QFAB at a glance


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Established in 2007, QFAB focuses on delivering robust, high quality and relevant bioinformatics services for life science researchers to analyse and manage large-scale datasets.

Our support ranges from experimental design, data capture and mining through to NGS, proteomic and metabolomic analyses. We are also expert in cross-domain integration with clinical data.

QFAB can work on specific projects, provide time against an ongoing need or become embedded in your organisation. Flexible, rapid and researcher oriented, QFAB has built a reputation for supporting the production of high quality outcomes which deliver those high impact publications or patents faster.


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QFAB at a glance

  1. 1. BIOINFORMATICS at a glance
  2. 2. Foundation Partners Contents 2 About QFAB 17 Tools & Platforms 3 QFAB Solutions - mixOmics 4 QFAB Governance - Systems Biology PlatformCollaborators 6 Testimonials 8 QFAB Team - Chemi-Biology Platform - Genomics Virtual Laboratory 10 QFAB Service - NCI-SFIMB – Institute for Molecular Bioscience - Next Generation Sequencing - Embl AustraliaEMBL Australia Bioinformatics Resource - Genotyping Data 18 Case Studies - Microarray Data - Featured project:Genomics Virtual Laboratory – Nectar - Integrated Systems Biology The embedded bioinformatician -Australian e-Health Research Centre - Mass Spectrometry Data QFAB research collaboration ARC Centre of Excellence in Bioinformatics - Cheminformatics - Southern Cross Univerity -NCI-Specialised Facility in Bioinformatics - Biostatistics Science Bioinformatics Support PlantIntersect Australia Ltd - Software and Web Development - Glycoselect statistical pipelineQCIF – Queensland Cyber Infrastructure Foundation - High Performance Computing - ArachnoServer, the world’s - Consulting first manually curatable resource forWound Management Innovation CRC - Training protein spider toxinsThe University of Auckland - EBI – Making AustralianUniversité de Toulouse Data DiscoverablePROOF Centre of Excellence, Canada 28 Publications 1
  3. 3. QFAB SolutionsMr Jeremy BarkerChief ExecutiveOfficer QFAB provides scalable and open solutions which enable experience and our broad suite of open source and scientists to extract the greatest value from their research commercial software and computational systems. data, across a variety of applications, technologies, and Flexible, rapid and researcher oriented, QFAB has built aAbout QFAB industries. reputation for supporting the production of high quality QFAB can work on specific projects, provide time against outcomes which deliver those high impact publications an ongoing need or become embedded in your or patents faster. organisation. Our solution will draw on the entire team’sWhat we do Who we do it forHowever you define bioinformatics, as broadly or narrowly Life science scientists are our clients. With a focus onas you wish, it fundamentally enables the modern client success, our skilled and expert team understandsday researcher to handle and analyse large and complex the biological question. We can help you define thedata – the big data challenge - an essential part of appropriate bioinformatics and biostatistics approachunderstanding biology. and apply the correct analyses to deliver on your project.Established in 2007, QFAB focuses on delivering robust, By unlocking the full value of your data, QFAB hashigh quality and relevant bioinformatics services for life become a leading provider of bioinformatics servicesscience researchers to analyse and manage large-scale to industry, clinical, applied and academic life sciencedatasets. researchers, including the biotechnology, pharmaceutical,We offer our clients a range of professional services clinical and research communities.– from contract research, project design and analysis, We operate nationally and internationally with a Technologies Applications Industriesscientific software development, to designing, deploying commitment to continuous engagement throughout We support evolving We design applications to We work with researchersand refining the high performance IT infrastructure the project. technologies used by life support: across a number of industries:that is required to support life science informatics. science researchers including:Our support ranges from experimental design, data What we stand forcapture and mining through to NGS, proteomic - Pathology/clinical data - Molecular biology research - Academic research Our highly experienced and skilled team is the foundationand metabolomic analyses. We are also expert in - Biomarker discovery - Healthcare of our success. As a team, we are committed to operating - Next generation sequencing: cross-domain integration with clinical data. ethically, with integrity and respect at all times. We believe Roche 454 GS-FLX, Illumina - Crop science and livestock - Pharma R&DQFAB’s training division provides integrated workshops that open communication, flexibility and honesty are the HiSeq, LifeTechnologies Solid, through to customised solutions in all facets of - Biodiversity - Clinical research keys to successful customer engagement. Ion Torrent databioinformatics. - Molecular diagnosis - Biotechnologies Early engagement means we can take the time to understand - Genotyping:We have a strong track record of delivering results which your goals and help derive the most efficient and - Drug discovery - Food industry ABI-LifeTechnologies, Illumina, are grounded in the team’s commitment to continuous cost-effective bioinformatics solutions, while the international Affymetrix, Agilent - Translational research - Environmentlearning and innovation, ensuring that our clients can experience brought to projects by our team memberstrust in the knowledge and integrity of our support. - Microarrays - Epidemiology - Biodiversity ensures the application of the relevant tools to the right data to answer your particular questions. - Mass spectrometry: - Pathway analysis - Energy We are the research data specialists: responsive, SELDI, MALDI, iTRACK - Clinical trials - Agricultural R&D professional, secure and quality focused.2 3
  4. 4. QFAB Specialist Advisory Group Dr Rhys Francis Dr Gregory Harper Dr Tim Littlejohn Warren Parker Dr Nadia Rosenthal Executive Director, Director, New Employee CEO, Director, Australian External Learning Lead, Scion, Australian eResearch Engagement, diversity, New Zealand Regenerative Infrastructure CSIRO life sciences, Forest Research Medicine Institute Council IBM Institute, New ZealandQFAB GovernanceMr Peter Turnbull seven management and advisory Chemistry and Computer Science Infectious Disease Research Program tradition of the Berkeley L0 project, Dr Andrew Lewis boards in molecular bioscience, and a PhD in Theoretical Chemistry at IHBI, which forms part of IHBI’s where he contributed a connectionistChairman Griffith University informatics and e-Research. at the Australian National University. Cells and Tissue Domain. Ken was synthesis of bottom-up andPeter is a company director and He has more than 160 peer-reviewed appointed to the role of IHBI Deputy top-down attentional systems as a Andrew is a Senior Research Specialistcorporate lawyer. Peter’s business in eResearch Services at Griffithinterests span many East Asian publications and research interests Dr Wayne Jorgensen Director in 2010. He has worked in model of spatial relations acquisition University. Andrew’s research expertise that include comparative, the area of mucosal immunology for and processing. Jim also leadsmarkets, Europe and the United Queensland Government includes parallel optimisation computational and evolutionary the past 25 years at the University of development of softwareStates. He is currently the Chairman genomics, high-throughput Wayne has over 25 years of research Alabama at Birmingham (UAB) and internationalisation work within algorithms for large numericalor a Director of various private and bioinformatics, high-performance experience in parasitology. Wayne the University of Newcastle prior Australia. simulations, including bio-inspiredunlisted public companies and is a computing, and technologies for has published over 70 research to moving to QUT. Ken’s current algorithms (particle swarm, ant colony,former Director of the Securities and papers in refereed, international spatial social networks, evolutionaryFutures Commission of Hong Kong. management and integration of journals and over 70 conference research interests focus on immunity Mr Jeremy Barker programming and extremal large datasets. to sexually transmitted infections,Peter has particular expertise in the papers at national and international QFAB optimisation), direct search algorithms in particular Chlamydia trachomatis.commercialisation of new technologies, conferences. He has written chapters Jeremy is the founding CEO of QFAB (simplex and pattern search methods)strategic planning, and complex Dr David Hansen on tick-borne diseases for the Office His research aims to define and (Queensland Facility for Advanced and gradient descent (quasi-Newton differentiate the immune parameterslegal, commercial and corporate CSIRO International des Epizooties, Bioinformatics) which he joined with BFGS update). He specialises of immune-mediated inflammatorygovernance transactions and alternate David is CEO of the Australian International Livestock Research pathology caused by Chlamydia full time in June 2007. Jeremy is in multi-objective optimisationdispute resolution strategies. He is a e-Health Research Centre. David Institute, Food and Agriculture infection from the immune responsible for the overall techniques for engineering design,recent past-President, and Chairman leads the research programs of the Organization of the United Nations, mechanisms that can protect against management of QFAB. He holds including the application of a varietyof Chartered Secretaries Australia, AeHRC, a joint venture between Parasitology Journal, and Merck. chlamydial infection to developing postgraduate qualifications in of algorithms to complex problems,and is a Fellow of the Australian CSIRO and the Queensland He is co-editor for Babesiosis in the effective chlamydial vaccines. science, commerce and governance methods of interactive optimisation,Institute of Company Directors. Government. Prior to joining CSIRO, International Consortium for Tick and has over 20 years of experience automated preference selection in David led development of the and Tick-borne Diseases Journal and in the management of life science Pareto-optimal sets, extension to Associate ProfessorProfessor Mark Ragan Sequence Retrieval System (SRS) at developed two international patents James Hogan organisations including a number of many-objective and dynamic LION Bioscience Ltd in Cambridge, on poultry coccidiosis vaccines. Board positions for biotechnology environments, and the developmentIMB QUT UK. SRS is the leading genomic data In 2008 Wayne received the Australia companies. In 2007, Jeremy was of automated, problem-solvingMark is the founding head of the and tool integration software, and Day award for contribution to awarded a Churchill Fellowship to frameworks. He also has expertise in Jim is an Associate Professor in theDivision of Genomics and is used by pharmaceutical and Queensland’s Primary Industries. undertake an international study parallel, distributed and grid computing Electrical Engineering and ComputerComputational Biology at the biotechnology companies, such as on ‘Management Best Practice in methods, including cluster-based, ad Science Faculty at QUT. His researchInstitute for Molecular Bioscience ofThe University of Queensland, and Glaxo Kline-Smith, Celera and Professor Ken Beagly interests include machine learning the Delivery of Bioinformatics to hoc grid, distributed, peer-to-peer Affymetrix, as well as academic and its application to cognitive Researchers’. He is a member of systems and cloud computing; andDirector of the Australian Research IHBI institutes, including The European science, and bioinformatics problems the Australian Institute of Company advanced visualisation techniques forCouncil Centre of Excellence in Bioinformatics Institute. David Ken is Deputy Director, Institute of Directors. scientific data analysis. and software engineering. Jim’s workBioinformatics. Mark is a Fellow of undertook a Bachelor of Science at Health and Biomedical Innovation is concerned with learning in visualthe Linnean Society of London, and the University of Queensland in (IHBI). He is a Professor of Immunology domains with associated text, in theserves on six editorial boards and at QUT and the leader of the4 5
  5. 5. The embedded bioinformatician “QFAB has assigned a successionof its research students and staff to work with our biologists and protein chemists, helping to design experiments and to interpret the data. As we were doing our research, QFAB was building up a pool of expertise in wound-healing bioinformatics.” Professor Zee UptonTestimonialsQFAB’s expertise in experimental design and analysis can be applied Professor Zee Uptonat any scale, from a simple microarray comparison of differential Wound Management Innovationgene expression, to a full-blown systems biology analysis integrating Cooperative Research Centregenomic, proteomic, metabolomic and clinical data. The Co-Program Leader of the Enabling Technologies Program in the Wound CRC, Professor Zee Upton, now Assistant Dean of Science atProfessor Glenn King Dr Roslyn Brandon Queensland University of Technology,Institute of Molecular Bioscience, Co-Founder, President and CEO says it was clear from the outset that theThe University of Queensland of Immunexpress (IXP) CRC was going to need high-order capabilities“QFAB has collaborated with us over a number of years “Since an initial collaborative project in 2010, IXP has in bioinformatics to make sense of the hugeto build a world-first spider toxin database that allows us significantly increased its work with QFAB as a contract volumes of DNA, SNP and proteomics datato combine data from publicly available databases including supplier of bioinformatics services. QFAB undertakes IXP’s flowing from its research.mRNA and protein sequences, 3D structures, and genomics multivariate data analytical work – a criticalfunctional information for hundreds of venom proteins. foundation for the development of our novel clinical In previous projects the bioinformaticiansIn our most recent project, QFAB worked with us to add diagnostic products. IXP is leading the world in applying were not physically co-located with thea number of new features to the database, including a its patented immune system blood biomarkers to improvingtoxin mass calculator, taxonomic target search, and the management of sepsis patients and those at risk of biological scientist generating the data.mechanisms to control the privacy of records. QFAB’s sepsis. Sepsis is a life-threatening immune response “That didn’t work as well as we hoped,”innovative approach and responsiveness has been to infection and is a leading cause of death in Intensive Professor Upton said.essential to the success of this project. I am happy to Care Units. QFAB works very effectively with our teamendorse QFAB as a provider of highly effective research to produce results time effectively and cost efficiently. “We found we needed a bioinformaticiandata management solutions.”  The QFAB project team is a mainstay for our business as our with specific expertise in handling product development processes rely heavily on world-class wound-healing data, so informatics. We have been very pleased with the quality and responsiveness of QFAB, and I am delighted to provide QFAB placed one of its researchers this testimonial for their client services.” in the CRC for two days a week.”6 7
  6. 6. QFAB TeamSeniorManagement Team Mr Jeremy Barker Dr Dominique Gorse Chief Executive Officer General Manager “QFAB is a vibrant and dynamic workplace, reflecting the variety of projects that attracted me to QFAB initially. I enjoy the challenge of working for an organisation that is at the cutting edge of bioinformatics Ms Mathilde Desselle Dr Mark Crowe Dr Stephen Rudd and the satisfaction gained from liberating more knowledge or productivity Business Development & Training & Outreach Manager Head of Computational for the customer by applying advanced bioinformatic solutions.” Marketing Manager Biology Dr Leo McHughComputational Biology Data Specialists Dr Kim-Anh Lê Cao Ms Roxane Legaie Dr Jeremy Parsons Ms Sarah Williams Biostatistician Bioinformatician Bioinformatician Bioinformatician Dr Xin-Yi Chua Ms Amanda Miotto Dr Leo McHugh Mr Pierre Chaumeil Ms Anne Kunert Mr Nick Rhodes Senior Bioinformatician eResearch Support Specialist Senior Computational Biologist Bioinformatician Bioinformatician Database and Systems Administrator8 9
  7. 7. QFAB ServicesQFAB is the research data specialist. We support the bioinformatics requirements ofresearch-intensive universities, institutions and companies and provide secure access tovery large databases, dedicated softwares, high-performance computing, terabyte storage,data integration technologies and advanced bioinformatics services.We pride ourselves in developing tailored, relevant bioinformatics solutions to meetresearch needs to:> Provide scalable infrastructure to meet future growth > Enable reasoning across data sources> Enable collaboration between scientists within > Develop workflows for easy and efficient data disparate research areas processing, analysis and visualisation.Our services include: Next Generation Sequencing Genomic capture > Adjustments of interpretation settings > Mutation and variant detection > Taxonomic trees Unlock the full value of your next-generation sequencing (NGS) data sets from Illumina > Identification and positioning of known and unknown > Samples comparison mutations RNAseq and microRNA HiSeq, Roche 454 GS-FLX and LifeTechnologies > Transcription: Influence of the mutation on the protein Solid and Ion Torrent platforms. RNAseq functionality QFAB provides tailored bioinformatics services to biologists > Changes in expression across the spectrum of computational techniques and ChipSeq > Detection of novel splice isoforms or transcripts services applicable to molecular biology and next generation > Mapping and genes identification sequencing. QFAB researchers design and implement > De novo transcriptome assembly > Comparison if samples regulated by the same custom bioinformatics approaches that are developed in transcription factor > Mutation detection consultation with researchers for specific questions in Annotation pipeline molecular biology. We can also integrate your genomics Exome data with other omics and clinical datasets. > Listing of identified mutations between the study > Prediction of coding regions Our NGS data analysis services include: samples and the reference: SNPs, InDels > Annotation of coding genes, non-coding RNA, tRNA, rRNA, miRNA… De Novo or reference genome assembly and > Identification of known mutations by comparing the annotation results to international databases > Repeat identification > Assembly and mapping > Influence of the mutation on the protein functionality > Statistics of annotation and analysis of GC content > Structural and functional annotation of the genome Metagenomics (ORF detection, assignment of genes,…) > Creation of reference database and alignment for or > Samples comparison ganisms identification10 11
  8. 8. Integrated Systems Biology QFAB supports systems biology research across the spectrum of interdisciplinary techniques. QFAB researchers work with biologists to define the nature of the biological systems under investigation in specific research projects. We develop or customise approaches for understanding these systems, or inferring the properties of such systems from high-throughput data sets: > Integration and simultaneous analysis of multiple omics or clinical datasets > Pathway and network analysis > Enrichment analysis > Gene regulation studies > Visualisation (correlations, networks, genome browsers). Genotyping Data Mass Spectrometry Data We can provide data filtering and genotype QFAB provides mass spectrometry data calling, as well as integration of your analysis, from design to protein identification, genotyping datasets into data management, annotation of secondary modifications, and visualisation, pathways network-based determination of the absolute or relative analysis or development of molecular abundance of individual proteins. diagnostic chip/IVD device. > Design QFAB researchers design and implement custom > Picks detection and protein identification bioinformatics approaches that are developed in > Annotation consultation with researchers for specific questions in > Quantitative analysis molecular biology: > Interpretation > SNP genotyping data We support data from most of the existing mass > Microsatellites / minisatellites genotyping data spectrometry platforms. > Genotyping by Sequencing data We support data from most of the existing genotyping and sequencing platforms. Cheminformatics QFAB supports drug discovery projects with Microarrays Data SAR analysis and SAR development using cheminformatics approaches. QFAB offers a wide range of statistical and > Prioritisation of compounds and assays bioinformatic analyses of microarray data, (Efficacy, Toxicity, ADME) ranging from design and quality control to > Provide databases and tools for compound samples comparison. registration and inventory > Design > HTS data handling, mining and reporting > Quality control > Design of compound libraries > Normalisation (diverse, focused or targeted) > Quantification: gene expression, exon level, > Combinatorial library design and library copy number enumeration > Differential samples comparison, and > Undesirable molecule elimination comparison with public datasets > Hit-to-lead optimization > Combination and integration with other data. > ADME and toxicity profiling.12 13
  9. 9. Biostatistics High Performance Computing QFAB provides expert biostatistical services to Mr Nick Rhodes support the design of biological experiments, Database and Systems Administrator biomarker identification, collection and QFAB’s HPC services include: analysis of data from experiments, and the > Hardware access / infrastructure interpretation of that data. > Cluster computing QFAB provides tailored data mining services to researchers who want to get more from their datasets. By creating > Cloud computing customised data mining solutions, QFAB can assist researchers > High memory servers. to get more from their existing data sets. By consulting with QFAB early, QFAB research staff can also provide detailed advice on the best methods for data capture, annotation Consulting and storage to maximise the benefits likely to result from Dr Dominique Gorse the application of data mining techniques. General Manager Our biostatistical services include: Discuss with us the design of your research project, > Combination and integration of multiple and evaluate bioinformatics analysis and support to be datasets types incorporated in your grant proposal. QFAB answers your > Univariate and multivariate analysis consulting need on a project basis, on a regular basis > Power calculation (number of days/ week-month-year), as well as through embedded staff model. > Classification QFAB can help scientists with access to the We undertake collaborations in clinical research informatics bioinformatics tools and the computational capability and research IT services with a growing number of clinical needed to meet the challenges of visualising disparate and translational research investigators. datasets which may use different or no ontologies and, at the social and regulatory levels, the need to maintain patient confidentiality through compliance with clinical records privacy laws. Building on our strengths in understanding and translating the needs of the researcher into the language of the bioinformatician and IT professional, QFAB can work closely with your research team to address both the data management and Software and Web Development bioinformatic aspects of your translational research project. Research computing resources offered by QFAB enable the visualisation and analysis of large biological data sets and to address Training complex biological problems. Dr Mark Crowe QFAB develops custom software tools, data management Training & Outreach Manager systems and web interface for life sciences researchers. QFAB understands the biological question and can help We support large collaborative research projects where the you unlock the answers from your data through our member groups are based in different locations. We develop specialised training programs. We provide a range of online tools for project participants to securely store their flexible modules, courses and workshops designed to suit own data, access other members’ data and allow real-time your needs – ranging from introductory project-focused communication between collaborative group members. courses to advanced bioinformatics. Our goal is to Our ICT services include: improve knowledge diffusion between experimental > Database development biologists and bioinformaticians, that is, increase the interaction between developers and users. > Web interface to biological databases Contact QFAB for details of how QFAB can meet your > Data analysis web applications. training needs. For more information on QFAB services, contact us: www.qfab.org14 15
  10. 10. Tools & PlatformsQFAB has a core team of software engineers Industry Collaborationand biologists who work together to help QFAB provides technical collaboration for:describe, formulate and build applications Embl Australia Bioinformatics Resourceto analyse and manage your research data.Our unique tools and platforms include: An online data resource replicating important components of the data and data services providedMixOmics by the European Bioinformatics Institute (EBI) -The integration of multiple ‘omics’ analyses enables a to provide Australian scientists with faster accessbetter understanding of a biological system as a whole. to EBI datasets and expanded collections ofQFAB’s mixOmics product is an R package dedicated Australian data.to the exploration and the integration of highly dimensional http://www.ebi.edu.au/data sets. MixOmics provides a strong focus on graphicalrepresentation, to better understand the relationshipsbetween the different types of data and to visualize the Genomics Virtual Laboratory (GVL)correlation structure between different measured entities.Systems Biology Platform The GVL provides Australian researchers with a community of accessible infrastructure, expertise Analysis of complex molecular networks which control and advocacy that connects genome researchers biological processes requires an integrated, highly capable with massive datasets, sophisticated analysis tools, bioinformatics platform. QFAB has developed a scalable and large-scale computational infrastructure.computational environment to analyse, model and inferbiomolecular networks. Our platform is unique in Australia, https://www.nectar.org.au/genomics-virtual-laboratorywith high-performance hardware and an integrated suiteof commercial software linked to curated datasets. NCI-SF in BioinformaticsChemi-Biology PlatformQFAB’s chemi-biology computational platform brings The National Computational Infrastructure,together complementary expertise in infectious disease Specialised Facility (NCI-SF) portal providesresearch and advanced computational methods to information on the hardware, software and services accelerate the drug discovery process. The platform aims available.at increasing the likelihood of discovering successful lead https://ncisf.org/compounds for anti-infective medicine. Unique in Australia,the platform consist of high-performance hardware andan integrated suite of open source and commercial softwarelinked to curated chemical and biological datasets. 17
  11. 11. Case StudiesQFAB collaborates with life scientists to help solve important challenges relating to theanalysis, management and visualisation of their research data. Read about some of ourprojects and collaborations.Indexp. 8 Featured project: The embedded bioinformatician - QFAB research collaboration 1p. 1 Southern Cross University - Plant Science Bioinformatics Support 2p. 3 Glycoselect statistical pipeline 2p. 4 Arachnoserver, the online data repository for spider toxin research 2p. 6 EBI – Making Australian Data Discoverable 2Featured project:Wound InnovationManagement CRC Dr Kim-Anh Lê Cao Mr Jeremy Barker, Professor Zee Upton, Biostatistician CEO, QFAB QUTThe embedded bioinformatician - QFAB research collaborationBy Graeme O’Neill theatre, a car accident, a farm The Co-Program Leader of the researchers in the CRC for two days help biologists to design be project-specific.A wound is a complex ecosystem, accident, or the consequence of Enabling Technologies Program a week. experiments and analyse the data “So they bring us this huge data set,seething with a diverse population necrosis associated with chronic in the Wound CRC, Professor Zee “Since then, QFAB has assigned a to answer the questions posed. saying they want do to this type ofof the patient’s cells, and a complex diabetes or a lifetime smoking habit. Upton, now Assistant Dean of succession of its research students As the cost of purchasing and analysis, hoping to get a certain result,community of microbes contending Over time, the wound’s microbial Science at Queensland University of and staff to work with our biologists operating high-speed DNA without fully understanding whatto colonise the wound. There is flora may vary with time, through Technology, says it was clear from and protein chemists, helping to sequencers has fallen, more research they’ve got from the experiment,constant communication between succession processes. the outset that the CRC was going design experiments and to interpret groups have been successful in or how to extract what they wantthem via a molecular intranet. Fibroblasts and other specialised to need high-order capabilities in the data. As we were doing our obtaining ARC infrastructure grants from the dataset. tissue-repair cells go about their bioinformatics to make sense of the research QFAB was building up a to buy these machines.”Some set outThe Wound Management Innovation “That’s where we can help. First, we business as the innate and adaptive huge volumes of DNA, SNP and pool of expertise in wound-healing to use the new equipment withoutCooperative Research Centre in can explain what their data will allow immune systems’ armies of natural proteomics data flowing from its bioinformatics.” really understanding how it can beBrisbane was established in 2010 them do, or how it might allow them killer cells, macrophages, B cells research. used,” he said.to explore these processes, and to And that’s the model QFAB is to do more than they expected.apply its findings to develop novel and T-cells swarm in to mount a In previous projects the bioinformati- offering to potential customers for its “They may have bought the machine “Secondly, we can help by showingtreatments to accelerate healing, coordinated defence of the breach cians were not physically co-located expertise and facilities. QFAB Chief after reading a paper in the scientific them how to do what they reallyreduce scarring, and prevent infection. against microbial invaders. with the biological scientist generating Executive Officer, Jeremy Barker says literature that used the same device. wanted to do, and help them design The high-speed DNA sequencers the data. “That didn’t work as the success of biological, medical It might describe the methodsEvery patient is genetically unique, experiments to produce the type of and various microarray technologies well as we hoped,” Professor Upton and pharmaceutical research will used to produce the data, and theand the microbes vying to colonise data they need to answer particular required to study the dynamics of said. “We found we needed a depend increasingly on the expertise conclusions, but reveals very littletheir wound will vary according to questions. Early engagement saves these processes over time, generate bioinformatician with specific of bioinformaticians who not only about the assumptions underlyinghow and where the wound occurred the costs involved in repeating enormous amounts of data. expertise in handling wound-healing understand the research, but can the methodology, which tend to– it might have been in an operating experiments. data, so QFAB placed one of its18 19
  12. 12. Barker says QFAB’s expertise in no reserve time to learn on the job. “We stay up to date with theexperimental design and That is the advantage of having a technologies out there, and thebioinformatics analysis can be larger team to draw on. specialised methodologies that goapplied at any scale, from a simple “Around 60 per cent of QFAB’s with them, so we will have a prettymicroarray comparison of differential recruits are PhDs. Everyone else is at good idea which technology is mostgene expression, to a full-blown least postgraduate trained, and we appropriate for each client’s project.systems biology analysis integrating have a core of experienced “The technology changes rapidly,genomic, proteomic, metabolomic bioinformaticians in senior positions and all bioinformaticians think theyand clinical data. to bring the necessary rigour to can produce a better algorithm“We engage with a prospective project planning. than the one described in the latestclient, discuss what they want, then “You need the depth of experience journal. submit it to our team for a think-tank provided by staff who have worked “We learn and adapt as needsession on how it might be done with on other projects before QFAB dictates. You don’t always have tothe expertise and resources that we recruited them.” reinvent the wheel; often, there ishave in-house, and at the client’s end. Dr Jeremy Parsons, Ms Roxane Legaie, “A bioinformatician joining the team already an algorithm that can do the Bioinformatician Bioinformatician“We then go back to the client with may have had experience working job. The trick is knowing that thea proposal detailing where and how on a particular class of cancers, or algorithm exists, and how to apply it.”we believe we can help.” on viral infections of mangoes, so As for data-crunching power, BarkerBarker says QFAB has served a they’re good with that type of data says the facility has just updated its Southern Cross University - Plant Science Bioinformatics Supportvariety of clients over the past seven and have that specialist knowledge computer cluster. It has seven nodes Brief description of the individuals of special interest to their all assemblies against each otheryears including CSIRO, Australia’s as well as the more general built around a 64-core processor, project research interests. This “de novo” and to related species to identifyuniversities, medical research institutes, bioinformatics skills. “Collectively each with 256 gigabits of RAM, approach to whole-genome assembly the best product for subsequentstate primary industry, fisheries and we can call upon a broad range of and terabyte storage capacities. The client is an Australian university from short shotgun reads is the most genomic analyses.forestry departments, and private expertise within our teams, and ask research team with broad genomic economical and fastest path to partial “That’s enough for most jobs,”biotech and pharmaceutical companies. them what they think about a experience and a special interest in What were the outcomes? he said. “But if it isn’t, we have genome reconstruction for novel particular question. genetics of Australian plants. QFAB organisms but it is problematic QFAB fully reconstructed twoBarker says bioinformatics is moving access to a supercomputer facility is providing a full genomic assembly when attempted without traditional organelle genomes and partially“at a mile a minute” so keeping , “We apply the team approach to at the University of Queensland that and analysis service on multiple guidance from physical clones assembled multiple plant nuclearabreast of the changes requires a every project, but we like to broaden runs a terabyte of RAM, which can organisms with direction and focus or genetic maps. The “de novo” genomes. Organelle genomes havecommitment to ongoing learning as the discussion on the projects we handle whole genome comparisons.” determined by the client. shotgun assembly method leads been shared privately and nuclearpart of the job and an investment have on the boil at any point in time, “With these facilities, our broadin the professional development of because someone from another expertise, and our data-integration Background to fragmented and isolated plant genomes for two Australian nativeQFAB’s team. team may have an insight into a nuclear chromosomal contigs which species have been assembled and abilities, we believe we offer a Recent dramatic cost reductions in particularly tricky question.” can be difficult to analyse. QFAB analysed for genes, repeats,Barker says he has seen an example service beyond the in-house shotgun genomic sequencing now and the client assembled multiple microsatellite SSRs, and inter-speciesof a research institute’s embedded Barker says clients can be certain bioinformatics capabilities of any enable biologists to cheaply and genomes using different DNA similarities. We have also preparedbioinformatician being rapidly that QFAB will have the best single institution or company in quickly sample the DNA sequence assembly programs and then compared genome size estimates.overwhelmed by data. “They have available expertise to do the job - Australia and the Asia Pacific region.” of an interesting species, or selected20 21
  13. 13. Boxplot samples 4 3 Outcometotal intensity 2 cancer normal 1 0 -1 -2 5 6 7 8 9 11 13 15 17 19 21 23 samples One of the outlier detection steps: boxplots of the biological samples coloured according to the outcome Dr Kim-Anh Lê Cao Biostatistician Glycoselect statistical pipeline Brief description of the pipeline needed to be deployed in proposed to process the data project the existing Glycoselect database to beforehand and remove potential identify biomarker signatures. outliers. The resulting process clearly Implementation of a statistical One of the challenges was to propose identified the outliers in the data pipeline in the Glycoselect database an appropriate methodology to deal enabling the researchers to remove for the identification of glycoprotein with data which include many zero these prior to selection of the biomarker signatures. values – many classical statistical biomarker panel. Background approaches (t-test, non parametric The R script was handed over to A new high-throughput test) do not apply in this case. the Glycoselect developer to be glycoproteomics technology is What were the outcomes? implemented into the Glycoselect being developed by the client to analytical pipeline. The outliner The statistical methodology uncover potential glycosylation detection methodology including developed by Lê Cao et al., 2011* changes in a complex mix of proteins visualisation of the analyses was also was proposed for this project and present in biological fluids such as provided to the client. produced very satisfying results. serum. The input data consists of The pipeline was developed using *Lê Cao K.-A., Boitard, S. and Besse, protein identification as determined this methodology and implemented P. (2011). Sparse PLS Discriminant by tandem mass spectrometry, in the R statistical programming Analysis: biologically relevant together with their binding affinities language. feature selection and graphical to a panel of lectins, which indicate displays for multiclass problems BMC An outlier detection step was also the glycan structure. A statistical Bioinformatics, 12:253 23
  14. 14. Cumulative Toxins Deposited by Year Toxin Distribution by Family Other 900 (86) Zodariidae Theraphosidae 800 (28) (201) 700 AgelenidaeNumber of Toxins (73) 600 500 Hexathelidae 400 (91) 300 Lyscosidae 200 (175) 100 Ctenidae (99) 0 1995 1990 1995 2000 2005 2010 Sicariidae Year (167) ArachnoServer, the world’s first manually curated resource for protein spider toxins Brief description of the These databases also require that 1) Allowing secure manual curation a single page and, where have been made available through Volker Herzig, David L. A. Wood, project their structure, data, and utility be of the toxin records by the expert available, a toxin’s structure can the web interface. First, similarity Felicity Newell, Pierre-Alain Chaumeil, appropriately modified over time team led by Professor Glenn King be dynamically displayed. searches can be made using BLAST. Quentin Kaas, Greta J. Binford; QFAB has worked in collaboration with new discoveries and changes using available literature and The solution chosen for ArachnoServer Secondly, signal peptide and Graham M. Nicholson; Dominique with Professor Glenn King to create in information priority. patent information. was to develop a Java Spring Model propeptide regions in spider-toxin Gorse; Glenn F. King (2011) Arachnoserver, the online data The aim of this project was to develop 2) Providing easy and powerful View Controller (MVC) application precursors can be predicted using ArachnoServer 2.0, an updated repository for spider toxin research. a robust, extensible and maintainable advanced search, browse and that uses a Hibernate Object SpiderP, a new tool developed for online resource for spider toxin Background software architecture that would view capabilities. ArachnoServer Relational Mapping (ORM) layer to ArachnoServer. sequences and structures. Nucleic High impact research requires the make ArachnoServer the world’s gold enables neuroscientists, a MySQL database. Using this ArachnoServer has become an Acids Research 39, D653-D657 wide and clear distribution of results. standard online data repository for pharmacologists, and toxinologists architecture, the application and international resource that is David LA Wood, Tomas Miljenović, This can be hampered by spider toxin research for years to come. to explore high quality toxin data model can be easily extended cross-referenced by the European Shuzhi Cai, Robert J Raven, Quentin bioinformatics web applications, information and rapidly answer or modified, as changes to the data Bioinformatics Institute’s UniProt Kaas, Pierre Escoubas, Volker Herzig, which often suffer from a lack of What were the outcomes? their research questions. model do not require SQL changes. knowledge base (UniProtKB). David Wilson and Glenn F King maintenance, leading to a decline in A web application was developed to Each toxin record is displayed in (2009) BMC Genomics 10:375  Two powerful bioinformatics tools http://www.arachnoserver.org/ data currency and subsequent accuracy. enable two key functions: 24 25
  15. 15. Dr Dominique Gorse General Manager EBI – Making Australian Data DiscoverableBrief description of the project The aim of this project was to develop The link between RDA and the EBI is > Identification of Australian species: sequences. A Java library was the primary data housed at the a set of software to allow nucleotide provided through the use of landing A list of Australian species was implemented which used EBI EBI. The webpage lists basic Populating Research Data Australia and protein sequence data of pages that are simple to use and sourced from the Atlas of Living hosted web services (http://www. metadata for the collectionwith collection descriptions of data Australian interest to be discoverable contain structured information useful Australia through the IBIS taxono ebi.ac.uk/Tools/webservices/) (eg a short description, synonyms held in the European Bioinformatics through RDA in the form of collections. to non-domain specialists who are my web services (http://www to query these databases. for the collection) as well asInstitute databanks. The project was funded by the unfamiliar with the content of the EBI ala.org.au/tools-services/ This library then inserted the displaying a list of recordsBackground Australian National Data Service databases (http://rda.ebi.edu.au). species-name-services/). extracted data into a MySQL (eg records of DNA or proteinThe European Bioinformatics through the DIISRTE Education Molecular data of Australian interest These species were assigned database. Other EBI databases sequences) relevant to thatInstitute (EBI, part of the European Infrastructure Fund. that is present on the EBI are now to approximately 800 higher were not interrogated as they collection. It also allows forMolecular Biology Laboratory, EMBL) more easily found, accessible and level taxonomic ranking groups either did not contain data that navigation back to the primary provides international access to data What were the outcomes? re-usable through RDA (eg genus, class, order) using the could be definitively identified as source at EBI and navigation to in molecular bioscience generated In this project, more than 13,000 (http://researchdata.ands.org.au). NCBI taxonomy (http://www.ncbi. Australian, or were not able to be related collections. The webpage by researchers worldwide, including collection records describing The technical solutions developed nlm.nih.gov/taxonomy). queried using the web services. was developed using JavaAustralia. In its present state, Australian-related content of the EBI for this project were: The higher order groupings were > Automatic generation of collections servlets, JSP and JavaScript.Australian specific data is difficult to nucleotide and protein sequence selected in consultation with and submission to RDA: Data The web interface is deployed on > Identification of Australianisolate within the EBI databases, databases were created. A large ANDS whilst the NCBI taxonomy stored in the MySQL database was an Apache Tomcat web server research institutions: A list of particularly for the non-domain user. effort was made to divide and was used for species assignment converted into ANDS compliant on an ESX server with RedHat relevant Australian research The establishment of the EMBL describe the content of large databases as this taxonomy is used in the EBI RIF-CS xml (using an ANDS enterprise Linux 5.4. institutions conducting biological Australia Bioinformatics Resource at into many smaller datasets that are databases. supplied RIF-CS Java library) and The software is freely available for research was compiled. This listthe University of Queensland has of potential interest to a wide and > Extraction of data from EBI made accessible to a RDA harvest download from Scourceforge under includes institutions identifiedprovided the opportunity for linking varied range of researchers. databases: Australian species or data source. More than 13,000 the GNU General Public Licence. through ARC and NHMRC grant data of Australian interest deposited The collections encompass two types research institutions were used as collections were generated. http://sourceforge.net/projects/ information and having a Nationalat the EBI, to Research Data Australia of Australian data: a) data submitted query items to interrogate the EBI ebi-rda-linkage/?source=directory Library of Australia (NLA) Party > Landing page for collections:(RDA), a cohesive repository of from Australian-based researchers; databases: Uniprot (http://www Persistent Identifier. Research The landing page is a webpage QFAB staff contact:research data collections enabling b) data associated with sets (and ebi.ac.uk/uniprot/) for protein institutions were then grouped by that is accessible from RDA and Dominique Gorse Project Manager Australian researchers to easily publish, subsets thereof) of Australian species.  sequences and ENA (http:// states and territories. acts as a link between RDA and discover, access and use research data. www.ebi.ac.uk/ena/) for nucleotide 26 27
  16. 16. PublicationsWe have supported our client’s successful grant applications worth over $56 million.The intellectual input of the QFAB Team provided clear bioinformatics strategies in theirexperimental design and valuable outcomes in the analyses.Recent publications in which QFAB Schroder, K., Irvine, K.M., Taylor, M.S., Bauer, D. C., Willadsen, K., Buske, F. feature selection and graphical BMC bioinformatics, 11, 498. untranslated regions. Nucleic Acidshas collaborated include: Bokil, N.J., Lê Cao, K.-A., Masterman, A., Lê Cao, K. A., Bailey, T. L., displays for multiclass problems. Res, 39((6)), 2393-2403. Degrelle, S. A., Lê Cao, K. A., K-A., Labzin, L.I., Semple, C.A., Dellaire, G., & Boden, M. (2011). BMC bioinformatics, 12, 253.Muscat GE, Eriksson NA, Byth K, Loi Heyman, Y., Everts, R. E., Campion, Taft, R. J, Simons, C., Nahkuri, S., Kapetanovic, R.A., Fairbairn, L., Sorting the nuclear proteome.S, Graham D, Jindal S, Davis MJ, Lingwood, B. E., Henry, A. M., E., Richard, C., Ducroix-Crépy, C., Oey, H., Korbie, D. J., Mercer, T. R., Akalin, A., Faulkner, G.J., Baillie , Bioinformatics, 27(13), i7-14.Clyne C, Funder JW, Simpson ER, d’Emden, M. C., Fullerton, A. M., Tian, X. C., Lewin, H. A., Renard, J. P., Holst, J., Ritchie, W., Wong, J. J., J.K., Gongora, M., Daub, C.O.,Ragan MA, Kuczek E, Fuller PJ, Tilley Herzig, V., Wood, D. L., Newell, F., Mortimer, R. H., Colditz, P. B., Robert-Granié, C., Hue, I. (2010). Rasko, J. E., Rokhsar, D. S., Degnan, Kawaji, H., McLachlan, G.J., Goldman,WD, Leedman PJ, Clarke CL. (2013). Chaumeil ,P. A., Kaas, Q., Binford, G. Lê Cao, K. A., Callaway, L. K. (2011). A small set of extra-embryonic genes B. M., Mattick, J. S. (2010). Nuclear- N., Grimmond, S.M., Carninci, P.,Research Resource: Nuclear J., Nicholson, G. M, Gorse, D., King, Determinants of body fat in infants defines a new landmark for bovine localized tiny RNAs are associated Suzuki, H., Hayashizaki, Y., Lenhard,Receptors as Transcriptome: G. F. (2011). ArachnoServer 2.0, an of women with gestational diabetes embryo staging Reproduction with transcription initiation and B., Hume, D.A., Sweet, M.J (2012).Discriminant and Prognostic Value updated online resource for spider mellitus differ with fetal sex. Diabetes 141(1), 79-89. splice sites in metazoans. Nature Conservation and Divergence inin Breast Cancer. Mol Endocrinol toxin sequences and structures. Care, 34(12), 2581-2585. Structural & Molecular Biology, 17(8), Toll-like Receptor 4-regulated gene Lê Cao, K. A., Meugnier, E., &27(2), 350-365. [Journal article]. Nucleic acids research, 1030-U1146. expression in primary human versus Choi, J., Davis, M. J., Newman, A. F., McLachlan, G. J. (2010). Integrative 39(Database issue), D653 - D657.Donald M. Gardiner, Megan C. mouse macrophages. Proceedings of & Ragan, M. A. (2010). A semantic mixture of experts to combine Shin, C. J., Davis, M. J., & Ragan, M.McDonald, Lorenzo Covarelli, Peter the National Academy of Sciences. Lê Cao, K.-A., & LeGall, C. (2011). web ontology for small molecules clinical factors and gene markers. A. (2009). Towards the mammalianS. Solomon, Anca G. Rusu, Mhairi Proc Natl Acad Sci 109(16), E944 - E953 Integration and variable selection of and their biological targets. J Chem Bioinformatics, 26(9), 1192-1198. interactome: Inference of a coreMarshall, Kemal Kazan, Sukumar ‘omics’ data sets with PLS: a survey Inf Model, 50(5), 732-741. mammalian interaction set in mouse. Yao, F., Coquery, J., & Lê Cao, Mercer, T. R., Wilhelm, D., Dinger,Chakraborty, Bruce A. McDonald, Journal de la Société Francaise de Proteomics, 9(23), 5256-5266. K.-A. (2012). Independent Principal Davis, M. J., Sehgal, M. S., & M.E., Soldà, G., Korbie, D. J., Glazov,John M. Manners (2012). Comparative Statistique, 152(2). Component Analysis for biologically Ragan, M. A. (2010). Automatic, E. A., Truong, V., Schwenke, M., Shin, C. J., Wong, S., Davis, M. J., &Pathogenomics Reveals Horizontally meaningful dimension reduction Lê Cao, K. A., Boitard, S., & Besse, context-specific generation of Gene Simons, C., Matthaei, K.I., Saint, R., Ragan, M. A. (2009). Protein-proteinAcquired Novel Virulence Genes of large biological data sets. BMC P. (2011). Sparse PLS discriminant Ontology slims. [Journal Article Koopman, P., Mattick, J. S. (2010). interaction as a predictor of subcellularin Fungi Infecting Cereal Hosts. bioinformatics, 13(1), 24. analysis: biologically relevant Research Support Non-U S Gov’t]. Expression of distinct RNAs from 3’ location. BMC Syst Biol, 3, 28.PLoS Pathog Sep, 8(9).28 29
  17. 17. www.qfab.orgQFAB BioinformaticsLevel 6, Queensland Bioscience PrecinctThe University of Queensland306 Carmody RoadSt Lucia QLD 4067AustraliaT +61 (0)7 3346 2604F +61 (0)7 3346 2101E contact@qfab.org