mathematics career in and what new and exciting areas are available to me in the future.
A presentation on the AMSI Intern program was included as part of the Careers Session. One of the aims of the AMSI Intern program is to maximise employability and help prepare research graduates to drive industry/private sector research. Are you hoping to work with industry? How important is this experience for researchers? Particularly in terms of offering career flexibility for women?
I’m not yet sure if I wish to work with industry/in the private sector, but regardless, the AMSI Intern Program sounds like an excellent opportunity that I may wish to participate in in the future.
The CHOOSEMATHS Grants are part of a broader program being delivered by AMSI Schools with support from BHP Billiton to turn the tide on Australia’s maths deficit and strengthen maths education and participation of women across the discipline. What do you see as the big challenges facing maths in Australia, particularly for women?
I think that one of the main challenges facing maths in Australia is that we tend to have a mindset that maths is not applicable to the “real world”, when in reality it is a vital skill for many careers. I’m not sure why particularly women are underrepresented in maths, but I’m certain that the problem is complex and multifaceted.
Did you always want to pursue a career in maths? Were you encouraged to study these subjects at school? Do any particular mentors come to mind? Any outstanding teachers?
Throughout high school I didn’t have any idea what I wanted for my career, beyond attending university. I chose maths because I did very well at it and I enjoyed it, but I may not have if not for my grade 11 and 12 maths teacher. He really encouraged me to pursue maths and made every one of his classes enjoyable for those two years.
Where do you see yourself in five or ten years time?
In five years time I see myself having finished my honours and working for a few years. In ten years time I see myself having established a career, perhaps with a PhD.
Any other feedback/comments you would like to provide on the CHOOSEMATHS grant or AMSI BioInfoSummer 2017?
BioInfoSummer was a great experience. I really enjoyed the speakers, and most of them provided enough foundation information for the biological topics that I was able to understand them, even coming from a maths and stats background.
Tahlia Perry
The University of Adelaide
Tahlia Perry is a PhD student at the University of Adelaide. She has always had a love for animals, fascinated with their biology and a passion for their conservation. Once Tahlia started her undergraduate degree in science, she also really enjoyed genetics, so through her studies she has been combining these two together. Tahlia acquired her first bioinformatics skills during her Honours degree where she analysed Next Generation Sequencing data from ancient DNA of an extinct mammal species. Now, during her PhD she is working on the iconic echidna, exploring many aspects of their genetics, such as reproduction and development, and developing tools to help with their conservation and captive breeding. As well as developing important laboratory and bioinformatics skills during her PhD, Tahlia has also created a citizen science project called EchidnaCSI, which has been hugely successful. She has also entered, and won, science communication competitions such as the 3 minute thesis and FameLab and had the opportunity to work with many media outlets including radio and television. Tahlia’s main aim in the future is to continue research that aids mammal conservation by bringing together fields of genetics, biochemistry and bioinformatics with ecology, conservation, and citizen science.
Can you give me a quick overview of the type of mathematics you are studying and its potential impacts for the broader community
For my PhD project I am working on our beloved echidnas, helping to understand more about their extraordinary biology, particularly their reproduction and development. One way in which I am doing this is by identifying the genes that are being turned on and off in the reproductive organs of adult echidnas compared to juveniles. By identifying these genes I can piece together the pathways that become active and control their reproduction and development.
In order for me to do this I have to analyse very large datasets and manipulate the programs that use complex mathematical models to accurately tell me which genes I should be focussing on based on how different they are in adults compared to juvenile echidnas.
By understanding echidna reproduction I can help inform the captive breeding programs here in Australia, which are becoming increasingly important as some populations of echidnas are endangered.
How important was receiving a CHOOSEMATHS grant in terms of your ability to attend and fully participate in the AMSI BioInfoSummer 2017 sessions throughout the week?
Conferences are an essential part of a PhD, providing the opportunity to showcase and share your research, but they can be very expensive to attend. As I was travelling from interstate it was incredibly important to have the CHOOSEMATHS Grant to assist with both travel and accommodation and allowed me to fully attend BioInfoSummer.
How important are initiatives such as the CHOOSEMATHS Grants in terms of fostering the participation and achievement of women in mathematics, particularly in terms of access to networking opportunities and further training opportunities?
I think offering the CHOOSEMATHS Grants for women really helps to encourage our participation in usually male-dominated areas such as bioinformatics and computer science. It is incredibly important to get our name and faces known in order for future careers and partnerships. Therefore, attending events like BioInfoSummer is particularly crucial for young researchers to learn these sorts of skills.
I particularly enjoyed the women’s lunch that was held on the first day. This event was a great ice-breaker, allowed us to meet new people straight away as well as share our similar experiences in our field of study. I think more events like this would make a huge impact for women in STEM.
In what ways has the experience impacted your maths studies? Has it influenced the direction of your research?
I am from a biology background and have had little training in bioinformatics and computer science, with the majority of my skills being self-taught. Attending BioInfoSummer helped immensely in giving direction to my research, as well as confirming that I am on the right track with my analyses. It also gave me a new found perspective on just how varied the field of bioinformatics is, with there being many people like myself who are from a biology background but also a significant amount of people who are from a pure maths background wanting to use their skills to solve biological problems. It really gave me an appreciation of how maths is really everywhere but in various forms.
What was the most valuable part of AMSI BioInfoSummer 2017 for you in terms of furthering your career in mathematical sciences?
When I was accepted for the CHOOSEMATHS grant, I then decided to make the most of the conference by presenting a poster. This required pushing myself to get as many results out during the weeks leading up to the conference, which was a great motivator. Presenting the poster allowed me to showcase my work and helped immensely with networking. Having this opportunity to share my research was incredibly powerful in terms of furthering my skills for a career in sciences. Winning the Best Poster Award also gave me great confidence that I am on the right path with both my science and communication skills.
A presentation on the AMSI Intern program was included as part of the Careers Session. One of the aims of the AMSI Intern program is to maximise employability and help prepare research graduates to drive industry/private sector research. Are you hoping to work with industry? How important is this experience for researchers? Particularly in terms of offering career flexibility for women?
I think it’s fantastic that there are more initiatives for PhD students to make contacts and work in industry, as it is well known that only a small percentage of postgraduate students actually continue with academic careers. Particularly for women, where research is still not as accommodating for those who choose to start a family, moving into private sectors or industry may offer more security. I, personally, am still interested in continuing a career in research but I am glad that these internships exist and I have the option to pursue them if I choose.
The CHOOSEMATHS Grants are part of a broader program being delivered by AMSI Schools with support from BHP Billiton to turn the tide on Australia’s maths deficit and strengthen maths education and participation of women across the discipline. What do you see as the big challenges facing maths in Australia, particularly for women?
I think maths, the same as many STEM subjects, lacks the encouragement of women to pursue these disciplines. It would be great to have more female role models for school age children as well as more information on where maths can lead to as a career. As we move up in our careers through PhD and beyond, I think the biggest problem is there needs to be a change in how females can balance work with lifestyle, especially when families are involved.
Did you always want to pursue a career in maths? Were you encouraged to study these subjects at school? Do any particular mentors come to mind? Any outstanding teachers?
I always loved maths growing up, I don’t know why but I always just got it and really enjoyed being able to solve problems. My teachers were always supportive and gave me extra work if I ever asked for it, which is likely what helped me to be top of my year 12 Maths Studies class by the end of high school. As I then pursued science through my undergraduate degree I am slightly disappointed that I didn’t continue to pursue maths subjects, as it was never encouraged. Maths and science go hand in hand and if I could go back and tell my past self anything, it would be to continue with maths, as it would help my current science research immensely.
Where do you see yourself in five or ten years time?
I have approximately 12-18 months left of my PhD, after that I plan on finding a postdoctoral position somewhere overseas, likely USA or the UK. I would love to work somewhere where I can utilise all of my skills and passion in molecular biology, bioinformatics and science communication in order to help with conservation of threatened species.
Any other feedback/comments you would like to provide on the CHOOSEMATHS grant or AMSI BioInfoSummer 2017?
I would just like to again thank AMSI for the CHOOSEMATHS grant and the ability to attend BioInfoSummer. It was a great conference and I loved the experience.
Loan Nguyen
The University of Queensland
Loan Nguyen is currently working as a lecturer at Vietnam National University of Agriculture. Her masters degree of Biotechnology at the University of Queensland in Australia was awarded in 2013. With great achievements from her master, Loan now holds a competitive UQ International Scholarship to support her PhD in the School of Chemistry and Molecular Biosciences. For her PhD, Loan is interested in understanding how genetics influence puberty in Brahman heifers, a dominant sub-species of cattle in tropical regions. Her PhD research has industry applications: finding potential candidate genes and furthering biological knowledge of puberty can help farmers improve the reproductive performance of Brahman heifers in Australia. In order to complete her PhD, Loan is well equipped with technologies: DNA sequencing, qPCR, genotyping, RNA sequencing and mass spectrometry as well as with bioinformatics tool.
Can you give me a quick overview of the type of mathematics you are studying and its potential impacts for the broader community
I am a PhD student at the University of Queensland, in the School of Chemistry & Molecular Biosciences. I am currently working on animal genetics. My project’s goal is to improve the reproductive performance of Brahman heifers in Australia. The research focuses on finding candidate genes and proteins as well as furthering biological knowledge of puberty in Brahman using computational strategies. This knowledge can bring the research one step closer towards the ultimate goal of enhancing genetics in Bos indicus cattle.
How important was receiving a CHOOSEMATHS grant in terms of your ability to attend and fully participate in the AMSI BioInfoSummer 2017 sessions throughout the week?
I knew about AMSI BioInfoSummer 3 years ago and I had chance to attend it in 2016 and in 2017. The CHOOSEMATHS Grant gave me opportunities to attend the full week and experience all sessions during the week. Attending talk sessions and networking events not only provided me opportunities to learn from lecturers and workshops but also gave me a chance to share my work and get advice from other fellows. Throughout the week, I also met experts who are working in the same area as well as different areas with me. Being able to network with these experts will open doors for my future career.
How important are initiatives such as the CHOOSEMATHS Grants in terms of fostering the participation and achievement of women in mathematics, particularly in terms of access to networking opportunities and further training opportunities?
I believe that CHOOSEMATHS give us, especially women, a place to meet other successful female scientists. Through this place, we then can encourage each other, participate in events, share knowledge and build a solid network.
In what ways has the experience impacted your maths studies? Has it influenced the direction of your research?
My background is in molecular biology and I am doing a PhD foussing on transcriptomic and proteomics. These high-throughput techniques generate a huge amount of data which I then need to use math, statistic and bioinformatics knowledge to handle. Attending BioInfoSummer 2017 gave me a broader understanding about research areas, current technologies: its advantage and disadvantage. Via this event, I can build my future direction for my research direction or career.
What was the most valuable part of AMSI BioInfoSummer 2017 for you in terms of furthering your career in mathematical sciences?
All sections of AMSI BioInfoSummer are valuable. Talks, lectures and poster presentations helped to broaden my knowledge in various area. The Career session brought me closer to successful female scientists and gave me a chance to learn from them. In terms of furthering my career in mathematical sciences, I think, the Combine Careers session was the most valuable part of AMSI BioInfoSummer 2017.
A presentation on the AMSI Intern program was included as part of the Careers Session. One of the aims of the AMSI Intern program is to maximise employability and help prepare research graduates to drive industry/private sector research. Are you hoping to work with industry? How important is this experience for researchers? Particularly in terms of offering career flexibility for women?
Working with industry may be a new challenge for me. It is quite different from academia. I started my first job as a lecturer in a University and then continued with my PhD overseas. But, If I have an opportunity to work with industry, I will definitely take it. There are huge varieties of different teams in industry, therefore, I can learn from experts in other disciplines and build up my knowledge.
Did you always want to pursue a career in maths? Were you encouraged to study these subjects at school? Do any particular mentors come to mind? Any outstanding teachers?
Honestly, I am not really good at maths. I completed my Bachelor and my master degree in Biotechnology. Therefore, my background is molecular biology. I started to learn about bioinformatics when I started my PhD project. It is so complicated but it is really helpful and powerful. I think Dr Toni Reverter helps and teaches me a lot. He is so smart and his knowledge encourages to learn and use bioinformatics tools for my study.
Where do you see yourself in five or ten years time?
I am going to complete my PhD soon. Therefore, my plan for my future career is to remain a researcher. Five years down the road I see myself growing into a senior researcher or lecturer where I think I will be able to use my skills to support, teach and help others.