Bioinformatics Training

This review provides a historical overview of the inception and development of bioinformatics research in the Netherlands. Rooted in theoretical biology by foundational figures such as Paulien Hogeweg (at Utrecht University since the 1970s), the developments leading to organizational structures supporting a relatively large Dutch bioinformatics community will be reviewed. We will show that the most valuable resource that we have built over these years is the close-knit national expert community that is well engaged in basic and translational life science research programmes. The Dutch bioinformatics community is accustomed to facing the ever-changing landscape of data challenges and working towards solutions together. In addition, this community is the stable factor on the road towards sustainability, especially in times where existing funding models are challenged and change rapidly.

is a bioinformatician with expertise and interest in systems biology approaches, de novo genome assembly, NGS data analysis, cloud computing and workshop development and delivery. Catherine A. Shang is a project manager working within large Australian collaborative systems biology research consortiums. Catherine is actively involved in establishing collaborative bioinformatics networks and developing and delivering open access bioinformatics training courses for the benefit of the Australian research community. Matthias Haimel is a bioinformatician working with different types of next-generation sequencing data, with a focus on assembling and analysing genomes. During the past 4 years, Matthias has been involved in developing and delivering next-generation sequencing courses either at the EBI or abroad. Myrto Kostadima is a PhD student at the European Bioinformatics Institute (EBI) with interest in transcription and the mechanisms of transcriptional regulation in humans. Myrto has been involved in organizing and delivering courses on next-generation sequencing for the past 3 years either at the EBI or abroad. Remco Loos is a postdoc working on understanding the mechanisms behind pluripotency and self-renewal in stem cells through next-generation sequencing, including Ribonucleic acid-sequencing (RNA-seq) and ChIP-seq, as well as sequencing approaches to epigenetic features (DNA methylation, histone modification, nucleosome positioning). In addition, Remco has been involved in developing and delivering training in next-generation sequencing analysis for the past 3 years. Nandan Deshpande is a bioinformatician with focus on systems biology-based data analysis and experience in genome assembly and de novo transcriptomics. Konsta Duesing Leads a team of bioinformaticians and statisticians engaged in genomics, epigenomics and metagenomics research. Konsta has developed and delivered training courses in NGS analysis and has a strong interest in systems approaches to biology and health. He is currently developing methods for the multiple 'omics' data space. Xi Li is a bioinformatician working on genome annotation, NGS data processing and web-based biodata analysis platforms, also with particular interests in developing computational algorithms for the study of gene regulation as well as NGS training workshops. Annette McGrath is the Bioinformatics Core Leader at the Commonwealth Scientific and Industrial Research Organisation. She leads a team of bioinformaticians involved in genomics research, bioinformatics infrastructure and tool development and provision and with a strong interest in training and development. Sean McWilliam is a bioinformatician with a focus on genome annotation, genome assembly and variant analysis. Simon Michnowicz assists researchers with high-performance computing requirements use the National Computational Infrastructure, hosted at Australian National University. He has a background in computational Proteomics. Paula Moolhuijzen is a bioinformatician experienced in the analysis of NGS genome, transcriptome and metagenomic data, with a particular interest is the development high-throughput workflows for bioinformatics analyses.

is a bioinformatician with expertise and interest in systems biology approaches, de novo genome assembly, NGS data analysis, cloud computing and workshop development and delivery. Catherine A. Shang is a project manager working within large Australian collaborative systems biology research consortiums. Catherine is actively involved in establishing collaborative bioinformatics networks and developing and delivering open access bioinformatics training courses for the benefit of the Australian research community. Matthias Haimel is a bioinformatician working with different types of next-generation sequencing data, with a focus on assembling and analysing genomes. During the past 4 years, Matthias has been involved in developing and delivering next-generation sequencing courses either at the EBI or abroad. Myrto Kostadima is a PhD student at the European Bioinformatics Institute (EBI) with interest in transcription and the mechanisms of transcriptional regulation in humans. Myrto has been involved in organizing and delivering courses on next-generation sequencing for the past 3 years either at the EBI or abroad. Remco Loos is a postdoc working on understanding the mechanisms behind pluripotency and self-renewal in stem cells through next-generation sequencing, including Ribonucleic acid-sequencing (RNA-seq) and ChIP-seq, as well as sequencing approaches to epigenetic features (DNA methylation, histone modification, nucleosome positioning). In addition, Remco has been involved in developing and delivering training in next-generation sequencing analysis for the past 3 years. Nandan Deshpande is a bioinformatician with focus on systems biology-based data analysis and experience in genome assembly and de novo transcriptomics. Konsta Duesing Leads a team of bioinformaticians and statisticians engaged in genomics, epigenomics and metagenomics research. Konsta has developed and delivered training courses in NGS analysis and has a strong interest in systems approaches to biology and health. He is currently developing methods for the multiple 'omics' data space. Xi Li is a bioinformatician working on genome annotation, NGS data processing and web-based biodata analysis platforms, also with particular interests in developing computational algorithms for the study of gene regulation as well as NGS training workshops. Annette McGrath is the Bioinformatics Core Leader at the Commonwealth Scientific and Industrial Research Organisation. She leads a team of bioinformaticians involved in genomics research, bioinformatics infrastructure and tool development and provision and with a strong interest in training and development. Sean McWilliam is a bioinformatician with a focus on genome annotation, genome assembly and variant analysis. Simon Michnowicz assists researchers with high-performance computing requirements use the National Computational Infrastructure, hosted at Australian National University. He has a background in computational Proteomics. Paula Moolhuijzen is a bioinformatician experienced in the analysis of NGS genome, transcriptome and metagenomic data, with a particular interest is the development high-throughput workflows for bioinformatics analyses.

The advent of Next Generation Sequencing (NGS) technologies has opened new possibilities for researchers. However, the more biology becomes a data-intensive field, the more biologists have to learn how to process and analyze NGS data with complex computational tools. Even with the availability of common pipeline specifications, it is often a time-consuming and cumbersome task for a bench scientist to install and configure the pipeline tools. We believe that a unified, desktop and biologist-friendly front end to NGS data analysis tools will substantially improve productivity in this field. Here we present NGS pipelines "Variant Calling with SAMtools", "Tuxedo Pipeline for RNA-seq Data Analysis" and "Cistrome Pipeline for ChIP-seq Data Analysis" integrated into the Unipro UGENE desktop toolkit. We describe the available UGENE infrastructure that helps researchers run these pipelines on different datasets, store and investigate the results and rerun the pipelines with the same parameters. These pipeline tools are included in the UGENE NGS package. Individual blocks of these pipelines are also available for expert users to create their own advanced workflows.

The advent of Next Generation Sequencing (NGS) technologies has opened new possibilities for researchers. However, the more biology becomes a data-intensive field, the more biologists have to learn how to process and analyze NGS data with complex computational tools. Even with the availability of common pipeline specifications, it is often a time-consuming and cumbersome task for a bench scientist to install and configure the pipeline tools. We believe that a unified, desktop and biologist-friendly front end to NGS data analysis tools will substantially improve productivity in this field. Here we present NGS pipelines "Variant Calling with SAMtools", "Tuxedo Pipeline for RNA-seq Data Analysis" and "Cistrome Pipeline for ChIP-seq Data Analysis" integrated into the Unipro UGENE desktop toolkit. We describe the available UGENE infrastructure that helps researchers run these pipelines on different datasets, store and investigate the results and rerun the pipelines with the same parameters. These pipeline tools are included in the UGENE NGS package. Individual blocks of these pipelines are also available for expert users to create their own advanced workflows.

She works on structural bioinformatics and teaches both academic and short training courses. She is Secretary of the Global Organisation for Bioinformatics Learning, Education and Training (GOBLET). Thomas Blicher is an Associate Professor at the NNF Center for Protein Research, University of Copenhagen. He is involved in teaching graduate and undergraduate students as well as developing methods for use of web-based tools in teaching.

As bioinformatics becomes increasingly central to research in the molecular life sciences, the need to train non-bioinformaticians to make the most of bioinformatics resources is growing. Here, we review the key challenges and pitfalls to providing effective training for users of bioinformatics services, and discuss successful training strategies shared by a diverse set of bioinformatics trainers. We also identify steps that trainers in bioinformatics could take together to advance the state of the art in current training practices. The ideas presented in this article MariaVictoria Schneider is the Training Programme Project Leader in the Outreach and Training Team at EMBL-EBI where she is responsible for developing and coordinating the in-house and external training activities of EMBL-EBI. James Watson is the Senior Scientific Training Officer in the Outreach and Training Team at EMBL-EBI, prior to this he was a postdoctoral researcher in the Thornton group looking at protein structure-function relationships. Teresa Attwood is professor of Bioinformatics at the University of Manchester; she coordinates and teaches the introductory module of the Bioinformatics Masters course, and has written several bioinformatics reference and textbooks .

Demand for training life scientists in bioinformatics skills led to the development of a trainthe-trainer collaboration between the European Molecular Biology Laboratory-European Bioinformatics Institute (EMBL-EBI) and 2 Australian organisations, Bioplatforms Australia and Commonwealth Scientific and Industrial Research Organisation (CSIRO) in 2012. The goal of the collaboration was to establish a group of trained instructors who could develop and deliver short bioinformatics courses nationally. A train-the-trainer course introduces instructors to aspects of andragogy and evidence-based learning principles to help them better design, develop, and deliver high-quality training. Since then, both the number of trainers in the network and the course portfolio have grown. Best practises have been developed and shared between the Australian cohort and EMBL-EBI to address common challenges in bioinformatics training. The Australian trainer cohort undertook a train-the-trainer instructor course, again with EMBL-EBI, and subsequently successfully delivered train-thetrainer courses to interested bioinformatics trainers within Australia. We conclude that a train-the-trainer approach can help build national capacity and maintain a critical mass of trained instructors. This is a PLOS Computational Biology Education paper.

The Bioinformatics Training Platform (BTP) has been developed to provide access to the computational infrastructure required to deliver sophisticated hands-on bioinformatics training courses. The BTP is a cloud-based solution that is in active use for delivering next-generation sequencing training to Australian researchers at geographically dispersed locations. The BTP was built to provide an easy, accessible, consistent and cost-effective approach to delivering workshops at host universities and organizations with a high demand for bioinformatics training but lacking the dedicated bioinformatics training suites required. To support broad uptake of the BTP, the platform has been made compatible with multiple cloud infrastructures. The BTP is an open-source and open-access resource. To date, 20 training workshops have been delivered to over 700 trainees at over 10 venues across Australia using the BTP.

There is a clear demand for hands-on bioinformatics training. The development of bioinformatics workshop content is both time-consuming and expensive. Therefore, enabling trainers to develop bioinformatics workshops in a way that facilitates reuse is becoming increasingly important. The most widespread practice for sharing workshop content is through making PDF, PowerPoint and Word documents available online. While this effort is to be commended, such content is usually not so easy to reuse or repurpose and does not capture all the information required for a third party to rerun a workshop. We present an open, collaborative framework for developing and maintaining, reusable and shareable hands-on training workshop content.

The Bioinformatics Training Platform (BTP) has been developed to provide access to the computational infrastructure required to deliver sophisticated hands-on bioinformatics training courses. The BTP is a cloud-based solution that is in active use for delivering next-generation sequencing training to Australian researchers at geographically dispersed locations. The BTP was built to provide an easy, accessible, consistent and cost-effective approach to delivering workshops at host universities and organizations with a high demand for bioinformatics training but lacking the dedicated bioinformatics training suites required. To support broad uptake of the BTP, the platform has been made compatible with multiple cloud infrastructures. The BTP is an open-source and open-access resource. To date, 20 training workshops have been delivered to over 700 trainees at over 10 venues across Australia using the BTP.

There is a clear demand for hands-on bioinformatics training. The development of bioinformatics workshop content is both time-consuming and expensive. Therefore, enabling trainers to develop bioinformatics workshops in a way that facilitates reuse is becoming increasingly important. The most widespread practice for sharing workshop content is through making PDF, PowerPoint and Word documents available online. While this effort is to be commended, such content is usually not so easy to reuse or repurpose and does not capture all the information required for a third party to rerun a workshop. We present an open, collaborative framework for developing and maintaining, reusable and shareable hands-on training workshop content.

Nathan S.Watson-Haigh is a bioinformatician with expertise and interest in systems biology approaches, de novo genome assembly, NGS data analysis, cloud computing and workshop development and delivery. Catherine A. Shang is a project manager working within large Australian collaborative systems biology research consortiums. Catherine is actively involved in establishing collaborative bioinformatics networks and developing and delivering open access bioinformatics training courses for the benefit of the Australian research community. Matthias Haimel is a bioinformatician working with different types of next-generation sequencing data, with a focus on assembling and analysing genomes. During the past 4 years, Matthias has been involved in developing and delivering next-generation sequencing courses either at the EBI or abroad. Myrto Kostadima is a PhD student at the European Bioinformatics Institute (EBI) with interest in transcription and the mechanisms of transcriptional regulation in humans. Myrto has been involved in organizing and delivering courses on next-generation sequencing for the past 3 years either at the EBI or abroad. Remco Loos is a postdoc working on understanding the mechanisms behind pluripotency and self-renewal in stem cells through next-generation sequencing, including Ribonucleic acid-sequencing (RNA-seq) and ChIP-seq, as well as sequencing approaches to epigenetic features (DNA methylation, histone modification, nucleosome positioning). In addition, Remco has been involved in developing and delivering training in next-generation sequencing analysis for the past 3 years. Nandan Deshpande is a bioinformatician with focus on systems biology-based data analysis and experience in genome assembly and de novo transcriptomics. Konsta Duesing Leads a team of bioinformaticians and statisticians engaged in genomics, epigenomics and metagenomics research. Konsta has developed and delivered training courses in NGS analysis and has a strong interest in systems approaches to biology and health. He is currently developing methods for the multiple 'omics' data space. Xi Li is a bioinformatician working on genome annotation, NGS data processing and web-based biodata analysis platforms, also with particular interests in developing computational algorithms for the study of gene regulation as well as NGS training workshops. Annette McGrath is the Bioinformatics Core Leader at the Commonwealth Scientific and Industrial Research Organisation. She leads a team of bioinformaticians involved in genomics research, bioinformatics infrastructure and tool development and provision and with a strong interest in training and development. Sean McWilliam is a bioinformatician with a focus on genome annotation, genome assembly and variant analysis. Simon Michnowicz assists researchers with high-performance computing requirements use the National Computational Infrastructure, hosted at Australian National University. He has a background in computational Proteomics. Paula Moolhuijzen is a bioinformatician experienced in the analysis of NGS genome, transcriptome and metagenomic data, with a particular interest is the development high-throughput workflows for bioinformatics analyses. Steve Quenette is the deputy director of the Monash eResearch Centre and project sponsor of the NeCTAR Research Cloud node at Monash University, with expertise in research platforms and productivity, and a research interest in computational science. Jerico Nico De Leon Revote is a developer involved in research collaborations, 3D immersive visualizations and the NeCTAR Australian national research cloud. Sonika Tyagi is a bioinformatician working in the genomics area with main focus on high-throughput sequence analysis. She is involved in developing computational methods and protocols for transcriptomics, post-transcription gene regulation analysis, exome and variation analysis. MariaV. Schneider is the Head of Training and Outreach for The Genome Analysis Centre (TGAC) where she is responsible for the strategic coordination of the in-house and external TGAC Training and Outreach activities. Before this, she was the User Training Coordinator at EMBL-EBI.

The Bioinformatics Training Platform (BTP) has been developed to provide access to the computational infrastructure required to deliver sophisticated hands-on bioinformatics training courses. The BTP is a cloud-based solution that is in active use for delivering next-generation sequencing training to Australian researchers at geographically dispersed locations. The BTP was built to provide an easy, accessible, consistent and cost-effective approach to delivering workshops at host universities and organizations with a high demand for bioinformatics training but lacking the dedicated bioinformatics training suites required. To support broad uptake of the BTP, the platform has been made compatible with multiple cloud infrastructures. The BTP is an open-source and open-access resource. To date, 20 training workshops have been delivered to over 700 trainees at over 10 venues across Australia using the BTP.

Nathan S.Watson-Haigh is a bioinformatician with expertise and interest in systems biology approaches, de novo genome assembly, NGS data analysis, cloud computing and workshop development and delivery. Catherine A. Shang is a project manager working within large Australian collaborative systems biology research consortiums. Catherine is actively involved in establishing collaborative bioinformatics networks and developing and delivering open access bioinformatics training courses for the benefit of the Australian research community. Matthias Haimel is a bioinformatician working with different types of next-generation sequencing data, with a focus on assembling and analysing genomes. During the past 4 years, Matthias has been involved in developing and delivering next-generation sequencing courses either at the EBI or abroad. Myrto Kostadima is a PhD student at the European Bioinformatics Institute (EBI) with interest in transcription and the mechanisms of transcriptional regulation in humans. Myrto has been involved in organizing and delivering courses on next-generation sequencing for the past 3 years either at the EBI or abroad. Remco Loos is a postdoc working on understanding the mechanisms behind pluripotency and self-renewal in stem cells through next-generation sequencing, including Ribonucleic acid-sequencing (RNA-seq) and ChIP-seq, as well as sequencing approaches to epigenetic features (DNA methylation, histone modification, nucleosome positioning). In addition, Remco has been involved in developing and delivering training in next-generation sequencing analysis for the past 3 years. Nandan Deshpande is a bioinformatician with focus on systems biology-based data analysis and experience in genome assembly and de novo transcriptomics. Konsta Duesing Leads a team of bioinformaticians and statisticians engaged in genomics, epigenomics and metagenomics research. Konsta has developed and delivered training courses in NGS analysis and has a strong interest in systems approaches to biology and health. He is currently developing methods for the multiple 'omics' data space. Xi Li is a bioinformatician working on genome annotation, NGS data processing and web-based biodata analysis platforms, also with particular interests in developing computational algorithms for the study of gene regulation as well as NGS training workshops. Annette McGrath is the Bioinformatics Core Leader at the Commonwealth Scientific and Industrial Research Organisation. She leads a team of bioinformaticians involved in genomics research, bioinformatics infrastructure and tool development and provision and with a strong interest in training and development. Sean McWilliam is a bioinformatician with a focus on genome annotation, genome assembly and variant analysis. Simon Michnowicz assists researchers with high-performance computing requirements use the National Computational Infrastructure, hosted at Australian National University. He has a background in computational Proteomics. Paula Moolhuijzen is a bioinformatician experienced in the analysis of NGS genome, transcriptome and metagenomic data, with a particular interest is the development high-throughput workflows for bioinformatics analyses. Steve Quenette is the deputy director of the Monash eResearch Centre and project sponsor of the NeCTAR Research Cloud node at Monash University, with expertise in research platforms and productivity, and a research interest in computational science. Jerico Nico De Leon Revote is a developer involved in research collaborations, 3D immersive visualizations and the NeCTAR Australian national research cloud. Sonika Tyagi is a bioinformatician working in the genomics area with main focus on high-throughput sequence analysis. She is involved in developing computational methods and protocols for transcriptomics, post-transcription gene regulation analysis, exome and variation analysis. MariaV. Schneider is the Head of Training and Outreach for The Genome Analysis Centre (TGAC) where she is responsible for the strategic coordination of the in-house and external TGAC Training and Outreach activities. Before this, she was the User Training Coordinator at EMBL-EBI.

Nathan S.Watson-Haigh is a bioinformatician with expertise and interest in systems biology approaches, de novo genome assembly, NGS data analysis, cloud computing and workshop development and delivery. Catherine A. Shang is a project manager working within large Australian collaborative systems biology research consortiums. Catherine is actively involved in establishing collaborative bioinformatics networks and developing and delivering open access bioinformatics training courses for the benefit of the Australian research community. Matthias Haimel is a bioinformatician working with different types of next-generation sequencing data, with a focus on assembling and analysing genomes. During the past 4 years, Matthias has been involved in developing and delivering next-generation sequencing courses either at the EBI or abroad. Myrto Kostadima is a PhD student at the European Bioinformatics Institute (EBI) with interest in transcription and the mechanisms of transcriptional regulation in humans. Myrto has been involved in organizing and delivering courses on next-generation sequencing for the past 3 years either at the EBI or abroad. Remco Loos is a postdoc working on understanding the mechanisms behind pluripotency and self-renewal in stem cells through next-generation sequencing, including Ribonucleic acid-sequencing (RNA-seq) and ChIP-seq, as well as sequencing approaches to epigenetic features (DNA methylation, histone modification, nucleosome positioning). In addition, Remco has been involved in developing and delivering training in next-generation sequencing analysis for the past 3 years. Nandan Deshpande is a bioinformatician with focus on systems biology-based data analysis and experience in genome assembly and de novo transcriptomics. Konsta Duesing Leads a team of bioinformaticians and statisticians engaged in genomics, epigenomics and metagenomics research. Konsta has developed and delivered training courses in NGS analysis and has a strong interest in systems approaches to biology and health. He is currently developing methods for the multiple 'omics' data space. Xi Li is a bioinformatician working on genome annotation, NGS data processing and web-based biodata analysis platforms, also with particular interests in developing computational algorithms for the study of gene regulation as well as NGS training workshops. Annette McGrath is the Bioinformatics Core Leader at the Commonwealth Scientific and Industrial Research Organisation. She leads a team of bioinformaticians involved in genomics research, bioinformatics infrastructure and tool development and provision and with a strong interest in training and development. Sean McWilliam is a bioinformatician with a focus on genome annotation, genome assembly and variant analysis. Simon Michnowicz assists researchers with high-performance computing requirements use the National Computational Infrastructure, hosted at Australian National University. He has a background in computational Proteomics. Paula Moolhuijzen is a bioinformatician experienced in the analysis of NGS genome, transcriptome and metagenomic data, with a particular interest is the development high-throughput workflows for bioinformatics analyses. Steve Quenette is the deputy director of the Monash eResearch Centre and project sponsor of the NeCTAR Research Cloud node at Monash University, with expertise in research platforms and productivity, and a research interest in computational science. Jerico Nico De Leon Revote is a developer involved in research collaborations, 3D immersive visualizations and the NeCTAR Australian national research cloud. Sonika Tyagi is a bioinformatician working in the genomics area with main focus on high-throughput sequence analysis. She is involved in developing computational methods and protocols for transcriptomics, post-transcription gene regulation analysis, exome and variation analysis. MariaV. Schneider is the Head of Training and Outreach for The Genome Analysis Centre (TGAC) where she is responsible for the strategic coordination of the in-house and external TGAC Training and Outreach activities. Before this, she was the User Training Coordinator at EMBL-EBI.

As bioinformatics becomes increasingly central to research in the molecular life sciences, the need to train non-bioinformaticians to make the most of bioinformatics resources is growing. Here, we review the key challenges and pitfalls to providing effective training for users of bioinformatics services, and discuss successful training strategies shared by a diverse set of bioinformatics trainers. We also identify steps that trainers in bioinformatics could take together to advance the state of the art in current training practices. The ideas presented in this article MariaVictoria Schneider is the Training Programme Project Leader in the Outreach and Training Team at EMBL-EBI where she is responsible for developing and coordinating the in-house and external training activities of EMBL-EBI. James Watson is the Senior Scientific Training Officer in the Outreach and Training Team at EMBL-EBI, prior to this he was a postdoctoral researcher in the Thornton group looking at protein structure-function relationships. Teresa Attwood is professor of Bioinformatics at the University of Manchester; she coordinates and teaches the introductory module of the Bioinformatics Masters course, and has written several bioinformatics reference and text-books. Kristian Rother is teaching structural bioinformatics, programming, and software development to bioinformaticians at the UAM Poznan. He is also contributor to the BioPython and PyCogent software libraries Aidan Budd is a computational biologist at the EMBL in Heidelberg, working in the Gibson Team. Working on a range of projects involving short protein linear motifs and phylogenies, he is also responsible for the training and outreach activities of the group. Jennifer McDowall is a Scientific Training Officer in the External Services Team at EMBL-EBI where she is responsible for developing and teaching patent-related training activities. AllegraVia is a researcher in

The widespread adoption of high-throughput next-generation sequencing (NGS) technology among the Australian life science research community is highlighting an urgent need to up-skill biologists in tools required for handling and analysing their NGS data. There is currently a shortage of cutting-edge bioinformatics training courses in Australia as a consequence of a scarcity of skilled trainers with time and funding to develop and deliver training courses. To address this, a consortium of Australian research organizations, including Bioplatforms Australia, the Commonwealth Scientific and Industrial Research Organisation and the Australian Bioinformatics Network, have been collaborating with EMBL-EBI training team. A group of Australian bioinformaticians attended the train-the-trai- ner workshop to improve training skills in developing and delivering bioinformatics workshop curriculum. A 2-day NGS workshop was jointly developed to provide hands-on knowledge and understanding of typical NGS data analysis workflows. The road show^style workshop was successfully delivered at five geographically distant venues in Australia using the newly established Australian NeCTAR Research Cloud. We highlight the challenges we had to overcome at different stages from design to delivery, including the establishment of an Australian bioinformatics training network and the computing infrastructure and resource development. A virtual machine image, workshop materials and scripts for configuring a machine with workshop contents have all been made available under a Creative Commons Attribution 3.0 Unported License. This means participants continue to have convenient access to an environment they had become familiar and bioinformatics trainers are able to access and reuse these resources.