Changes between Initial Version and Version 2 of Ticket #1440


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Timestamp:
Nov 18, 2009, 12:54:17 PM (14 years ago)
Author:
Nicklas Nordborg
Comment:

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  • Ticket #1440

    • Property Owner changed from everyone to Nicklas Nordborg
    • Property Status new → assigned

  • Ticket #1440 – Description

    initial v2  
    1 The BaseFileSet (BFS) file format is a new file format that is intended to be used for passing data between BASE and external plug-ins. The intention is that it should complement the existing BASEfile format, which is sometimes hard to parse by external programs (for example R).
     1The !BaseFileSet (BFS) file format is a new file format that is primarily intended to be used for passing data between BASE and external plug-ins. The intention is that it should complement the existing BASEfile format, which is sometimes hard to parse by external programs (for example R).
     2
     3A secondary objective is that the BFS format should be re-usable in other use cases.
    24
    35The main idea is to use multiple files:
    4   * One parameter/metadata file that contains information about what kind of data that is found in the other files.
    5   * One assay information file that contains id, name, annotations, etc for each assay.
    6   * One reporter information file that contains id, name, annotations, etc, for each reporter.
    7   * One or more data files that contains the actual spot data.
     6  * A parameter/metadata file that contains information about what kind of data that is found in the other files.
     7  * Annotation files that contains additional information about various items, such as reporter, assays, etc.
     8  * One or more data files that contains the actual data.
    89
    9 A data file can contain either:
    10  * A single value per position for all assays. For example, one file can hold ch1 intensity, a second file holds ch2 intensity.
    11  * Multiple values per position for one assay. For example, one file holds both ch1 and ch2 intensity for one assay, a second file holds the same values for another assay.
     10The parameter/metadata file is structured in section with key/value pairs. The annotation files are simple tab-separated tables with configurable number of columns with varying data types. The data files are plain-matrix data files with no row or column headers.
    1211
    13 This ticket is about documenting the file format for the four types of files. Working drafts should be attached to this ticket. The final BFS file format should be documented in the docbook documentation.
     12This ticket is about documenting the file format for the various file types, generically and specifically for the plug-in execution use case. Working drafts should be attached to this ticket. The final BFS file format should be documented in the docbook documentation.