2012 Web Discussion: Difference between revisions
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===Learn about Small Angle Scattering=== | ===Learn about Small Angle Scattering=== | ||
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Revision as of 22:53, 29 July 2012
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:
Software for small angle scattering
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")
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]
ARR - There is a page listing neutron reflectometers and software for neutron reflectometry at: http://material.fysik.uu.se/Group_members/adrian/reflect.htm .
Dates meetings and 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
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
FRMII http://www.frm2.tum.de/en/index.html Julich Centre for Neutron Science http://www.fz-juelich.de/jcns/EN/Home/home_node.html
SANS KWS-1 High resolution Small Angle Scattering http://www.fz-juelich.de/jcns/DE/Leistungen/Instruments2/Structures/KWS1/_node.html KWS-2 High intensity Small Angle Scattering http://www.fz-juelich.de/jcns/DE/Leistungen/Instruments2/Structures/KWS2/_node.html KWS-3 Very Small Angle Scattering http://www.fz-juelich.de/jcns/DE/Leistungen/Instruments2/Structures/KWS3/_node.html SANS-1 http://www.frm2.tum.de/en/science/diffraction/sans-1/index.html Reflectometer MARIA Magnetic Reflectometer with high Incident Angle http://www.fz-juelich.de/jcns/DE/Leistungen/Instruments2/Structures/MARIA/_node.html REFSANS http://www.frm2.tum.de/en/science/diffraction/refsans/index.html N-REX+ http://www.frm2.tum.de/en/science/diffraction/n-rex/index.html Booklet http://www.frm2.tum.de/en/science/experimental-facilities-booklet/index.html
SINQ: The Swiss Spallation Neutron Source http://www.psi.ch/sinq/
SANS SANS-I Small-angle neutron scattering camera, 40m http://kur.web.psi.ch/sans1/ SANS-II Small-angle neutron scattering camera, 12m http://kur.web.psi.ch/sans2/ Reflectometer AMOR Apparatus for multi optional reflectometry http://kur.web.psi.ch/amor/ MORPHEUS 2-axes neutron diffractometer & reflectometer, zero-field spin-echo as future option http://kur.web.psi.ch/morpheus/ NARZISS Polarized neutron reflectometer http://kur.web.psi.ch/narziss/
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/
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/
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
| Downloads | ||||||||
|---|---|---|---|---|---|---|---|---|
| Application | Description | Author | Documentation | Windows | Linux | Unix | Mac | |
| BS-2D | A Windows-based version of BSL. | N Koubassova | Documentation | W32 | n/a | n/a | n/a | |
| 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 | |
| FIT2D | General-purpose & specialist data analysis and visualisation program. | A Hammersley | Documentation | W32 | n/a | n/a | OSX | |
| 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 | |
| XOTOKO | ||||||||
| Downloads | ||||||||
|---|---|---|---|---|---|---|---|---|
| Application | Description | Author | Documentation | Windows | Linux | Unix | Mac | |
| FISH | A sophisticated, tried & tested, model-fitting program with a Java GUI. | R Heenan | Documentation | W32 | Linux | n/a | n/a | |
| SANSView | A sophisticated model-fitting program built around C++/Python, supporting Python model plugins, and utilising NIST-developed model functions. | DANSE SANS Project | Documentation | W32/W64 | Linux | n/a | OSX | |
| 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 | |
| FD2BSL | CCP13 | |||||||
| FDSCALE | CCP13 | |||||||
| FTOREC | CCP13 | |||||||
| FibreFix | A GUI-driven program environment integrating XCONV, XFIX, FTOREC & LSQINT. NB: requires MS .NET Framework 1 which is incompatible with Windows 7. | CCP13 | ||||||
| HELIX | CCP13 | |||||||
| LSQINT | CCP13 | |||||||
| MusLABEL | CCP13 | |||||||
| Sample | CCP13 | |||||||
| WinLALS | Linked-Atom Least-Squares (LALS) program for building molecular and crystal structures of helical polymers and refining them to fit X-ray fiber diffraction data. | K Okuyama | Documentation | W32 | n/a | n/a | n/a | |
| Downloads | ||||||||
|---|---|---|---|---|---|---|---|---|
| Application | Description | Author | Documentation | Windows | Linux | Unix | Mac | |
| CORFUNC | CCP13 | |||||||
| CORFUNC Java | CCP13 | |||||||
| XFIT | A GUI-driven peak-fitting program. | CCP13 | ||||||
| Downloads | ||||||||
|---|---|---|---|---|---|---|---|---|
| Application | Description | Author | Documentation | Windows | Linux | Unix | Mac | |
| CELLREF | Lattice refinement routine. | K Gardner | ||||||
| DSPACE | Calculates and sorts d-spacings. | K Gardner | ||||||
| EXPAND | Expands a BSL format data frame. | D Marvin | ||||||
| FIT2D2RKH | Simple utility to convert FIT2D ASCII format data into ISIS SANS ASCII format data. Useful as a prelude to converting the data into BSL format with XCONV. | S King | n/a | W32 | n/a | n/a | n/a | |
| XCONV | Converts several different X-ray detector (and reduced ISIS SANS) data formats to BSL format. | CCP13 | ||||||
| XML Loader | For loading SASXML format data into IGOR | M Wasbrough | Documentation | IGOR ipf | n/a | n/a | IGOR ipf | |
