2011 Strategic roadmap for Australian research infrastructure

The 2011 Roadmap articulates the priority research infrastructure areas of a national scale (capability areas) to further develop Australia’s research capacity and improve innovation and research outcomes over the next five to ten years. The capability areas have been identified through considered analysis of input provided by stakeholders, in conjunction with specialist advice from Expert Working Groups   It is intended the Strategic Framework will provide a high-level policy framework, which will include principles to guide the development of policy advice and the design of programs related to the funding of research infrastructure by the Australian Government. Roadmapping has been identified in the Strategic Framework Discussion Paper as the most appropriate prioritisation mechanism for national, collaborative research infrastructure. The strategic identification of Capability areas through a consultative roadmapping process was also validated in the report of the 2010 NCRIS Evaluation. The 2011 Roadmap is primarily concerned with medium to large-scale research infrastructure. However, any landmark infrastructure (typically involving an investment in excess of $100 million over five years from the Australian Government) requirements identified in this process will be noted. NRIC has also developed a ‘Process to identify and prioritise Australian Government landmark research infrastructure investments’ which is currently under consideration by the government as part of broader deliberations relating to research infrastructure. NRIC will have strategic oversight of the development of the 2011 Roadmap as part of its overall policy view of research infrastructure

Bin3C: Exploiting Hi-C sequencing data to accurately resolve metagenome-assembled genomes

© 2019 The Author(s). Most microbes cannot be easily cultured, and metagenomics provides a means to study them. Current techniques aim to resolve individual genomes from metagenomes, so-called metagenome-assembled genomes (MAGs). Leading approaches depend upon time series or transect studies, the efficacy of which is a function of community complexity, target abundance, and sequencing depth. We describe an unsupervised method that exploits the hierarchical nature of Hi-C interaction rates to resolve MAGs using a single time point. We validate the method and directly compare against a recently announced proprietary service, ProxiMeta. bin3C is an open-source pipeline and makes use of the Infomap clustering algorithm (https://github.com/cerebis/bin3C)

Readiness for research data management in the life sciences at the University of the Witwatersrand

Because of the importance of Research Data Management (RDM) in the life sciences, where vast amounts of research data in different complex formats are being produced, this study aimed to assess the state of RDM readiness in the life sciences at Wits to ascertain what support is needed with regards to RDM. In order to achieve the aim, the current RDM practices and needs of researchers, as well as the challenges they face, were investigated. The Jisc Research Data Lifecycle (Jisc, 2021a) was used to guide the literature review, frame data collection, analyse data and advise on some of the main findings and recommendations. A mixed methods approach and an explanatory sequential design were used to achieve the research objectives. For the quantitative phase of research, an online questionnaire was used to collect data. As the total target population (282) was not big, a census was conducted. The questionnaire was administered using SurveyMonkey software. During the qualitative part of the research, semi-structured interviews were used to explain the quantitative results. Five participants were purposively sampled to take part in interviews. The statistical package, MS Excel, was used to analyse quantitative data whilst qualitative data were analysed by thematic analysis. The study showed that life sciences researchers at Wits have adopted many RDM practices, and researchers are increasingly becoming aware of the importance of the openness of data. However, they are dealing with similar RDM issues as their peers worldwide. Results highlighted challenges of, amongst others, the lack of an RDM policy as well as the lack of, or unawareness of, appropriate RDM training and support at Wits. As formal implementation of RDM still needs to take place at Wits, it is recommended that Wits puts an RDM policy in place, followed by suitable RDM infrastructure and awareness making of current services

iLearnPlus: a comprehensive and automated machine-learning platform for nucleic acid and protein sequence analysis, prediction and visualization

Sequence-based analysis and prediction are fundamental bioinformatic tasks that facilitate understanding of the sequence(-structure)-function paradigm for DNAs, RNAs and proteins. Rapid accumulation of sequences requires equally pervasive development of new predictive models, which depends on the availability of effective tools that support these efforts. We introduce iLearnPlus, the first machine-learning platform with graphical- and web-based interfaces for the construction of machine-learning pipelines for analysis and predictions using nucleic acid and protein sequences. iLearnPlus provides a comprehensive set of algorithms and automates sequence-based feature extraction and analysis, construction and deployment of models, assessment of predictive performance, statistical analysis, and data visualization; all without programming. iLearnPlus includes a wide range of feature sets which encode information from the input sequences and over twenty machine-learning algorithms that cover several deep-learning approaches, outnumbering the current solutions by a wide margin. Our solution caters to experienced bioinformaticians, given the broad range of options, and biologists with no programming background, given the point-and-click interface and easy-to-follow design process. We showcase iLearnPlus with two case studies concerning prediction of long noncoding RNAs (lncRNAs) from RNA transcripts and prediction of crotonylation sites in protein chains. iLearnPlus is an open-source platform available at https://github.com/Superzchen/iLearnPlus/ with the webserver at http://ilearnplus.erc.monash.edu/.Zhen Chen, Pei Zhao, Chen Li, Fuyi Li, Dongxu Xiang, Yong-Zi Chen, Tatsuya Akutsu, Roger J. Daly, Geoffrey I. Webb, Quanzhi Zhao, Lukasz Kurgan, and Jiangning Son

Defining virus-antibody interplay during the development of HIV-1 neutralization breadth to inform vaccine design

A thesis submitted to the School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Doctor of Philosophy. Johannesburg, 2016Human Immunodeficiency Virus Type 1 (HIV-1) infects approximately two million people annually, highlighting the need for a preventative vaccine. An effective HIV-1 vaccine will likely need to elicit broadly neutralizing antibodies (bNAbs), which arise naturally in some infected individuals and recognize the envelopes (Env) of multiple HIV-1 strains. Understanding the molecular events that contribute to bNAb development during infection may provide a blueprint for vaccine strategies. Here we investigated the development of a V1V2-directed bNAb lineage in the context of viral co-evolution in an HIV-1 superinfected participant (CAP256). For this, clonally-related monoclonal antibodies (mAbs), with a range of neutralization breadth, were isolated. We determined their developmental pathway from strain-specificity towards neutralization breadth and identified viral variants responsible for initiating and maturing this bNAb lineage. MAbs were isolated by memory B cell culture or trimer-specific single B cell sorting and extensively characterized by Env-pseudotyped neutralization, cell surface-expressed Env binding, electron microscopy and epitope-predictive algorithms. Antibody next-generation sequencing (NGS) at multiple time-points enabled the inference of the unmutated common ancestor (UCA) of this lineage. Viral co-evolution was investigated using Env single genome amplification and V1V2 NGS. A family of 33 clonally-related mAbs, CAP256-VRC26.01-33, was isolated from samples spanning four years of infection. The UCA of this lineage possessed an unusually long heavy chain complementarity determining region 3 (CDRH3), which resulted from a unique recombination event. Surprisingly, this UCA potently neutralized later viral variants that had evolved from the superinfecting virus, which we termed bNAb-initiating Envs. Viral diversification, which peaked prior to the development of neutralization breadth, created multiple immunotypes at key residues in the V1V2 epitope. Exposure to these immunotypes allowed adaptation of some mAbs to tolerate this variation and thus mature towards neutralization breadth. Based on these data, we proposed a four-step immunization strategy which includes priming with bNAb-initiating Envs to engage rare B cells with a long CDRH3; followed by three sequential boosts (including select V1V2 immunotypes) to drive antibody maturation. In conclusion, this study has generated a testable HIV-1 vaccine immunization strategy through the delineation of mAb-virus co-evolution during the development of neutralization breadth.MT201

Designing the Library of the Future

The University of Technology, Sydney (UTS) has embarked on a major redevelopment of its City Campus. A key element of this redevelopment is the planned construction of a new University Library at the centre of the redeveloped campus on the current site of Building 2, adjoining the UTS Tower, Building 1. This Library of the Future, which is planned to open for academic year 2015, will be a new kind of academic library which will aim to set a standard for the future. The focus of this report is on envisaging a Library of the Future, what it might be when it opens and how it might develop to retain its novelty so that it will continue to surprise and excite. To endeavour to imagine and create a Library of the Future is a daring and humbling enterprise: it must be designed to foster an effective academic community in the long term at UTS through its role as the knowledge hub of the University