Flow Cytometry Data Standards / News: Recent posts

A minor revision of Gating-ML 1.5 has been posted at
https://sourceforge.net/project/showfiles.php?group_id=175725&package_id=202309

The revision 1.5.081030 fixes identified errors and incorporates suggestions from the developers as follows:

Gating-ML specification
- A typo has been fixed in the formula defining the negative part of the EH (hyperlog) transformation (bracket removed in Eq. 25, 26) and in the MathML documentation.
- The definition of valid rectangular gates have been updated: if both the min and the max attributes are specified then the value of the min attribute shall be less than the value of the max attribute.... read more

A minor revision of Gating-ML 1.5 has been posted at
https://sourceforge.net/project/showfiles.php?group_id=175725&package_id=202309

The revision 1.5.081007 fixes identified errors in the Gating-ML specification and the Gating-ML compliance test suite as follows:

Gating-ML specification (PDF document)
- The specification was ambiguous in the definition of the hyperbolic sinus transformation. Specifically, Eq. 23 in the PDF did not match definitions in the XML schema and MathML Central generated documentation (parameters a and b were flipped). The formula has been fixed to f(argument, a, b) = (sinh(argument / b)) / a, which also corresponds to a and b usage in the asinh transformation.
- Minor extension/improvement of the documentation.... read more

Hi,

Gating-ML is now published (http://www.ncbi.nlm.nih.gov/pubmed/18773465) and developers started implementing it and running all the provided compliance tests. This identified few errors in the current version of the test suite.

Details can be found in our new "FAQs and Issues document" (ComplianceTests_FAQs_and_Issues_20081003.zip), which can be downloaded from the Gating-ML download page at https://sourceforge.net/project/showfiles.php?group_id=175725&package_id=202309.... read more

An alfa version of a list mode data converter has been released. The application performs conversion between files conforming to FCS and netCDF - Proposed Conventions for List Mode Binary Data File.

More information, download, usage info, Java WebStart, etc. available at:
http://flowcyt.sourceforge.net/netcdf/converter/

Cheers,
Josef

Based on received feedback we have revised the Gating-ML proposal. While keeping separate XML schemas, we have harmonized the Gating-ML, Transformation-ML, and Compensation-ML proposals and merged these into a single Gating-ML standard. Since the previous version, we have added some elementary transformations (e.g., transition, ratio) and improved design, consistency, and documentation. Compensation is considered as one of the transformations that can now also be placed in a Gating-ML XML file. We have removed the "new names" approach and removed two data transformations that are only available under restrictive licensing conditions to some community members.... read more

We have been investigating formats reusable for binary list mode data (one of the components of the proposed ACS container). We believe that the cytometry community could benefit from adopting the Network Common Data Form (NetCDF) for this purpose.

NetCDF is a well matured open standard that has been adopted in approximately 30 different fields to accommodate for array-oriented scientific data over the past 20 years. NetCDF is a set of freely available software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. Many groups, including NASA and the Los Alamos National Laboratory, have adopted NetCDF as a standard way to represent some forms of scientific data. ... read more

We suggest using ZIP as the file format for the Analytical Cytometry Standard container. This approach has been adopted by other groups including for purposes such as Java JAR files, OpenDocument and Office Open XML formats, Google Earth KMZ files, Mozilla Firefox Add-ons, Nokia's mobile phone themes, WinAmp and Windows Media Player skins, Magic Draw UML files and many others.

Download the whole proposal from:
https://sourceforge.net/project/showfiles.php?group_id=175725&package_id=202340... read more

The proposal version 0.8 of the Analytical Cytometry Standard (ACS) version 1.0 (formerly discussed as FCS4.0) has been released. Detailed list of changes including rationale is included as part of the package. The proposed standard has been named Analytical Cytometry Standard (ACS) due to the large number of changes, which separate it from FCS (though the content is a subset of the data in FCS with no new keywords) and as it also facilitates inclusion of metadata from analysis procedures other than flow cytometry.

MIFlowCyt proposal has been officially submitted for review by the Data Standards Task Force of the International Society of Analytical Cytology (ISAC). The latest version of the proposal is available in the download section.

Test files have been added to Compensation-ML, Gating-ML, and Transformation-ML packages. They are suitable to test compatibility of a particular software implementation with Compensation-ML/Gating-ML/Transformation-ML specifications. They have been attached to the particular packages as ZIP collections including an instructions/overview file.

Minor update of the proposal for FCS4 has been done to clarify using of the TIME parameter without the $TIMESTAMP keyword (the semantic of the time parameter value is the exact relative time stamp for each event as an XDR-encoded floating point in seconds).

We have updated the FCS4 proposal based on discussions with instrument and software developers during the Flow Informatics and Computational Cytometry Society (FICCS) meeting in Seattle, Nov. 7-8, 2006. There are two (2) changes in the latest proposal:

1) Remove $PnR
For each fluorescence and scatter parameter, the $PnR value used to represent the maximum that could be achieved for the parameter. We propose to fix $PnR to one (1) for each fluorescence and scatter parameter, i.e., stored event values are relative amounts of measured fluorescence on a linear scale with the maximum of 1. The $PnR keyword is removed from the FCS text segment. Historically, the $PnR value also suggested internal precision of the flow cytometry instrument used to generate the FCS file. This is not true with several contemporary instruments anymore. We suggest storing instrument precision along with other metadata, either in the instrumentation description XML file or using RDF.... read more

The FICCS OMWG group committed to evaluate possibilities of building an FCM-specific object model based on existing technologies and models; possibly reusing and sharing common concepts with other ‘omics’ sciences. Representatives of the working group met for a development workshop in Dallas, TX, USA, in October 2006. The main purpose of the workshop was to closely evaluate whether the Functional Genomics Experiment (FuGE) Object Model is useful as the core for the FCM object model, and, based on the results, specify methodology and strategy to develop the first initial draft of the model. FICCS OMWG chose FuGE as the core for the FCM object model. The main areas to start extending FuGE were identified as: ... read more

The UML model has been reverse engineered for documentation purposes from the FACEJava source code. It is available in 3 formats (mdzip, rich xmi, and xmi).

The updated version:
1) The model has not changed but several diagrams have been added to provide simplified vizualization.
2) Java profile has been included in the distribution for convenience of MagicDraw Community Edition users.

The UML model has been reverse engineered for documentation purposes from the FACEJava source code. It is available in 3 formats (mdzip, rich xmi, and xmi). For your convenience, the main diagrams are also stores as hi resolution PNG pictures in the UML-pictures directory.

New version of MIFACE Guidelines (1.1 of Sept 19th, 2006) has been published. The changes are included in the release notes (go to download and click on the book icon of the relevant package).

New version of the Proposal for FCS 4.0 (of Sept 15th, 2006) has been published. The changes are included in the release notes (go to download and click on the book icon of the relevant package).

Manuscript on development of bioinformatics standards for flow cytometry published in OMICS: A Journal of Integrative Biology: Spidlen J., Gentleman R.C., Haaland P.D., Langille M., Le Meur N., Ochs M.F., Schmitt Ch., Smith A.C., Treister A.S., and Brinkman R.R. (2006). Data standards for flow cytometry. Omics 10, 209-214.

http://www.liebertonline.com/doi/abs/10.1089/omi.2006.10.209