2012 Web Discussion

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(Instruments/facilities)
(Software)
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===Software===
 
===Software===
 
ATSAS package for biological scattering: http://www.embl-hamburg.de/biosaxs/software.html
 
  
 
Small Angle Scattering toolbox: http://sastbx.als.lbl.gov/wiki/index.php/Main_Page
 
Small Angle Scattering toolbox: http://sastbx.als.lbl.gov/wiki/index.php/Main_Page
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{| border="1"
 
{| border="1"
 
|+'''For SAS Data Reduction & Visualisation'''
 
|+'''For SAS Data Reduction & Visualisation'''
! || || || || colspan="7" | Downloads
+
! || || || || colspan="5" | Downloads
 
|-
 
|-
! Application || Description || Author || Documentation || Windows || Linux || Unix || Unix || Unix || Mac
+
! Application || Description || Author || Documentation || Windows || Linux || Unix || Mac
 +
|-
 +
| BSL
 +
| An antiquated line-mode data manipulation package developed for 2D SAXS image data.
 +
| J Bordas & G Mant
 +
| [http://www.small-angle.ac.uk/small-angle/Software/BSL.html Documentation]
 +
| n/a
 +
| [http://www.small-angle.ac.uk/dms/small-angle/linux/bsl-tar/bsl.tar.gz Linux]
 +
| [http://www.small-angle.ac.uk/dms/small-angle/solaris7/bsl.Z Solaris]
 +
| n/a
 
|-
 
|-
 
| GDA
 
| GDA
|  
+
| A customisable Jython-based software framework to operate experiments on synchrotron facilities, visualise and analyse the data.
|  
+
| [http://www.opengda.org/ opengda.org]
|  
+
| [http://www.opengda.org/OpenGDA/Documentation.html Documentation]
|  
+
| n/a
|  
+
| [http://www.opengda.org/OpenGDA/Download.html Linux]
|  
+
| n/a
|  
+
| n/a
|
+
|
+
 
|-
 
|-
 
| Mantid
 
| Mantid
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| [http://download.mantidproject.org/ W32/W64]
 
| [http://download.mantidproject.org/ W32/W64]
 
| [http://download.mantidproject.org/ Redhat/Ubuntu]
 
| [http://download.mantidproject.org/ Redhat/Ubuntu]
| n/a
 
| n/a
 
 
| n/a
 
| n/a
 
| [http://download.mantidproject.org/ OSX]
 
| [http://download.mantidproject.org/ OSX]
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{| border="1"
 
{| border="1"
|+'''For Analysing SAS from Bio-molecular Systems'''
+
|+'''For Model-Fitting SAS Data'''
! || || || Downloads
+
! || || || || colspan="5" | Downloads
 
|-
 
|-
! Application || Description || Author || Documentation || Windows || Linux || Unix || Unix || Unix || Mac
+
! Application || Description || Author || Documentation || Windows || Linux || Unix || Mac
 
|-
 
|-
 +
| FISH
 
|  
 
|  
 
|  
 
|  
 
|  
 
|  
 +
|
 +
|
 +
|
 +
|
 +
|-
 +
| SANSView
 
|  
 
|  
 
|  
 
|  
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|-
 
|-
 
|}
 
|}
 +
 +
 +
{| border="1"
 +
|+'''For Analysing SAS from Bio-molecular & Fibre Systems'''
 +
! || || || || colspan="5" | Downloads
 +
|-
 +
! Application || Description || Author || Documentation || Windows || Linux || Unix || Mac
 +
|-
 +
| ATSAS
 +
| A program suite for small-angle scattering data analysis from biological macromolecules.
 +
| D Svergun
 +
| [http://www.embl-hamburg.de/biosaxs/software.html Programs]
 +
| [http://www.embl-hamburg.de/biosaxs/download.html W32/W64]
 +
| [http://www.embl-hamburg.de/biosaxs/download.html Redhat/Ubuntu/Debian]
 +
| n/a
 +
| [http://www.embl-hamburg.de/biosaxs/download.html OSX]
 +
|-
 +
|}
 +
 +
 +
{| border="1"
 +
|+'''For Analysing Other Types of SAS Data '''
 +
! || || || || colspan="5" | Downloads
 +
|-
 +
! Application || Description || Author || Documentation || Windows || Linux || Unix || Mac
 +
|-
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|
 +
|-
 +
|}
 +
  
 
----
 
----

Revision as of 08:57, 29 July 2012

Contents

Pre-meeting

  • The following is the agenda of work posted under business for canSAS-2012 under the Web Portal topic. Please add comments here:
    • define scope, purpose, and goal of portal
    • list content type to which such a portal should give access.
    • Suggest method for hosting
      •  ?more distributed or more centralized,
      •  ?under auspices of a particular facility or SAS commission
      •  ? .. or both etc)
    • Build a working straw landing page prototype
    • Build at least 2 or 3 subpages and/or designs on paper
    • plan for presentations
      • SAS 2012
      • SAS commission


There are a number of places on the www with information about small-angle scattering. A portal needs to provide links to relevant information and extra content. The working group needs to find a way to make information readily available in an attractive way for different categories of people that will include scientists curious about the technique but unfamiliar, potential users, experienced users, etc. Some current pages are:

IUCr SAS Commission

Software for small angle scattering

smallangles.net

SAXIER website

World Directory of SANS Instruments

BioSAXS data analysis software (EMBL Hamburg)

Wikipedia Small-angle Scattering

SAS Toolbox from LBL - mostly software and on-line calculators

Manfred Kriechbaums's page on small-angle scattering

These pages are examples of what is already available. The challenge is to provide access and to integrate information.

   ARR:  A challenge is to find a means to keep the portal maintained and updated.  We will need some continuing
         commitment to this task. 
   SMK:  If you type 'small angle scattering' into Google - what I suspect most people would do in the first instance
         if looking for information on the topic - you get a Wikipedia article (which then subdivides into further
         articles on SANS & SAXS). Do we know who wrote these articles?
   ARR:  I agree that people will find readily the Wikipedia articles.  I suppose that the 'portal for the
         community' should aim to provide further information (some that is not considered suitable for Wikipedia 
         articles).  These topics might include links to software descriptions, lists of conferences, access 
         to mailing list archives, etc. 
   SMK:  Yes, I agree. I think I was thinking more in terms of 'a portal to the portal'!?
   SMK:  On a different point, I have been in contact with the IUCr Webmaster. IUCr Commissions, such as the
         CSAS, have two sets of pages on the IUCr servers: an "official" page at
         http://www.iucr.org/iucr/commissions/small-angle-scattering maintained directly by the IUCr Executive
         Secretary, and their own pages, http://www.iucr.org/resources/commissions/small-angle-scattering
         maintained directly by the Commission (which has effective autonomy over the content although technically
         is subject to scrutiny by the IUCr Executive Committee). Content for the latter is managed using the
         web-based package Squiz Matrix (http://manuals.matrix.squizsuite.net/). Authorship rights to the
         CSAS's pages are currently vested in the CSAS Chairman. However the IUCr is currently trialing co-existing,
         'lightweight', satellite websites (see, for example, http://blogs.iucr.net/) based on Wordpress. Content
         on these satellite sites could be promoted as "in association with the SAS Commission". The caveat is that
         this is a very new departure, as yet untested, and currently only informally backed-up. The IUCr also
         haven't yet made a long-term commitment to maintain these sites.
   ARR:  Thanks for finding out about the IUCr developments.  I see quite a lot of diversity on the commission 
         web sites.  Some even direct to external servers (e.g. the Commission on Electron Crystallograpy goes 
         to http://www.emzm.uni-mainz.de/iucr_cec/.  Other Commissions have quite a lot of material on the IUCr 
         site.  Perhaps someone will be able to find out what the SAS commission plans?  At the moment even the 
         few extra pages are not really recent.  For example, there is no link to the proceedings of the Oxford 
         SAS conference.
   ARR:  I think that the proposed SAS portal will have to go beyond 'blogs' even if these are a useful addition 
         to the IUCr site.
   PDB:  I have a couple of comments regarding the issue of what is the first page of entry on search engine:
         *A very important part of any effort at building any site and even more so one that wants to be a portal
          is to develop a site in a way that maximizes its SEO score (search engine optimization) There are companies 
          devoted to that sort of thing as this is a very big deal.
         *I agree (I think) with Stephen -- ours should be a portal to the portal in some way (though whether we
          ever show up above the wikipedia entry in a search is questionable:-) but as Adrian says the portal we
          are discussing should target a very different audience and include much more than an encyclopedic entry
         (i.e. be a portal to ALL things SAS)
         *The wikipedia entries seem pretty decent, but contributing to these might also be a goal.  Not sure how
          to find out who originally wrote those pages, but suspect we know them (the community isn’t that big).
          Not sure how we find out as it would be nice to work together.
   PDB:  IUCr and CSAS sites.  I believe that Duncan is involved in those efforts as a member of CSAS.  Pete Jemian
         is also a member of the CSAS I believe.  Perhaps we can have them say a few words in a plenary session
         about the current status of the CSAS thinking there and where the opportunities might be.  As Adrian
         suggested at the beginning one challenge will be the long term support which IUCr could perhaps help with
         even if just by giving broader legitimacy and thus easier to secure commitment from other SAS sources.
   PDB:  Another topic dear to my heart which I think the portal could provide is to use the portal to build a
         “community” in the true sense of the word.  Besides helping to speed exchange of ideas and generating the
         interest required to propel the site to the status of a true portal, it could be the source of some of the
         effort that would be required to actively maintain it.  Of course the difficulty is always in managing that
         kind of engagement so that it doesn’t become a free for all that turns people away.  That may be too difficult
         a task but I think worth thinking about anyway.
   SMK:  So, if I've interpreted Wikipedia's FAQ correctly, the Small-Angle Scattering page was first constructed in
         Oct 2006 by http://en.wikipedia.org/wiki/User:Iepeulas. It was then subsequently modified by several people,
         the more meaningful names of which are: Tocharianne, Stemonitis (who would seem to be a biologist), Tpikonen
         (who would appear to be into X-ray spectroscopy), Booers, Yen Zotto (not sure if that's a real name), Uvainio
         (a physicist in Germany), and Alltat (which I think must be a moniker), and someone with an unhelpful ID but
         who claims to be a professor and has made a raft of contributions that would seem to suggest they are quite
         knowledgeable in physics). Do we recognise any of these user ID's as the names of small-angle scatterers?
   ARR:  Ulla Vainio has worked at DESY since she finished her Ph.D. at the University of Helsinki in 2007.
         Her work has involved a lot of SAXS and anomalous SAXS.  I think (but am not certain) that Tpikonen
         is Teemo Ikonen who was also in Helsinki and moved to SLS at PSI.  Several people in Helsinki were
         active in maintaining Wikipedia.
   ARR:  In respect of 'community building' mentioned by PDB, it might be useful to discuss why the features
         such as the SAS mail list (IUCr) and the discussion board (SAXIER) are not very widely known or 
         used.  How can these be better publicised and exploited?
   ARR:  A useful preliminary analysis might be to think about what resources are available already on the 
         www in this area.  One could then ask are these adequately maintained, what is needed for 
         the maintenance, is provision of links to other sites is sufficient in some fields this will reduce
         the necessary work to provide content that is not available elsewhere.
   PDB:  Agree on both points above.  The first and foremost problem is knowing something exits at the time I'm looking
         for the kind of thing it offers.  This is probably the biggest challenge for the portal project.  Creating a
         simple portal to lots of useful information that is well branded with an easy to remember name is a start. 
         Showing up as a top hit when doing a google search is another.  Getting facilities, instrument scientists and
         SAS bigshots to tell everyone is another.  Getting linked from a lot of appropriate places another etc..  The
         nest most difficult task will be figuring out/organizing the long term support and maintenance.  With regards
         to using whatever is out there rather than re-invent the wheel that will be required to keep the effort levels
         manageable.  I think identifying the kinds of things should be on a portal should go simultaneously with looking
         for what is out there as one may inform the other.

Day 1 design and technical details

Design questions: KEEP IT SIMPLE. Use wikipedia landing page as inspiration. Need to choose small set of topic areas that will send to more full secondary portal pages. Mock up of concept is provided in figure. Note that yellow tags are for main topic areas while blue are some subtopics that would go under the topic are. Green labels represent sites which we would like to get to link to the portal. Under calendar we are thinking of a goolge calendar that keeps track of beam time proposal submission deadlines and possibly upcoming meetings. Under education interactive web tools/tutorials would be really good for new users (see e.g. Brian Maranville's NIST summer school tutorial "toys")

Portaldesign1.png

Question of using an actual wiki as authoring software. ultimately want a wikipedia type of contributions to the final knowledge base but perhaps not enforced in the same way?


Other issues

  • Content authorship
    • SEPARATE portal issue from content (what machine things reside on is irrelevant)
    • Should use existing content as much as possible
    • Encourage/recruit people to provide missing content (on their servers of choice or we give space on ours)
    • Can try to provide some content ourselves -- but that is same as above?
  • hosting
    • Easiest for initial start up is to keep the UTK servers
    • Longer term we would like to get some mirror sites at the very least
    • Probably not host directly on IUCr servers
  • Domain branding
    • use smallangle.org
    • don't advertise but if we can get smallangles.org have it point to same place.
  • What is proper/best role for IUCr
    • probably as a representative with editing access to site and part of group maintaining portal?
  • High impact content
    • calendar of proposal deadlines
    • Glossay of terms
    • interactive tutorials
    • breaking news maybe?
  • management - best ad hoc by group of interested volunteers but practically may need some level of foramlized committe to point to in order for community to be comfortable? How does wikipedia do it? What level of editorial control should be maintained and by whom?
  • SAS meeting questions
    • Ask for volunteers for various missing content
    • Reflection, LS, and grazing incidence are all part of IUCr SAS commission remit. How much should the portal cover and how? Group believe LS is out of purview as too much, and that reflectivity should be included at some lever but not "separately"

Content

AJJ - Adrian mentioned metadata and search engine optimization. This is an important issue - Google has a document about this: [Google SEO Guide]



Dates/meetings/calendar


Learn about Small Angle Scattering

Wikipedia

http://en.wikipedia.org/wiki/Small-angle_scattering

http://en.wikipedia.org/wiki/Small-angle_neutron_scattering

http://en.wikipedia.org/wiki/Small-angle_X-ray_scattering

Tutorials

SANS at NIST, movies and pdfs: http://www.ncnr.nist.gov/programs/sans/tutorials/index.html

Boualem Hammouda's polymer based tutorial for SANS: http://www.ncnr.nist.gov/staff/hammouda/

List of EMBO courses for biological macromolecues, with recommended reading links: http://www.embl-hamburg.de/biosaxs/courses/

BIOISIS (ALS at Berkeley) tutorial for biological macromolecules studied with SAXS. Includes sample preparation, measurement, reduction and analysis: http://bioisis.net/tutorial

ORNL SANS (PDF links only): http://neutrons.ornl.gov/research/techniques.shtml

Diamond, UK, "Beginner's guide to SAXS" (PDFs) and useful links: http://www.diamond.ac.uk/Home/Beamlines/small-angle/Beginners-Guide-to-SAXS.html

RKT SANS applets: http://rkt.chem.ox.ac.uk/techniques/smallanglescattering.html



Instruments/facilities

Worldwide neutron sources: http://www.neutron.anl.gov/

Worldwide synchrotron sources: http://www.lightsources.org/cms/

Worldwide directory of SANS instruments (not fresh): http://www.ill.eu/instruments-support/instruments-groups/groups/lss/more/world-directory-of-sans-instruments/

Anton Paar SAXS: http://www.anton-paar.com/SAXS/59_Corporate_en?productgroup_id=107

Bruker SAXS: http://www.bruker-axs.com/nanostar.html


Facilities and their SAS & Refelctometery instruments

Oak Rdge National Laboratory (ORNL): http://www.sns.gov/

SNS: http://www.sns.gov/facilities/SNS/
 SANS
  EQ-SANS: http://neutrons.ornl.gov/instruments/SNS/EQ-SANS/
  USANS(in coming): http://www.sns.gov/tofusans/
 Reflecrometer
  LR(Liquid Refelctometer: http://neutrons.ornl.gov/instruments/SNS/LR/
HFIR http://neutrons.ornl.gov/facilities/HFIR/
 SANS
  GP-SANS: http://neutrons.ornl.gov/instruments/HFIR/CG2/
  Bio-SANS: http://neutrons.ornl.gov/instruments/HFIR/CG3/

ISIS: http://www.isis.stfc.ac.uk/

SANS
 LOQ: http://www.isis.stfc.ac.uk/instruments/loq/
 SANS2d: http://www.isis.stfc.ac.uk/instruments/sans2d/
 NIMROD: http://www.isis.stfc.ac.uk/instruments/nimrod/nimrod2468.html
 Lamor (NSE-SANS, in coming): http://www.isis.stfc.ac.uk/instruments/larmor/larmor8239.html
Reflecrometer
 CRIPS: http://www.isis.stfc.ac.uk/instruments/crisp/crisp2466.html
 Inter: http://www.isis.stfc.ac.uk/instruments/inter/inter2471.html
 Offspec (with NSE): http://www.isis.stfc.ac.uk/instruments/offspec/offspec3048.html
 Polref: http://www.isis.stfc.ac.uk/instruments/offspec/offspec3048.html
 Surf: http://www.isis.stfc.ac.uk/instruments/surf/surf2469.html

Institut Laue-Langevin (ILL): http://www.ill.eu/

SANS
 D11: http://www.ill.eu/instruments-support/instruments-groups/instruments/d11/
 D22: http://www.ill.eu/instruments-support/instruments-groups/instruments/d22/
 D33(in coming): http://www.ill.eu/instruments-support/instruments-groups/instruments/d33/
 D16:  http://www.ill.eu/instruments-support/instruments-groups/instruments/d16/
Reflectometer
 Super Advanced Reflectometer for the Analysis of Materials: 
       http://www.ill.eu/instruments-support/instruments-groups/instruments/superadam/
 D17: http://www.ill.eu/instruments-support/instruments-groups/instruments/d17/
 FIGARO (Fluid Interfaces Grazing Angles ReflectOmeter): 
      http://www.ill.eu/instruments-support/instruments-groups/instruments/figaro/

Laboratoire Leon Brillouin, Saclay, CEA http://www-llb.cea.fr/en/

SANS        
 Pace: Small Angle Neutron Spectrometer (isotropic scattering) 
       http://www-llb.cea.fr/en/fr-en/pdf/pace-llb.pdf
 Paxy: Small Angle Neutron Spectrometer (high resolution) 
       http://www-llb.cea.fr/en/fr-en/pdf/paxy-llb.pdf
 Paxe: Small Angle Neutron Spectrometer http://www-llb.cea.fr/en/fr-en/pdf/paxe-llb.pdf
 TPA : Very Small Angle Neutron Spectrometer TPA : Very Small Angle Neutron Spectrometer 
Reflectometer
 Eros: Time of flight reflectometer http://www-llb.cea.fr/en/fr-en/pdf/eros-llb.pdf
 Prism: 2 axis with polarized neutrons and polarization analysis 
       http://www-llb.cea.fr/en/fr-en/pdf/prism-llb.pdf

NIST Center for Neutron Research http://www.nist.gov/ncnr/

SANS
 NG3 SANS http://www.nist.gov/ncnr/ng3-sans-small-angle-neutron-scattering.cfm
 NG7 SANS http://www.nist.gov/ncnr/ng7sans.cfm
 BT5 USANS http://www.nist.gov/ncnr/bt5-usans-ultra-small-angle-neutron-scattering.cfm
Reflectometer
 NGD Off-Specular Reflectometer(MAGIK) http://www.ncnr.nist.gov/instruments/magik/
 NG-1 Reflectometer (Polarized) http://www.ncnr.nist.gov/instruments/ng1refl/
 NG7 Horizontal Neutron Reflectometer http://www.ncnr.nist.gov/instruments/ng7refl/

Los Alamos Neutron Science Center: http://lansce.lanl.gov/ Lujian Neutron Center: http://lansce.lanl.gov/lujan/index.shtml

SANS
 Low-Q Diffractometer(LQD): http://lansce.lanl.gov/lujan/instruments/LQD.shtml
Reflectometers
 Asterix(Polarized): http://lansce.lanl.gov/lujan/instruments/ASTERIX.shtml
 Surface Profile Analysis Reflectometer(SPEAR):
                     http://lansce.lanl.gov/lujan/instruments/SPEAR.shtml

NRC Canadian Neutron Beam Centre: http://www.nrc-cnrc.gc.ca/eng/ibp/cnbc.html

Reflecrometer
 D3 Reflectometer: http://www.nrc-cnrc.gc.ca/eng/facilities/cnbc/spectrometers/d3.html

News

Small angle scattering mailling list server archive and instructions for joining: http://www.iucr.org/__data/iucr/lists/sa_scat/


Resources

X-ray anomalous scattering resources (primarily for crystallography, useful for aSAXS: http://skuld.bmsc.washington.edu/scatter/

ATSAS forums: http://www.saxier.org/forum/index.php

NIST Scattering Length Density calculator: http://www.ncnr.nist.gov/resources/sldcalc.html

Another scattering length density calculator: http://sld-calculator.appspot.com/

Neutron scattering lengths: http://www.ncnr.nist.gov/resources/n-lengths/

Peptide property calculator (can caluclate amino acid volumes): http://www.basic.northwestern.edu/biotools/proteincalc.html


Software

Small Angle Scattering toolbox: http://sastbx.als.lbl.gov/wiki/index.php/Main_Page

List of SAS software (ISIS): http://www.small-angle.ac.uk/small-angle/Software.html


For SAS Data Reduction & Visualisation
Downloads
Application Description Author Documentation Windows Linux Unix Mac
BSL An antiquated line-mode data manipulation package developed for 2D SAXS image data. J Bordas & G Mant Documentation n/a Linux Solaris n/a
GDA A customisable Jython-based software framework to operate experiments on synchrotron facilities, visualise and analyse the data. opengda.org Documentation n/a Linux n/a n/a
Mantid MantidPlot is a version of QtiPlot customised to present a technique-independent data analysis framework for Neutron and Muon data. It is built around C++/Python and supports Python plugins and scripting. mantidproject.org Documentation W32/W64 Redhat/Ubuntu n/a OSX


For Model-Fitting SAS Data
Downloads
Application Description Author Documentation Windows Linux Unix Mac
FISH
SANSView


For Analysing SAS from Bio-molecular & Fibre Systems
Downloads
Application Description Author Documentation Windows Linux Unix Mac
ATSAS A program suite for small-angle scattering data analysis from biological macromolecules. D Svergun Programs W32/W64 Redhat/Ubuntu/Debian n/a OSX


For Analysing Other Types of SAS Data
Downloads
Application Description Author Documentation Windows Linux Unix Mac



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