Cross-WG Conference Calls
- July 25, 2007: FICCS Development Conference Call - Summary.
- July 11, 2007: FICCS Development Conference Call - Summary.
- June 27, 2007: FICCS Development Conference Call - Summary.
- June 13, 2007: FICCS Development Conference Call - Summary.
- May 30, 2007: FICCS Development Conference Call - Summary.
- May 16, 2007: FICCS Development Conference Call - Summary.
- May 2, 2007: FICCS Development Conference Call - Summary.
- April 21, 2007: FICCS Development Conference Call - Summary.
- February 21, 2007: FICCS Development Conference Call - Summary.
- January 24, 2007: FICCS Development Conference Call - Summary.
- January 10, 2007: FICCS Development Conference Call - Summary.
- December 13, 2006: FICCS Development Conference Call - Summary.
- November 29, 2006: FICCS Development Conference Call - Summary.
- November 22, 2006: FICCS Development Conference Call - Summary.
Algorithms
Currently, high throughput flow cytometry techniques can analyze thousands of samples per day. However, managing the generated data presents a significant challenge, as each data set can consist of multiparametric descriptions of millions of individual cells. To date only rudimentary bioinformatics tools exist to manage, analyze, present and disseminate this data, and there is considerable demand for appropriate tools and new algorithms to be developed. The Algorithms Working Group (ALWG) addresses these shortcomings by developing new algorithms for analysing and viewing multi parametric flow cytometry data.
Object Model
Several object models have been developed by various groups. However, the lack of a standardized approach prevents from sharing these data, resulting in limited possibilities of cooperation among independent research groups.
A comprehensive flow cytometry object model is being developed by the Object Model Working Group (OMWG). It is based on FuGE and should include a model of the metadata describing the experiment design and protocol, the primary results generated by the cytometer, the metadata describing the processing of the primary results and the derived data emanating from the analytical processing.
Download current version of the extended FuGE model from subversion source control.
R Packages
R Packages Working Group (RPWG) developes statistical packages for processing flow cytometry data. New packages will be based on RFlowCyt and Prada; they will also be available as part of the Bioconductor package and they will implement new algorithms and proposed standards.
Proposed packages:
- flowCore: read/write FCS and XML based standards, provide summary statistics, support for data filtering and unitests
- flowViz: visualization of flow cytometry data (density plots, stacked histograms, parallel coordinates)
- flowQ: quality control and assurance support, e.g., control charts, Levy Jennon chart, summary.
- flowUtil: Other utilities to analyze flow cytometry data.
- plateCore: Support for high throughput flow cytometry, n-samples on a plate, panels, etc., including plate metadata.
- flowDataset: Future support for accessing data and metadata above local file system, e.g., in databases, via web services, etc.
Data Standards
Lately, the importance of flow cytometry as an analytical tool in varied research/clinical areas has widely increased. However, current data standards do not capture the full scope of flow cytometry experiments, i.e., there are no standards to report flow cytometry experiments and thus the experiments are irreproducible and unverifiable by independent researchers. Moreover, the lack of standardization prevents a variety of collaborative opportunities to recreate experimental methods and results.
To address these shortcomings we have brought together the Data Standards Working Group (DSWG) - a unique cross-disciplinary international collaborative group of bioinformaticists, computational statisticians, software developers and clinician scientists, from both academia and industry (including both software and hardware suppliers) to collaborate on development of data standards in flow cytometry.