Talk:canSAS-2012: Difference between revisions

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== brief notes ==


== 2012-07-28 Notes ==
----
== 2012-07-28 Notes of Discussions ==


*IUCr World Database of Crystallographers
=== Data storage formats ===
** Is this list contemporary?
see: [[2012_Data_Discussion]] and [[User:Boesecke | discussion from Peter Boesecke]]
*** Who are the consumers of this information?
*** Are standard terms codified?
*** Search for "small-angle" or "small angle" is not as useful as "SAXS" or "SANS"
*** SAS does not consider itself under "Crystallography"


*NeXus main page
* sasCIF
**  How to find links to Definitions and Examples? Make better main page links.
* [http://scripts.iucr.org/cgi-bin/paper?S0907444912012073 newer standard] for publishing bio SAXS data in IUCr journals (doesn't specify format, but includes data validation)
*** NAPI examples don't work (Ron Ghosh).  What is the problem?  Fix?
* canSAS1d
*** Needs more help oriented for data consumers
* NeXus
* IUCr Diffraction Data Deposition Working Group proposal, SAS Commission response to proposal, & whether proposal would impact SAS data standardization
* discussed use of standard formats to ensure some level of integrity in publications


*Data storage formats
----
**  sasCIF
 
*** newer standard for publishing bio SAXS data in IUCr journals
====  Considerations for the design of a canSAS-multid format ====
*** canSAS1d
* What is the definition of reduced SAS data?
*** NeXus
* purpose of the format?
*** DDDWG and its impact for SAS data standardization
* ease of use?
* ease of maintainability?
* user support?
* what content?
* can it handle 'big data'?
* can it cope with sparse data?
* build in coordinate specifications
*Compatibility with multiple techniques:
** SAXS+WAXS, ASAXS, GISAXS, SAXS(t), XPCS, ...
* extensibility?
* well-defined?
* ensure it gets used!
 
----
 
=== NeXus main page ===
 
see:  http://www.nexusformat.org
 
* How to find links to [http://download.nexusformat.org/doc/html/ClassDefinitions-Application.html Definitions] and [http://download.nexusformat.org/doc/html/Examples.html Examples]?  Make better [http://www.nexusformat.org/ main page] links.
** NAPI examples don't work (Ron Ghosh).  What is the problem?  Fix?
** Needs more help oriented for data consumers
* [http://download.nexusformat.org/doc/html/ClassDefinitions-Application.html#NXsas NXsas]: a definition for raw SAS data
*  [http://download.nexusformat.org/doc/html/ClassDefinitions-Application.html#NXiqproc NXiqproc]: general definition, might work for reduced SAS or at least be considered a starting point
 
----
 
=== IUCr World Database of Crystallographers ===
 
http://www.iucr.org/people/wdc
 
* Is this list contemporary?
* Who are the consumers of this information?
* Are standard terms codified?
* Search for "small-angle" or "small angle" is not as useful as "SAXS" or "SANS"
* SAS does not consider itself under "Crystallography"
 
----
 
=== SAS Portal ===
*  There can be only one!
*  Considerations for the design of a portal
** who is the target audience?
** should it support languages other than English?
** should it just be links to existing content or 'more dynamic', perhaps with a 'SAS news' section, recent results, etc?
** include an FAQ?
** incorporate social media?
** should it 'involve' the IUCr SAS Commission?
** how should it be promoted to the SAS community?
* What role should canSAS take?
* What do we recommend the IUCr provide through the [http://www.iucr.org/iucr/commissions/small-angle-scattering IUCr/CSAS] web site?
 
----
 
=== PDB data deposition task force ===
 
(Information from email chat with Jill Trewhella)
 
'''Task force remit:''' 
Bio-molecular Small-Angle Scattering Data and Interpretation; Data Deposition and Model Archiving
 
'''Task Force Membership:'''  Helen Berman, Wayne Hendrickson, Gerard Kleywegt, Guy Montelione, Mamuro Sato, Torsten Schwede, Dmitri Svergun, John Tainer, Jill Trewhella
 
'''Preliminary Recommendations:'''
 
* Need a standard dictionary for definitions of terms for data collection and for managing a data repository.  X-rays and neutrons.
* Need a data repository that holds standard data set, is searchable, internationally accessible for download.   
* Bead and atomistic models based on SAS data should be archived in a searchable data base and (given that the underlying data are not atomic resolution) there be specific information in regard to the quality/reliability/uniqueness of the result.  Criteria for these assessments need to be defined; issues chi squared, error propagation, sensible stereo-chemistry requirement is argued and needs yet to be agreed.
* Need a meeting of key people from different task forces to come together to define what the pdb should be archiving.
 
We also discussed what might be in the PDB and what might be in a parallel "hybrid model" data base that is distinct from the PDB, but with a common interface.  By this means it would be easy to communicate that the hybrid models are not based purely on data that can provide atomistic (or something close to it) information.
 
 
ADDITIONAL COMMENTS:
*While a database of data is desirable from the PDB perspective, it is not clear who should be the steward
*Data should include information about sample and its history/preparation etc., and treatment of background (and potentially storing background data as well)
*A lunchtime session has been scheduled at SAS 2012 (Sydney, November) to discuss these standards with the community
*Ideas from [http://scripts.iucr.org/cgi-bin/paper?S0907444912012073 Acta Cryst. D, 68, 620–626 (2012)] are embodied in this

Latest revision as of 13:27, 28 July 2012

2012-07-28 Notes of Discussions

Data storage formats

see: 2012_Data_Discussion and discussion from Peter Boesecke

  • sasCIF
  • newer standard for publishing bio SAXS data in IUCr journals (doesn't specify format, but includes data validation)
  • canSAS1d
  • NeXus
  • IUCr Diffraction Data Deposition Working Group proposal, SAS Commission response to proposal, & whether proposal would impact SAS data standardization
  • discussed use of standard formats to ensure some level of integrity in publications

Considerations for the design of a canSAS-multid format

  • What is the definition of reduced SAS data?
  • purpose of the format?
  • ease of use?
  • ease of maintainability?
  • user support?
  • what content?
  • can it handle 'big data'?
  • can it cope with sparse data?
  • build in coordinate specifications
  • Compatibility with multiple techniques:
    • SAXS+WAXS, ASAXS, GISAXS, SAXS(t), XPCS, ...
  • extensibility?
  • well-defined?
  • ensure it gets used!

NeXus main page

see: http://www.nexusformat.org

  • How to find links to Definitions and Examples? Make better main page links.
    • NAPI examples don't work (Ron Ghosh). What is the problem? Fix?
    • Needs more help oriented for data consumers
  • NXsas: a definition for raw SAS data
  • NXiqproc: general definition, might work for reduced SAS or at least be considered a starting point

IUCr World Database of Crystallographers

http://www.iucr.org/people/wdc

  • Is this list contemporary?
  • Who are the consumers of this information?
  • Are standard terms codified?
  • Search for "small-angle" or "small angle" is not as useful as "SAXS" or "SANS"
  • SAS does not consider itself under "Crystallography"

SAS Portal

  • There can be only one!
  • Considerations for the design of a portal
    • who is the target audience?
    • should it support languages other than English?
    • should it just be links to existing content or 'more dynamic', perhaps with a 'SAS news' section, recent results, etc?
    • include an FAQ?
    • incorporate social media?
    • should it 'involve' the IUCr SAS Commission?
    • how should it be promoted to the SAS community?
  • What role should canSAS take?
  • What do we recommend the IUCr provide through the IUCr/CSAS web site?

PDB data deposition task force

(Information from email chat with Jill Trewhella)

Task force remit: Bio-molecular Small-Angle Scattering Data and Interpretation; Data Deposition and Model Archiving

Task Force Membership: Helen Berman, Wayne Hendrickson, Gerard Kleywegt, Guy Montelione, Mamuro Sato, Torsten Schwede, Dmitri Svergun, John Tainer, Jill Trewhella

Preliminary Recommendations:

  • Need a standard dictionary for definitions of terms for data collection and for managing a data repository. X-rays and neutrons.
  • Need a data repository that holds standard data set, is searchable, internationally accessible for download.
  • Bead and atomistic models based on SAS data should be archived in a searchable data base and (given that the underlying data are not atomic resolution) there be specific information in regard to the quality/reliability/uniqueness of the result. Criteria for these assessments need to be defined; issues chi squared, error propagation, sensible stereo-chemistry requirement is argued and needs yet to be agreed.
  • Need a meeting of key people from different task forces to come together to define what the pdb should be archiving.

We also discussed what might be in the PDB and what might be in a parallel "hybrid model" data base that is distinct from the PDB, but with a common interface. By this means it would be easy to communicate that the hybrid models are not based purely on data that can provide atomistic (or something close to it) information.


ADDITIONAL COMMENTS:

  • While a database of data is desirable from the PDB perspective, it is not clear who should be the steward
  • Data should include information about sample and its history/preparation etc., and treatment of background (and potentially storing background data as well)
  • A lunchtime session has been scheduled at SAS 2012 (Sydney, November) to discuss these standards with the community
  • Ideas from Acta Cryst. D, 68, 620–626 (2012) are embodied in this
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