Kieran O'Neill

RchyOptimyx: Cellular hierarchy optimization for flow cytometry

Analysis of high‐dimensional flow cytometry datasets can reveal novel cell populations with poorly understood biology. Following discovery, characterization of these populations in terms of the critical markers involved is an important step, as this can help to both better understand the biology of these populations and aid in designing simpler marker panels to identify them on simpler instruments and with fewer reagents (i.e., in resource poor or highly regulated clinical settings). However, current tools to design panels based on the biological characteristics of the target cell populations work exclusively based on technical parameters (e.g., instrument configurations, spectral overlap, and reagent availability). To address this shortcoming, we developed RchyOptimyx (cellular hieraRCHY OPTIMization), a computational tool that constructs cellular hierarchies by combining automated gating with dynamic programming and graph theory to provide the best gating strategies to identify a target population to a desired level of purity or correlation with a clinical outcome, using the simplest possible marker panels. RchyOptimyx can assess and graphically present the trade‐offs between marker choice and population specificity in high‐dimensional flow or mass cytometry datasets. We present three proof‐of‐concept use cases for RchyOptimyx that involve 1) designing a panel of surface markers for identification of rare populations that are primarily characterized using their intracellular signature; 2) simplifying the gating strategy for identification of a target cell population; 3) identification of a non‐redundant marker set to identify a target cell population. Published 2013 Wiley‐Periodicals, Inc.

Dasty2, an Ajax protein DAS client

SUMMARY Dasty2 is a highly interactive web client integrating protein sequence annotations from currently more than 40 sources, using the distributed annotation system (DAS). AVAILABILITY Dasty2 is an open source tool freely available under the terms of the Apache License 2.0, publicly available at http://www.ebi.ac.uk/dasty/.

Enhanced flowType/RchyOptimyx: a Bioconductor Pipeline for Discovery in High-dimensional Cytometry Data

We present a significantly improved version of the flowType and RchyOptimyx BioConductor-based pipeline that is both 14 times faster and can accommodate multiple levels of biomarker expression for up to 96 markers. With these improvements, the pipeline is positioned to be an integral part of data analysis for high-throughput experiments on high-dimensional single-cell assay platforms, including flow cytometry, mass cytometry and single-cell RT-qPCR.

OntoDas – a tool for facilitating the construction of complex queries to the Gene Ontology

BackgroundOntologies such as the Gene Ontology can enable the construction of complex queries over biological information in a conceptual way, however existing systems to do this are too technical. Within the biological domain there is an increasing need for software that facilitates the flexible retrieval of information. OntoDas aims to fulfil this need by allowing the definition of queries by selecting valid ontology terms.ResultsOntoDas is a web-based tool that uses information visualisation techniques to provide an intuitive, interactive environment for constructing ontology-based queries against the Gene Ontology Database. Both a comprehensive use case and the interface itself were designed in a participatory manner by working with biologists to ensure that the interface matches the way biologists work. OntoDas was further tested with a separate group of biologists and refined based on their suggestions.ConclusionOntoDas provides a visual and intuitive means for constructing complex queries against the Gene Ontology. It was designed with the participation of biologists and compares favourably with similar tools. It is available at http://ontodas.nbn.ac.za