Gating-ML revision 1.5.081030 has been posted

Ryan Brinkman — Thu, 30 Oct 2008 21:29:52 -0000

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.

Gating-ML compliance test suite
- Gating-ML files 01Rectangular.xml, 09Ellipsoids.xml, 10PolytopeGates.xml, 24TrExp.xml, 28TrEH.xml, and 30TrInvSplitScale.xml have been updated affecting 15 out of 461 gates in the test suite.
- Detailed expected results have been added for the 09Ellipsoids/Ellipsoid_19i gate and updated for the 32TrCompensation2/comp2G5 gate.
- Typo has been corrected in the text segment of the int-10_events_8_parameters.fcs file.
- Floating point precision issues have been addressed using appropriate machine constants.

Detailed revision history is part of (i) Annex B of the Gating-ML specification PDF and (ii) the readme.pdf of the Gating-ML compliance test suite, respectively.

My apologies for any inconvenience that this may have introduced.

Best regards,
Josef

Minor revision of Gating-ML 1.5 specification and tests

Ryan Brinkman — Wed, 08 Oct 2008 18:39:14 -0000

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.

Gating-ML XML schemas
- No changes, original XML schemas have been kept.

Gating-ML compliance test suite
- Expected results for the following gates have been updated: prt_02, prt_03, prt_08, prt_19, prt_23, prt_p08, and prt_p09 (all defined in 17ParentIdTest.xml). This fixes rounding errors effecting events close to the boundary of some ellipsoid gates.
- Typos have been fixed in parameter names in the LComb_4 transformation (19TrCombination.xml) and prt_05 gate (17ParentIdTest.xml).

Detailed revision history is part of (i) Annex B of the Gating-ML specification PDF and (ii) the readme.pdf of the Gating-ML compliance test suite, respectively.

My apologies for any inconvenience that this may have brought you.

Best regards,
Josef

Gating-ML Compliance Tests Issues and FAQs

Ryan Brinkman — Fri, 03 Oct 2008 17:50:34 -0000

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.

In a brief summary, issues have been identified for the following tests:
- 26TrSinH.xml: TrSHG1, TrSHG2, TrSHG3, TrSHG4, TrSHG5, TrSHG6
- 17ParentIdTest.xml: prt_p08, prt_p09, prt_23, prt_19, prt_08, prt_02, prt_03
- 19TrCombination.xml: typo in a parameter name in the Lcomb_4 transformation

These issues are related to Gating-ML.v1.5.080311.Compliance-tests.080902.zip (Compliance tests version 080902 to Gating-ML version 1.5.080311). We are working on a new revision of the compliance test suite to provide correct expected results for these test gates.

Cheers,
Josef

List-mode data converter released

Ryan Brinkman — Tue, 19 Feb 2008 19:45:42 -0000

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

Gating-ML proposal updated

Ryan Brinkman — Fri, 16 Nov 2007 18:13:48 -0000

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.

The updated Gating-ML proposal is available at:
https://sourceforge.net/project/showfiles.php?group_id=175725&package_id=202309

NetCDF proposed to store list mode data in ACS containers

Ryan Brinkman — Fri, 16 Nov 2007 18:03:35 -0000

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.

Please see the “conventions” PDF document at
https://sourceforge.net/project/showfiles.php?group_id=175725&package_id=202340
for motivation and details on how we propose to use NetCDF to capture binary list mode data.

ZIP for ACS

Ryan Brinkman — Fri, 16 Nov 2007 17:56:13 -0000

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

FCS4.0 / ACS1.0, proposal released

Ryan Brinkman — Tue, 13 Feb 2007 01:31:52 -0000

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 being reviewed by ISAC

Ryan Brinkman — Thu, 08 Feb 2007 18:25:40 -0000

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.

*ML compatibility testing

Ryan Brinkman — Tue, 06 Feb 2007 01:30:48 -0000

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.

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