#44 Sarah's comments Sofware

#44 (comment)
4dn-dcic · Sep 14, 2024 · 32ee024 · 32ee024
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diff --git a/docs/source/allowable_value_lists.rst b/docs/source/allowable_value_lists.rst
@@ -17,6 +17,12 @@ Allowable value lists
     - SI units of `Length <https://en.wikipedia.org/wiki/SI_base_unit>`_
     - nm, micron, mm, etc.
     - micron
+  * - 2
+    - ``Software_Type``
+    - The type of this Software used to produce results recorded in this table.
+    - SpotLoc, Tracing, SpotLoc+Tracing, Segmentation, QC, Other
+    - Not Applicable
+    - Not Applicable
   * - 2
     - ``Time_unit``
     - The unit used to represent a time interval.

diff --git a/docs/source/bio.rst b/docs/source/bio.rst
@@ -31,7 +31,7 @@ File Header
 - The first line in the header is always ``##FOF-CT_Version=vX.X``.
 - The second line in the header is always ``##Table_Namespace=4dn_FOF-CT_bio``.
 
-The header **MUST** contain a mandatory set of fields that describe any algorithm that was used to produce/process data in this table. In case more than one algorithm were used, please use the same set of fields for each of them.
+.. tip:: If applicable, the header **MUST** contain a mandatory set of fields that describe any Software tool that was used to produce/process data in this table. If more than one software tool was used, please repeat a set of Software-fields for describing each of them.
 
 The header **MUST** include a detailed description of each Optional Column used. 
 

diff --git a/docs/source/cell.rst b/docs/source/cell.rst
@@ -29,6 +29,8 @@ File Header
 - The first line in the header is always ``##FOF-CT_Version=vX.X``.
 - The second line in the header is always ``##Table_Namespace=4dn_FOF-CT_cell``.
 
+.. tip:: If applicable, the header **MUST** contain a mandatory set of fields that describe any Software tool that was used to produce/process data in this table. If more than one software tool was used, please repeat a set of Software-fields for describing each of them.
+
 The header **MUST** include a detailed description of each optional columns used.
 
 .. tip:: The table **MUST** contain at least 1 Optional Column. 

diff --git a/docs/source/core.rst b/docs/source/core.rst
@@ -55,10 +55,7 @@ File Header
 - The first line in the header is always ``##FOF-CT_Version=vX.X``.
 - The second line in the header is always ``##Table_Namespace=4dn_FOF-CT_mapping``.
 
-The header **MUST** contain a mandatory set of fields that describe the
-algorithm(s) that were used to identify and localize bright Spots and to
-connect them to form Traces. In case more than one algorithm were used,
-please use the same set of fields for each of the algorithm used.
+.. tip:: The header **MUST** contain a mandatory set of fields that describe any Software tool that was used to produce/process data in this table. If more than one software tool was used, please repeat a set of Software-fields for describing each of them.
 
 All columns for this table are mandatory and do not need to be described
 in the header.

diff --git a/docs/source/demultiplexing.rst b/docs/source/demultiplexing.rst
@@ -28,9 +28,7 @@ File Header
 - The first line in the header is always ``##FOF-CT_Version=vX.X``.
 - The second line in the header is always ``##Table_Namespace=4dn_FOF-CT_mapping``.
 
-The header **MUST** contain a mandatory set of fields that describe any
-algorithm that was used to produce/process data in this table.
-In case more than one algorithm were used, please use the same set of fields for each of them.
+.. tip:: The header **MUST** contain a mandatory set of fields that describe any Software tool that was used to produce/process data in this table. If more than one software tool was used, please repeat a set of Software-fields for describing each of them.
 
 The header **MUST** include a detailed description of each optional columns used.
 

diff --git a/docs/source/extracell.rst b/docs/source/extracell.rst
@@ -27,6 +27,8 @@ File Header
 - The first line in the header is always ``##FOF-CT_Version=vX.X``.
 - The second line in the header is always ``##Table_Namespace=4dn_FOF-CT_extracell``.
 
+.. tip:: If applicable, the header **MUST** contain a mandatory set of fields that describe any Software tool that was used to produce/process data in this table. If more than one software tool was used, please repeat a set of Software-fields for describing each of them.
+
 The header **MUST** include a detailed description of each Optional Columns used. 
 
 .. tip:: The table **MUST** contain at least 1 Optional Column. 

diff --git a/docs/source/mapping.rst b/docs/source/mapping.rst
@@ -66,6 +66,8 @@ File Header
 - The first line in the header is always ``##FOF-CT_Version=vX.X``.
 - The second line in the header is always ``##Table_Namespace=4dn_FOF-CT_mapping``.
 
+.. tip:: If applicable, the header **MUST** contain a mandatory set of fields that describe any Software tool that was used to produce/process data in this table. If more than one software tool was used, please repeat a set of Software-fields for describing each of them.
+
 The header **MUST** include a detailed description of each optional columns used.
 
 .. csv-table::

diff --git a/docs/source/quality.rst b/docs/source/quality.rst
@@ -33,9 +33,7 @@ File Header
 - The first line in the header is always ``##FOF-CT_Version=vX.X``.
 - The second line in the header is always ``##Table_Namespace=4dn_FOF-CT_mapping``.
 
-The header **MUST** contain a mandatory set of fields that describe any
-algorithm that was used to produce/process data in this table.
-In case more than one algorithm were used, please use the same set of fields for each of them.
+.. tip:: The header **MUST** contain a mandatory set of fields that describe any Software tool that was used to produce/process data in this table. If more than one software tool was used, please repeat a set of Software-fields for describing each of them.
 
 The header **MUST** include a detailed description of each optional columns used. 
 

diff --git a/docs/source/rna.rst b/docs/source/rna.rst
@@ -46,10 +46,7 @@ File Header
 - The first line in the header is always ``##FOF-CT_Version=vX.X``.
 - The second line in the header is always ``##Table_Namespace=4dn_FOF-CT_mapping``.
 
-The header **MUST** contain a mandatory set of fields that describe the
-algorithm(s) that were used to identify and localize bright Spots.
-In case more than one algorithm were used, please use the same set of fields
-for each of them.
+.. tip:: The header **MUST** contain a mandatory set of fields that describe any Software tool that was used to produce/process data in this table. If more than one software tool was used, please repeat a set of Software-fields for describing each of them.
 
 The header **MUST** include a detailed description of each optional columns used.
 

diff --git a/docs/source/rna_bio.rst b/docs/source/rna_bio.rst
@@ -31,7 +31,7 @@ File Header
 - The first line in the header is always ``##FOF-CT_Version=vX.X``.
 - The second line in the header is always ``##Table_Namespace=4dn_FOF-CT_rna_bio``.
 
-The header **MUST** contain a mandatory set of fields that describe any algorithm that was used to produce/process data in this table. In case more than one algorithm were used, please use the same set of fields for each of them.
+.. tip:: If applicable, the header **MUST** contain a mandatory set of fields that describe any Software tool that was used to produce/process data in this table. If more than one software tool was used, please repeat a set of Software-fields for describing each of them.
 
 The header **MUST** include a detailed description of each optional columns used. 
 

diff --git a/docs/source/rna_quality.rst b/docs/source/rna_quality.rst
@@ -33,9 +33,7 @@ File Header
 - The first line in the header is always ``##FOF-CT_Version=vX.X``.
 - The second line in the header is always ``##Table_Namespace=4dn_FOF-CT_rna_quality``.
 
-The header **MUST** contain a mandatory set of fields that describe any
-algorithm that was used to produce/process data in this table.
-In case more than one algorithm were used, please use the same set of fields for each of them.
+.. tip:: The header **MUST** contain a mandatory set of fields that describe any Software tool that was used to produce/process data in this table. If more than one software tool was used, please repeat a set of Software-fields for describing each of them.
 
 The header **MUST** include a detailed description of each optional columns used.
 

diff --git a/docs/source/subcell.rst b/docs/source/subcell.rst
@@ -28,6 +28,8 @@ File Header
 - The first line in the header is always ``##FOF-CT_Version=vX.X``.
 - The second line in the header is always ``##Table_Namespace=4dn_FOF-CT_subcell``.
 
+.. tip:: If applicable, the header **MUST** contain a mandatory set of fields that describe any Software tool that was used to produce/process data in this table. If more than one software tool was used, please repeat a set of Software-fields for describing each of them.
+
 The header **MUST** include a detailed description of each optional columns used.
 
 .. tip:: The table **MUST** contain at least 1 Optional Column. 

diff --git a/docs/source/tables/bio_header.csv b/docs/source/tables/bio_header.csv
@@ -8,8 +8,8 @@ Name,Description,Example,Conditional requirement conditions
 **#Experimenter_Name:**,name of the person performing the experiment.,John Doe,
 **#Experimenter_Contact:**,email address of the person performing the experiment.,[email protected],
 **#Description:**,"A free-text, description of the experiment and of the data recorded in this table. This description should provide a clear understanding of the process utilized to produce the data and contain sufficient details to ensure interpretation and reproducibility.",,
-*#Software_Title:*,The name of the Software(s) that were used in this case for localizing individual FISH-omics bright Spots and/or to produce three-dimensional (3D) polymeric chromatin Traces.,AlgorithmXYZ,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table.
-*#Software_Type:*,"The type of this Software. Allowed values: SpotLoc, Tracing, SpotLoc+Tracing, Segmentation, QC, Other",Segmentation,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table.
+*#Software_Title:*,"The name of the Software tool that was used to produce the results reported in this table. If more than one software tool was used, please repeat a set of Software-fields for describing each of them.",AlgorithmXYZ,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table.
+*#Software_Type:*,"The type of this Software used to produce results recorded in this table. Allowed values: SpotLoc, Tracing, SpotLoc+Tracing, Segmentation, QC, Other",Segmentation,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table.
 *#Software_Authors:*,"The Name(s) of the individual Author(s) of this Software. In case there are more than one Authors, individual names should be listed as follows, Doe, John; Smith, Jane; etc,.",John Doe,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table.
 *#Software_Description:*,"A free-text, description of this Software. This description should provide a detailed understanding of the algortithm and of the analysis parameters that were used, in order to guarantee interpretation and reproducibility.",A pretty clear description,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table.
 *#Software_Repository:*,The URL of any repository or archive where the Software executable release can be obtained.,https://github.com/repo_name_goes_here,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table.

diff --git a/docs/source/tables/cell_header.csv b/docs/source/tables/cell_header.csv
@@ -10,8 +10,8 @@ Name,Description,Example,Conditional requirement conditions
 **#Experimenter_Name:**,name of the person performing the experiment.,John Doe,
 **#Experimenter_Contact:**,email address of the person performing the experiment.,[email protected],
 **#Description:**,"A free-text, description of the experiment and of the data recorded in this table. This description should provide a clear understanding of the process utilized to produce the data and contain sufficient details to ensure interpretation and reproducibility.",,
-*#Software_Title:*,"The name(s) of the Software(s) that were used here for localizing individual FISH-omics bright Spots, to produce three-dimensional (3D) polymeric chromatin Traces or for segmentation to identify individual cells, subcellular structures or extra-cellular entities, as applicable.",AlgorithmXYZ,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table.
-*#Software_Type:*,"The type of this Software. Allowed values: Loc, SpotLoc, Tracing, SpotLoc+Tracing, Segmentation, QC, Distance, Other",Segmentation,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table.
+*#Software_Title:*,"The name of the Software tool that was used to produce the results reported in this table. If more than one software tool was used, please repeat a set of Software-fields for describing each of them.",AlgorithmXYZ,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table.
+*#Software_Type:*,"The type of this Software used to produce results recorded in this table. Allowed values: SpotLoc, Tracing, SpotLoc+Tracing, Segmentation, QC, Other",Segmentation,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table.
 *#Software_Authors:*,"The Name(s) of the individual Author(s) of this Software. In case there are more than one Authors, individual names should be listed as follows, Doe, John; Smith, Jane; etc,.",John Doe,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table.
 *#Software_Description:*,"A free-text, description of this Software. This description should provide a detailed understanding of the algortithm and of the analysis parameters that were used, in order to guarantee interpretation and reproducibility.",A pretty clear description,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table.
 *#Software_Repository:*,The URL of any repository or archive where the Software executable release can be obtained.,https://github.com/repo_name_goes_here,Conditional requirement: this MUST be reported any time a software is used to produce data associated with this table.

diff --git a/docs/source/tables/core_columns.csv b/docs/source/tables/core_columns.csv
@@ -1,7 +1,7 @@
 core_columns,,,,
 Name,Description,Example,Conditional requirement conditions,
 **Spot_ID**,A unique identifier for this bright DNA Spot.,1,,
-**Trace_ID**,"In case of **ball-and-stick** Chromatin Tracing experiments, tracing algorithms are used to interlink individual DNA Spots in 3D polymeric traces delineating the conformation of chromatin fibers (such as in ORCA; https://doi.org/10.1038/s41596-020-00478-x). As such, this fields reports a unique identifier for the DNA trace the Spot belongs to. **Note**: this is used to connect Spots that are part of the same polymeric Trace. It is also used to connect data in this table with any other Trace global measurements reported elsewhere in the dataset (i.e., :ref:`trace` and :ref:`rna`).",1,,
+**Trace_ID**,"In **ball-and-stick** Chromatin Tracing experiments, tracing algorithms are used to interlink individual DNA Spots in 3D polymeric traces delineating the conformation of chromatin fibers (such as in `ORCA <https://doi.org/10.1038/s41596-020-00478-x>`_). As such, this fields reports a unique identifier for the Trace each Spot belongs to. **Note**: The purpose of this field is to connect Spots that are part of the same polymeric Trace. It is also used to connect individual Traces recorded in this table with global Trace properties reported elsewhere in the dataset (i.e., :ref:`trace` and :ref:`rna`).",1,,
 **X**,The sub-pixel X coordinate of this bright Spot. NOTE: the reported X position is understood to be the one resulting from any performed post-processing correction procedures (i.e. drift correction; chromatic correction etc).,14.43,,
 **Y**,The sub-pixel Y coordinate of this bright Spot. NOTE: the reported Y position is understood to be the one resulting from any performed post-processing correction procedures (i.e. drift correction; chromatic correction etc).,41.43,,
 **Z**,The sub-pixel Z coordinate of this bright Spot. NOTE: the reported Z position is understood to be the one resulting from any performed post-processing correction procedures (i.e. drift correction; chromatic correction etc).,1.23,,