Anna Syme

• Senior Bioinformatician, The University of Melbourne/Australian Biocommons
• Science Lead, Galaxy Australia
• Most of my recent work is with Galaxy Australia - a webpage (connected to computing resources) where people can analyse data.

Peer-reviewed publications Conferences, seminars, workshops Galaxy Training Network tutorials Galaxy Top Tips Zenodo tutorials and datasets WorkflowHub workflows IWC workflows Galaxy Australia published workflows Professional memberships and reviewing Books Theses Community engagement Contact me

Peer-reviewed publications

• Simpson L, et al. [incl. Syme AE]. (2025). The Genomics for Australian Plants (GAP) framework initiative—developing genomic resources for understanding the evolution and conservation of the Australian flora. Australian Systematic Botany 38(3). doi:10.1071/SB24022
• Hyde C, Syme AE, Batut B, Zierep PF, Mok W, Bacon WA, Price GR. (2025). Community-curated Galaxy interfaces with the Galaxy Labs Engine. Preprint: doi:10.20944/preprints202508.0199.v1
• The Galaxy Community [incl. Syme AE]. (2024). The Galaxy platform for accessible, reproducible, and collaborative data analyses: 2024 update. Nucleic Acids Research 52(W1): W83–W94. doi:10.1093/nar/gkae410
• Brown T, et al. [incl. Syme AE]. (2024). Genome annotation and other post-assembly workflows for the Tree of Life. BioHackrXiv preprint. doi:10.37044/osf.io/vvadp
• Mu A, et al. [incl. Syme AE]. (2023). Integrative omics identifies conserved and pathogen-specific responses of sepsis-causing bacteria. Nature Communications 14: 1530. doi:10.1038/s41467-023-37200-w
• Hiltemann S, et al. [incl. Syme AE]. (2023). Galaxy Training: a powerful framework for teaching! PLOS Computational Biology 19(1): e1010752. doi:10.1371/journal.pcbi.1010752
• The Galaxy Community [incl. Syme AE]. (2022). The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. Nucleic Acids Research 50(W1): W13–W51. doi:10.1093/nar/gkac247
• Syme AE, McLay TGB, Udovicic F, Cantrill DJ, Murphy DJ. (2021). Long-read assemblies reveal structural diversity in genomes of organelles – an example with Acacia pycnantha. Gigabyte. doi:10.46471/gigabyte.36
• Georgeson P, Syme AE, et al. (2019). Bionitio: demonstrating and facilitating best practices for bioinformatics command-line software. GigaScience 8(9): giz109. doi:10.1093/gigascience/giz109
• Minhas V, et al. [incl. Syme AE]. (2019). Capacity to utilize raffinose dictates pneumococcal disease phenotype. mBio 10(1): e02596-18. doi:10.1128/mBio.02596-18
• Foster CSP, et al. [incl. Syme AE]. (2016). Molecular phylogenetics provides new insights into the systematics of Pimelea and Thecanthes (Thymelaeaceae). Australian Systematic Botany 29: 185–196. doi:10.1071/SB16013
• McCallum AW, et al. [incl. Syme AE]. (2014). Productivity enhances benthic species richness along an oligotrophic Indian Ocean continental margin. Global Ecology and Biogeography. doi:10.1111/geb.12255
• Poore GCB, et al. [incl. Syme AE]. (2014). Invertebrate diversity of the unexplored marine western margin of Australia: taxonomy and implications for global biodiversity. Marine Biodiversity 45: 271–286. doi:10.1007/s12526-014-0255-y
• Syme AE, Udovicic F, Stajsic V, Murphy DJ. (2013). A test of sequence-matching algorithms for a DNA barcode database of invasive grasses. DNA Barcodes 1: 19–26. doi:10.2478/dna-2012-0002
• Syme AE, Oakley TH. (2012). Dispersal between shallow and abyssal seas and evolutionary loss and re-gain of ostracod compound eyes in cylindroleberidid ostracods. Systematic Biology 61(2): 314–336. doi:10.1093/sysbio/syr085
• Syme AE. (2012). Diversification rates in the Australasian endemic grass Austrostipa – 15 million years of constant evolution. Plant Systematics and Evolution 298(1): 221–227. doi:10.1007/s00606-011-0529-z
• Syme AE, Murphy DJ, Holmes GD, Gardner S, Fowler R, Cantrill DC. (2012). An expanded phylogenetic analysis of Austrostipa (Poaceae: Stipeae) to test infrageneric relationships. Australian Systematic Botany 25: 1–10. doi:10.1071/SB11016
• Lebel T, Syme AE. (2012). Sequestrate Agaricus and Macrolepiota from Australia: new combinations and species, and their position in a calibrated phylogeny. Mycologia 104: 496–520. doi:10.3852/11-078
• Jenkins GP, Syme AE, Macreadie PI. (2011). Feeding ecology of King George whiting Sillaginodes punctatus recruits in seagrass and unvegetated habitats. Journal of Fish Biology 78: 1561–1573. doi:10.1111/j.1095-8649.2011.02978.x
• Rivera AS, et al. [incl. Syme AE]. (2010). Gene duplication and the origins of morphological complexity in pancrustacean eyes, a genomic approach. BMC Evolutionary Biology 10: 123. doi:10.1186/1471-2148-10-123
• Syme AE, Poore GCB. (2008). A supplementary description of Cypridina mariae, type species of Cylindroleberis, and rediagnosis of the genus (Ostracoda: Myodocopa: Cylindroleberididae). PLoS ONE 3(4): e1960. doi:10.1371/journal.pone.0001960
• Lum KE, Syme AE, Schwab AK, Oakley TH. (2008). Euphilomedes chupacabra (Ostracoda: Myodocopida: Philomedidae), a new demersal marine species from coastal Puerto Rico with male-biased vespertine swimming activity. Zootaxa 1684: 35–57. doi:10.11646/zootaxa.1684.1.2
• Syme AE, Poore GCB. (2006). Three new species of the Cylindroleberididae from coastal Australian waters (Crustacea: Ostracoda). Zootaxa 1305: 51–67. doi:10.11646/zootaxa.1305.1.5
• Syme AE, Poore GCB. (2006). A checklist for species of the Cylindroleberididae (Crustacea: Ostracoda). Museum Victoria Science Reports 9: 1–20. doi:10.24199/j.mvsr.2006.09

Conferences, seminars, workshops

• Nelson, TM, et al. [incl. Syme AE] (2026). Poster (Nelson T presenter). Genomics infrastructure to support Australian researchers. 47th Lorne Genome Conference, Australia.
• Syme AE. (2023, 2024, 2025). Asia-Pacific regional lead for the Galaxy Training Academy (GTA). Galaxy Training Academy, annual international event. The 2024 event attracted over 3,000 participants; the 2025 event reached a record 3,574 from 122 countries.
• Syme AE. (2025). Co-technical lead for Galaxy Australia at the Singapore Biology League (SBL 2025): approximately 500 student teams used Galaxy Australia for a major competition practical, 12 July 2025. (online) July 2025. sgbioleague.org
• Syme AE. (2025). The Power of Workflows in Galaxy Australia. Talk with live demonstration. Australian BioCommons Genomics Community Meeting, March 2025.
• Syme AE. (2024). Galaxy Australia: genome assembly workflows. Demonstration. Fungi Bioinformatics Workshop, Australian BioCommons / Galaxy Australia, 2024.
• Price G, [Galaxy Australia team incl. Syme AE], et al. (2024). Talk (Price G presenter). State of Galaxy Australia. Galaxy Community Conference (GCC2024), Brno, Czech Republic, June 2024. Syme AE recognized for IWC (Intergalactic Workflow Commission) contributions to high-quality workflows and for contribution to ELIXIR’s 2023 Biohackathon (https://www.biocommons.org.au/blogs/gcc2024).
• Nelson, TM, et al. [incl. Syme AE] (2024). Poster (Nelson T presenter). Establishing genomics infrastructure for Australian researchers. ELIXIR All-Hands Meeting, Uppsala, Sweden, June 2024. https://f1000research.com/posters/13-607
• Silver L, Syme AE, Ward N, Hogg C. (2024). Talk (Silver L presenter). Empowering Bioinformaticians and Conservation Managers: Generating Workflow Solutions in Galaxy. Genetics Society of Australasia Conference, Macquarie University, June 30 – July 3, 2024. https://genetics.org.au/wp-content/uploads/2025/03/GSA24_AbstractBook_Oficial.pdf
• Connolly K, et al. [incl. Syme AE]. (2023, 2024). Galaxy Australia – making use of national and commercial GPGPU resources. Talk (co-author; Connolly K presenter). eResearch Australasia, Brisbane, October 2023; eResearch Australasia, Melbourne, October–November 2024.
• Syme AE et al. (2024). BPA Functional Fungi bioinformatics workshop. Workshop (co-lead trainer) for 38 researchers. Australian National University, Canberra, November 2024. Developed customised training materials and six template workflows spanning QC through annotation and comparative genomics; delivered eight hands-on Galaxy sessions. All materials, 15 example histories and six workflows published on Zenodo (December 2024; >1,200 downloads). Link: https://zenodo.org/records/14498677 doi:10.5281/zenodo.14498676
• Nelson TM, et al. [incl. Syme AE] (2024). Establishing genomics infrastructure for the Australian research community. Poster. Galaxy Community Conference (GCC2024), F1000Research 2024, 13(ELIXIR):607. doi:10.7490/F1000RESEARCH.1119744.1
• Syme AE, et al. (2023). Poster. Building a Galaxy Lab for genomics. Galaxy Community Conference (GCC2023), Brisbane, July 2023. Scientific Program Committee member.
• Brown T, et al. [incl. Syme AE]. (2023). Genome annotation workflows for the Tree of Life. BioHackathon Europe, Barcelona, October–November 2023. Led Australian team. Outputs: preprint doi:10.37044/osf.io/vvadp
• Syme AE, Bassetti M, Mok W, Hyde C, Ward N, Price G. (2023). Making bioinformatics more user-friendly with custom interfaces. Talk (Price G, presenter). International Conference on Bioinformatics (InCoB), 2023.
• Syme AE. (2023). Melbourne Bioinformatics workshops (mid-2023): Introduction to Galaxy and Galaxy Workflows; Introduction to Galaxy and Quality Control. Workshops (presenter). Melbourne Bioinformatics, University of Melbourne, 2023.
• Price G, Syme AE. (2022). Bioinformatics Training: Galaxy Global Platform for the Analysis of SARS-CoV-2 Data and Variants. Training session. 53rd Meeting of the Asia Pacific Advanced Network (APAN53), Bangladesh (online/hybrid), 7 March 2022. Coordinated by eResearch Network for South East Asia (eRSEA). apan53.apan.net
• Syme AE, et al. (2021). Driving workforce transition in Australian life science research. Poster. Galaxy Community Conference (GCC2021), July 2021 (online). Scientific Program Committee member. Workshop (presenter): Genome Assembly – lecture and hands-on tutorial (Syme AE, Gladman S).
• Syme AE. (2021). Assembling genomes on Galaxy Australia. Presentation. Australian BioCommons Showcase, Melbourne, 4 November 2021. Panelist: Galaxy Partnerships – Partnering with the international community (Ward N, Price G, Gladman S, Syme AE).
• Syme AE. (2021). What can long reads tell us about genome structure? Presentation. Melbourne Bioinformatics Group Meeting, March 2021.
• Syme AE. (2021). Asia/Pacific Facilitator for several multi-day international Galaxy workshops: Galaxy Smorgasbord training week (>1,000 participants); SARS-CoV-2 Data Analysis and Monitoring with Galaxy; Plant Transcriptomics with Galaxy.
• Syme AE, et al. (2021). Driving workforce transition in Australian life science research. Poster. Galaxy Community Conference, F1000Research. doi:10.7490/f1000research.1118591.1
• Pope B, et al. [incl. Syme AE]. (2020). Best practices in bioinformatics command-line software with Bionitio. Talk (co-author; Pope B presenter). ABACBS Annual Conference, November 2020 (online).
• Syme AE. (2020). What do researchers want to know? Presentation. Australian BioCommons BYOD Project Presentation, November 2020.
• Pope B, Syme AE. (2020). Bionitio – building better bioinformatics tools with batteries included. Workshop (co-presenter). Bioinformatics Community Conference (BCC2020), 18 July 2020.
• Syme AE. (2020). Chloroplast genome assembly using Galaxy Australia. Webinar. Australian BioCommons, 10 December 2020.
• Pope B, et al. [incl. Syme AE]. (2020). Bionitio. Talk (co-author; Pope B presenter). Bioinformatics Community Conference (BCC), July 2020 (online).
• Syme AE. (2020). GAP Reference Genomes Pilot. Presentation. BioPlatforms Australia Facilities Meeting, May 2020.
• Price G, et al. [incl. Syme AE]. (2019). Galaxy Australia – inside the national vision of a data commons. Talk (co-author; Price G presenter). Galaxy Community Conference (GCC2019), Freiburg, Germany, 2 July 2019. Session chair: Transcriptomics and Genomics (3 July 2019).
• Hiltemann S, et al. [incl. Syme AE]. (2019). Train the Galaxy Trainer. Workshop (co-presenter). Galaxy Community Conference (GCC2019), Freiburg, Germany, 3 July 2019. Overview: gcc2019.sched.com/event/MDTV
• Lariviere D, Syme AE. (2019). Assembly and annotation of bacterial genomes. Workshop (co-presenter). Galaxy Community Conference (GCC2019), Freiburg, 4 July 2019.
• Session co-chair: Plant genomics. Australasian Genomic Technologies Association (AGTA) Conference, Melbourne, 8 October 2019.
• Pope B, Syme AE, Cameron D. (2018). Best practices in bioinformatics software development. Workshop (co-presenter). ABACBS Conference, Melbourne, 30 November 2018.
• Price G, et al. [incl. Syme AE]. (2018). Enabling Australian Genomics research through enhancements to the Genomics Virtual Lab. Talk (co-author; Price G presenter). eResearch Australasia Conference, Melbourne, October 2018.
• Syme AE. (2018). Long-read genome assembly. Workshop (presenter/developer). Melbourne Bioinformatics Genome Assembly Workshop, October 2018 (Syme AE, Seemann T, Gladman S) and March 2018 (Syme AE, Seemann T).
• Syme AE. (2018). National Hybrid Training. Workshop (developer and co-presenter). Galaxy Australia / Australian BioCommons, 2018. Four workshops across Australia: (1) Genome Assembly and Annotation, 22 August; (2) Finding Genetic Variants in Bacterial Sequence Data, 12 September; (3) Differential Gene Expression from Bacterial RNA-Seq Data, 23 October; (4) Metagenomics, 14 November. Facilitator Training for Hybrid Training, Melbourne, 26–27 July.
• Pope B, Syme AE. (2018). Bionitio for bioinformatics command-line software. Workshop (co-presenter). Melbourne Bioinformatics, July 2018.
• Syme AE, et al. (2017). Galaxy training for microbial genomics. Poster (presenter). ABACBS Annual Conference, Adelaide, November 2017.
• Syme AE. (2017). Building genomics tutorials in Galaxy, for biologists. Talk (presenter). Galaxy Australasia Meeting (GAMe), Melbourne, February 2017.
• Kwong JC, et al. [incl. Syme AE]. (2017). Combined genomic and epidemiological investigation of a state-wide, multi-institution outbreak of KPC-producing Enterobacteriaceae. Poster (co-author). European Congress of Clinical Microbiology and Infectious Diseases (ECCMID), Vienna, April 2017.
• Syme AE. (2017). Long-read genome assembly. Workshop (presenter/developer). Melbourne Bioinformatics Genome Assembly Workshop, October 2017.
• Gladman S, Syme AE. (2017). Galaxy, Assembly, Annotation, Useful tools, Moving data, Variant calling. Workshop (co-presenter). Genomics Workshop for Faculty of Veterinary and Agricultural Sciences, University of Melbourne, November 2017.
• Gladman S, Syme AE. (2017). Bacterial genomics using the Galaxy platform. Workshop (co-presenter). Genomics Workshop for Intersect, Sydney, December 2017.
• Syme AE. (2017). The Genomics Virtual Laboratory and Omics Platform. Workshop/demonstration (presenter). eResearch South Australia, Adelaide, April 2017.
• Syme AE. (2017). Genome size from k-mer counting. Melbourne Bioinformatics, September 2017.
• Syme AE. (2016). Using DNA to understand eye evolution. Melbourne Bioinformatics, June 2016.
• Syme AE. (2016). Complete genomes from long and short reads. Melbourne Bioinformatics, October 2016.
• Syme AE, Seemann T, Gladman S, Bulach D. (2016). Complete genomes: the long and the short of it. Poster (presenter). ABACBS Annual Conference, Brisbane, November 2016. Published: F1000Research 5: 2589. doi:10.7490/f1000research.1113338.1
• Syme AE, Seemann T, Gladman S, Bulach D, et al. (2016). RDS Omics Training Material – antibiotic resistant pathogens. Project update (presenter). RDS/BPA Omics Consortium Meeting, Melbourne, November 2016.
• Gladman S, Syme AE. (2016). A next-generation sequencing workshop: assembly, annotation, variant calling. Workshop (co-presenter). UWA Microbial Genomics Workshop, Perth, November 2016. Event: combine.org.au
• Syme AE, Stefani F. (2012). Phylogenetic methods using BEAST, R and Geneious. Presentation and workshop. Melbourne Systematics Forum, May 2012.
• Syme AE, Udovicic F. (2011). Investigating rbcL gene duplication in grasses. Talk (presenter). Session chair: Barcoding Grasses. Fourth International Barcode of Life Conference, Adelaide, 2011.
• Syme AE, Udovicic F. (2011). A multi-gene study of relationships within the Australian grass genus Austrostipa. Talk (presenter). XVIII International Botanical Congress, Melbourne, 2011.
• Udovicic F, Syme AE, Murphy D, Stajsic V. (2011). DNA barcodes for stipoid grasses: developing a better tool for biosecurity. Talk (co-author; Udovicic F presenter). XVIII International Botanical Congress, Melbourne, 2011.
• Cross H, Murphy D, Brown A, Gardner S, Syme AE, Jardine D, Cantrill D, Lowe A. (2011). Utilizing grass DNA barcodes to explore Australian ecosystems. Talk (co-author; Cross H presenter). XVIII International Botanical Congress, Melbourne, 2011.
• Syme AE, Oakley TH. (2008). How quickly are eyes lost? A phylogenetic study of deep sea and shallow water cylindroleberidid ostracods. Talk (presenter). Society for Integrative and Comparative Biology (SICB) Annual Conference, San Antonio, Texas, 2008.
• Syme AE. (2005). Towards a phylogeny of the Cylindroleberididae (Crustacea: Ostracoda). Poster (presenter). Sixth International Crustacean Congress, Glasgow, 2005.

Galaxy Training Network tutorials

• Anna Syme, Nicola Soranzo, A short introduction to Galaxy (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-short/tutorial.html [Total pageviews: 89,100; 2025 pageviews: 19,500]
• Anna Syme, Chloroplast genome assembly (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/assembly/tutorials/chloroplast-assembly/tutorial.html [Total pageviews: 12,900; 2025 pageviews: 2,300]
• Anna Syme, Large genome assembly and polishing (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/assembly/tutorials/largegenome/tutorial.html [Total pageviews: 10,300; 2025 pageviews: 3,800]
• Delphine Lariviere et al. [incl Anna Syme], Vertebrate genome assembly using HiFi, Bionano and Hi-C data - Step by Step (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/assembly/tutorials/vgp_genome_assembly/tutorial.html [Total pageviews: 25,500; 2025 pageviews: 5,400]
• Anna Syme, Torsten Seemann, Simon Gladman, Genome annotation with Prokka (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/genome-annotation/tutorials/annotation-with-prokka/tutorial.html [Total pageviews: 32,300; 2025 pageviews: 3,100]
• Anna Syme, Simon Gladman, Torsten Seemann, Microbial Variant Calling (Galaxy Training Materials). https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/microbial-variants/tutorial.html [Total pageviews: 24,800; 2025 pageviews: 3,000]
• GTN contributor profile: training.galaxyproject.org/hall-of-fame/annasyme/

Galaxy Top Tips (YouTube series)

• Syme AE. (2024). Saving time when uploading data. Galaxy Top Tips, Australian BioCommons, 2024.
• Syme AE. (2024). Automate your data analyses with workflows. Galaxy Top Tips, Australian BioCommons, 2024.

Zenodo tutorials and datasets

• Syme AE. (2021). Tutorial: Assemble a large genome using Galaxy. Zenodo. doi:10.5281/zenodo.5655813 [327 downloads]
• Syme AE. (2020). Tutorial: Assemble and annotate a chloroplast genome. Zenodo. doi:10.5281/zenodo.3971667 [502 downloads]
• Syme AE. (2020). Chloroplast genome sequencing reads from snow gum [dataset]. Zenodo. doi:10.5281/zenodo.3600662 [267 downloads]
• Syme AE. (2019). Chloroplast genome sequencing reads from sweet potato [dataset]. Zenodo. doi:10.5281/zenodo.3567224 [3,686 downloads]
• Schwessinger B, et al. [incl. Syme AE]. (2024). BPA Functional Fungi bioinformatics workshop: training materials, 15 example histories and 6 workflows. Zenodo. https://zenodo.org/records/14498677 [1,218 downloads]

WorkflowHub workflows

Source: workflowhub.eu/people/200/workflows

• Syme A. (2021). Data QC. WorkflowHub. https://doi.org/10.48546/workflowhub.workflow.222.1 [8,167 views; 840 downloads]
• Syme A. (2021). kmer counting - Meryl. WorkflowHub. https://doi.org/10.48546/workflowhub.workflow.223.1 [9,513 views; 794 downloads]
• Syme A. (2021). Trim and filter reads - Fastp. WorkflowHub. https://doi.org/10.48546/workflowhub.workflow.224.1 [15,999 views; 784 downloads]
• Syme A. (2021). Assembly with Flye. WorkflowHub. https://doi.org/10.48546/workflowhub.workflow.225.1 [10,788 views; 859 downloads]
• Syme A. (2021). Assembly polishing. WorkflowHub. https://doi.org/10.48546/workflowhub.workflow.226.1 [10,394 views; 813 downloads]
• Syme A. (2021). Racon polish with long reads, x4. WorkflowHub. https://doi.org/10.48546/workflowhub.workflow.227.1 [9,481 views; 840 downloads]
• Syme A. (2021). Racon polish with Illumina reads, x2. WorkflowHub. https://doi.org/10.48546/workflowhub.workflow.228.1 [8,281 views; 757 downloads]
• Syme A. (2021). Assess genome quality. WorkflowHub. https://doi.org/10.48546/workflowhub.workflow.229.1 [8,132 views; 768 downloads]
• Syme A. (2021). Combined workflows for large genome assembly. WorkflowHub. https://doi.org/10.48546/workflowhub.workflow.230.1 [8,411 views; 870 downloads]
• Syme A. (2022). QC of RADseq reads. WorkflowHub. https://workflowhub.eu/workflows/346 [8,131 views; 675 downloads]
• Syme A. (2022). Stacks RAD-seq reference-guided workflow. WorkflowHub. https://workflowhub.eu/workflows/347 [9,418 views; 763 downloads]
• Syme A. (2022). Stacks RAD-seq de novo workflow. WorkflowHub. https://workflowhub.eu/workflows/348 [8,915 views; 694 downloads]
• Syme A. (2022). Partial de novo workflow: ustacks only. WorkflowHub. https://workflowhub.eu/workflows/349 [7,494 views; 732 downloads]
• Syme A. (2022). Partial de novo workflow: c-s-g-pops only. WorkflowHub. https://workflowhub.eu/workflows/350 [7,358 views; 718 downloads]
• Syme A. (2022). Partial ref-guided workflow - bwa mem only. WorkflowHub. https://workflowhub.eu/workflows/351 [7,369 views; 676 downloads]
• Syme A. (2022). Partial ref-guided workflow - gstacks and pops. WorkflowHub. https://workflowhub.eu/workflows/352 [7,427 views; 695 downloads]
• Silver L, Syme A. (2024). QC and trimming of RNAseq reads - TSI. WorkflowHub. https://doi.org/10.48546/workflowhub.workflow.876.1 [5,215 views; 649 downloads]
• Silver L, Syme A. (2024). Find transcripts - TSI. WorkflowHub. https://doi.org/10.48546/workflowhub.workflow.877.1 [5,428 views; 589 downloads]
• Silver L, Syme A. (2024). Combine transcripts - TSI. WorkflowHub. https://doi.org/10.48546/workflowhub.workflow.878.1 [5,381 views; 615 downloads]
• Silver L, Syme A. (2024). Extract transcripts - TSI. WorkflowHub. https://doi.org/10.48546/workflowhub.workflow.879.1 [5,260 views; 603 downloads]
• Silver L, Syme A. (2024). Convert formats - TSI. WorkflowHub. https://doi.org/10.48546/workflowhub.workflow.880.1 [5,464 views; 712 downloads]
• Silver L. (2024). Fgenesh annotation - TSI. WorkflowHub. https://doi.org/10.48546/workflowhub.workflow.881.5 [8,759 views; 2,284 downloads]
• Silver L, Syme A. (2024). Repeat masking - TSI. WorkflowHub. https://doi.org/10.48546/workflowhub.workflow.875.3 [7,158 views; 1,500 downloads]
• Syme A. (2024). Genome assembly workflow for nanopore reads, for TSI. WorkflowHub. https://doi.org/10.48546/workflowhub.workflow.1114.1 [4,376 views; 505 downloads]
• Farquharson K, Price G, Tang S, Syme A. (2024). Genome-assessment-post-assembly. WorkflowHub. https://doi.org/10.48546/workflowhub.workflow.403.7 [13,323 views; 3,052 downloads]

IWC workflows

• Syme AE. (2024). Assembly with Flye. Galaxy workflow, Intergalactic Workflow Commission (IWC). https://workflowhub.eu/workflows/750 [5,950 views; 21,778 downloads]
• Syme AE. (2023). Polish with long reads. Galaxy workflow, Intergalactic Workflow Commission (IWC). https://workflowhub.eu/workflows/563 [6,193 views; 7,656 downloads]

Galaxy Australia published workflows

Selected workflows; owner/creator AE Syme

• Create manifest for fastq files for Qiime2 (2025). https://usegalaxy.org.au/u/anna/w/create-manifest-for-fastq-files-for-qiime2
• QC of Illumina data (2025). https://usegalaxy.org.au/u/anna/w/qc-illumina-data
• Combined fungi assembly and annotation workflow - Version 1 (2024). https://usegalaxy.org.au/u/anna/w/combined-fungi-assembly-and-annotation-workflow
• Conditional workflows simple example - Version 1 (2024). https://usegalaxy.org.au/u/anna/w/copy-of-demo-workflow-for-conditional-statements-1
• Create pairwise FASTA list (2024). https://usegalaxy.org.au/u/anna/w/create-pairwise-fasta-list
• Demonstration conditional workflow (2024). https://usegalaxy.org.au/u/anna/w/demonstration-conditional-workflow
• Examples of optional and restricted inputs - Version 1 (2024). https://usegalaxy.org.au/u/anna/w/examples-of-optional-and-restricted-inputs
• Fungi: Assembly QC, Blast, RagTag - Version 1 (2024). https://usegalaxy.org.au/u/anna/w/fungi-assembly-qc
• Fungi: Illumina data QC and assembly - Version 1 (2024). https://usegalaxy.org.au/u/anna/w/fungi-illumina-assembly
• Fungi: repeat masking, annotation with Helixer, Funannotate, Fgenesh (2024). https://usegalaxy.org.au/u/anna/w/fungi-annotation
• Pre-Alphafold workflow to create list of target-candidate pairs - Version 1 (2024). https://usegalaxy.org.au/u/anna/w/create-target-candidate-pairs
• Run a tool if more than x reads - Version 1 (2024). https://usegalaxy.org.au/u/anna/w/copy-of-demonstration-conditional-workflow
• What is in my sequencing reads? - Version 1 (2024). https://usegalaxy.org.au/u/anna/w/what-is-in-my-sequencing-reads
• Workflow example with workflow report - Version 1 (2024). https://usegalaxy.org.au/u/anna/w/workflow-example-with-workflow-report
• Assembly polishing (2021). https://usegalaxy.org.au/u/anna/w/assembly-polishing
• Assembly with Flye (2021). https://usegalaxy.org.au/u/anna/w/assembly-with-flye
• Assess genome quality (2021). https://usegalaxy.org.au/u/anna/w/assess-genome
• Combined workflows for large genome assembly (2021). https://usegalaxy.org.au/u/anna/w/combined-large-genome-workflow
• Data QC (2021). https://usegalaxy.org.au/u/anna/w/data-qc
• kmer counting - meryl (2021). https://usegalaxy.org.au/u/anna/w/kmer-counting-meryl
• Prepare test data - remove chloroplast reads and subsample to 10% (2021). https://usegalaxy.org.au/u/anna/w/prepare-test-data-remove-chloro-subsample-10-pc
• Racon polish with Illumina reads (R1 only), x2 (2021). https://usegalaxy.org.au/u/anna/w/racon-polish-with-illumina-reads-x2
• Racon polish with long reads, x4 (2021). https://usegalaxy.org.au/u/anna/w/racon-polish-with-long-reads-x4
• Trim and filter reads - fastp (2021). https://usegalaxy.org.au/u/anna/w/trim-and-filter-reads-fastp

Professional memberships and reviewing

• Editorial Board member, Gigabyte (since 2020): gigabytejournal.com/editorial-board
• Australian Bioinformatics and Computational Biology Society (ABACBS): Education Sub-Committee member.
• Galaxy Outreach and Training Committee member. Galaxy Community Conference Scientific Committee member (2020, 2021, 2023).
• Peer reviewer for: GigaByte; GigaScience; Journal of Crustacean Biology; Proceedings of the Biological Society of Washington; Zootaxa; Australian Biological Resources Study; Deep Sea Research.
• Associate Editor, Muelleria. Botanical research journal of the Royal Botanic Gardens Victoria (2010-2012)

Books

• Wilson R, Norman M, Syme AE. (2007). An Introduction to Marine Life. Museum Victoria / CSIRO Publishing. 144 pp. ISBN: 9780975837054.
• Poore GCB, Syme AE. (2009). Barnacles. Museum Victoria / CSIRO Publishing. 36 pp. ISBN: 9780980381351.

Theses

• Syme AE. (2007). A Systematic Revision of the Cylindroleberididae (Crustacea: Ostracoda: Myodocopa). PhD thesis, The University of Melbourne. minerva-access.unimelb.edu.au/items/c2d1a62c-1c48-58f5-914b-21d2065f452b
• Syme AE. (1998). Food Limitation and Daily Ration of Post-settlement King George Whiting (Sillaginodes punctatus) in Port Phillip Bay. BSc(Hons) thesis, The University of Melbourne.

Community engagement

• Collaborator, evolutionary biologist/bioinformatician consultant: “Gene Tree Project - the sound of art and science; E Goodrich” (2016 – 2020). Supported by: Australia Council for the Arts, Australia Arts Music Fund, Creative Victoria, City of Melbourne/ Creative Spaces, Culture_Lab14. The project is a dynamic collaboration between composer and musician Elissa Goodrich, dramaturge Nadja Kostich and evolutionary biologist Dr Anna Syme.
• Blindside Festival - On The Verge: composer Elissa Goodrich + biologist Dr Anna Syme in conversation with writer/broadcaster Melissa Cranenburgh. The Kelvin Club, August 31, 2016. // Interview: Frankie magazine, Jan/Feb 2017 issue