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LECIS should be recast into XML. The first step is to create some strongly
typed schemas. I have already taken a very small part of Digital Imaging and
Communications in Medicine (DICOM) and reused it for CytometryML. I used
constant attributes to provide a linkage to the original DICOM data types.
The schemas and a publication describing their creation is available on the
CytometryML page of www.newportinstruments.com
Bob Leif

________________________________________
From: Sanjaya Joshi [mailto:sanjay@...]
Sent: Monday, May 19, 2003 10:07 AM
To: lecis-post@yahoogroups.com

Since AniML is atleast a year or more away, I would recommend getting a
group of focused individuals to revise the Core LECIS areas (maybe in-line
with the AniML). I would, however, caution not to get too carried away and
set a strict deadline to compelete the revision.
 
The areas:
1. Reduction of the handshake protocol
2. More emphasis on the TCP layer (perhaps the IPv6 service layer?)
3. An implementation model
4. An error and reporting model

Thanks,
Sanjay
-----Original Message-----
From: Torsten [mailto:tstaab@...]
Sent: Monday, May 19, 2003 10:02 AM
To: lecis-post@yahoogroups.com
Subject: [lecis-post] ASTM LECIS is up for review
Hello all,

The ASTM LECIS standard is coming up for review. So we need to decide
collectively what we would like to do about the ASTM standard. According to
Dr. Gary Kramer, who is heading ASTM E13.15 subcommittee that will deal with
LECIS, we have three options:

1. Say it's fine and leave it as it is for another 5 years. 
2. Say it's obsolete and kill it. 
3. Get a task group together to revise what needs fixing. 

I would like to get everyone's feedback on this no later than May 30, 2003.
In case we end up deciding to go with option 3, I will need some volunteers
and revision suggestions asap.
Please e-mail your thoughts on this either to the list
(lecis-post@yahoogroups.com) or me (tstaab@...).

Thanks,
Torsten

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>Date: Mon, 14 Apr 2003 11:42:13 -0400
>From: "Gary W. Kramer" <gary.kramer@...>
>Subject: ASTM E13.15 ANIML Development Meeting at ASTM Hdqrts
>
>Hi folks,
>This is a reminder that we will hold an ASTM E13.15 ANIML development meeting
>at ASTM Headquarters on April 23 and 24.  The meeting will start at 1:00
>PM on
>Wednesday, 4/23.  We'll reconvene at 9:00 AM on Thursday, 4/24 and try to
>finish up by 2:30 PM.  Directions to ASTM can be found on their website
>(www.astm.org).
>
>As this is a development meeting, we will not have a strict agenda.  However,
>since our PittCon meeting, several of us have been thinking about our
>challenge and have put together an initial list of discussion topics:
>
>1. Review the Model to make sure that we like it and that it will work.
>
>2. Discuss how encapsulation will work (i.e. incorporating other schemas).
>
>3. Discuss the allowable data types that can be used in the Core.
>
>4. Discuss the concept and consequences of versioning and versions.
>
>There are many other areas that we will have to consider; so, if your
>favorite
>topic is not on this list, let me know, and we'll try to schedule some
>discussion time for it at this meeting or at a future workshop.
>
>Information on the ANIML model can be found on the ANIML sourceforge site
>(http://animl.sourceforge.net) in my SpectroML presentation.  You may recall
>that we have agreed to reuse as much as we can from previous efforts.  So, in
>preparation for the workshop, I think it would be useful to take a look at
>some related work, including:  the discussion of data types in the generic
>JCAMP 6.0 draft document (see www.jcamp.org under "drafts") as well as the
>other JCAMP docs found on the same site under "protocols."  It would also be
>useful to take a peek at the MATML (Materials Markup Language) site
>(www.matml.org). We may find a lot of what we need in the way of sample
>description has already been done in MATML.  Finally, the information on GAML
>can be found at www.gaml.org, and the SpectroML stuff can be had at ftp://
>caals.nist.gov/pub/download.
>
>I hope to see you at ASTM on April 23rd.
>
>Cheers,
>Gary Kramer
>
>
>
>
>Gary W. Kramer, Ph.D.
>Leader, Molecular Spectrometry and Microfluidic Methods Group
>Analytical Chemistry Division
>Chemical Science and Technology Laboratory
>National Institute of Standards and Technology
>Building 227, Room A-163
>Gaithersburg, MD  20899-8394
>(301) 975-4132   (301) 977-0587 fax
>gary.kramer@...

X-Mailer: InterCon tcpCONNECT4 4.0 (Macintosh)
Date: Sun, 30 Mar 2003 20:25:55 -0500
From: "Gary W. Kramer" <gary.kramer@...>
To: 106363.3566@..., adam.patkin@...,
   almutin@..., anhdao.nguyen@..., antony.williams@...,
   bewilson2@..., bill.town@..., bill.town@...,
   blair@..., blankge@..., borutapa@...,
   brenda.kesler@..., brian_rohrback@...,
   bruce_c_schaeffer@..., bryan_miller@..., bs-sc@...,
   bstinnett@..., bwlyttle@..., carol.jantzen@...,
   carroll.davis@..., cdehne@..., cdollar@...,
   christopher.lynch@..., chsieh@...,
   clacraver@..., claracraver@..., clifford.buffett@...,
   craig.fellows@..., craig.walla@...,
   craig.walla@..., d_martinsen@..., dale.rushneck@...,
   dan_holmes@..., dave.blaha@...,
   dave.michelsen@..., david.varley@...,
   dcsilv@..., debbie_zink@..., dermin.fan@...,
   dgossman@..., dheld@..., dlevy@...,
   don.kuehl@..., douglas.bigwood.b@..., dperry@...,
   drbobby@..., dweiss@..., dwinsten@...,
   edward.colbert.b@..., edward_kikta@..., egavin@...,
   elena.mendoza@..., emmert.clevenstine@..., enviroed@...,
   esvastit@..., fcverna@..., forraw@...,
   frank.tontala@..., friedrich.brunzema@..., ftontala@...,
   gary.kramer@..., gary.mallard@..., gcollins@...,
   ggeiger@..., gmingxin@..., hen@...,
   hlmark@..., hmcclard@..., hoe@..., hooverhl@...,
   huffman@..., hughes_philip_f@..., james.duckworth@...,
   jay_powell@..., jbergen@..., jbfugere@...,
   jean-louis.excoffier@..., jeff.dann@...,
   jerrym@..., jim.myers@..., jiri.jirat@...,
   joe.meier@..., john.rumble@..., john.travis@...,
   jturpin@..., julian_randall_k@..., jwebber@...,
   jworkman@..., kageyama@...,
   kdammers@..., ken-blick@..., khabramo@...,
   klemens.bley@..., lewis_kenneth@..., lsidisky@...,
   manishimura@..., mar@..., marie.scandone@...,
   mark.bayliss@..., mark.f.bean@..., mark.russo@...,
   mark_harnois@..., markus.hemmer@...,
   martin.peschke@..., mbayliss@..., merrerr@...,
   michael@..., michael_boruta@..., michel@...,
   mike.garry@..., mil55244@..., miloslav.nic@...,
   minor@..., moored@..., panromek@...,
   paul.derose@..., paul.fjeldsted@...,
   peter.linstrom@..., pkilz@..., pm286@...,
   polyspec@..., puskarica@...,
   r_d_mcdowall@..., raf7k@..., rich@...,
   rjlanc@..., rkjulian@..., rlarsensdt@...,
   rmcdjcamp@..., rob.b.myers@..., robert.dragoset@...,
   robert.williams@..., roger.mcintosh@...,
   rok@..., ron@..., ron_graham@...,
   sanjay@..., sanjay@...,
   schaefer@..., schweifk@...,
   scot.ellis@..., scubbedge@..., sgadgil@...,
   sherry.hemmingsen@..., shorten@...,
   simon.kaalman@..., simonc@...,
   smrichard@..., smwishnies@..., ssimpson@...,
   stephen.best@..., stephen.heller@...,
   stephen.w.gaarenstroom@..., steve.leicester@...,
   steve.leich@..., steve.stein@..., steve@...,
   terry.sheehan@..., tgilmore@..., thomas.allison@...,
   thomas.weber@..., thomas_r_sharp@...,
   thorsten.froehlich@..., tmalt@...,
   todd_miller@..., tom.tuzzeo@...,
   tony.davies@..., tony.johnson@...,
   tony@..., tony_brand@..., totoole@...,
   trichter@..., tstaab@..., ttauber@...,
   ty_abshear@..., uro@..., ute_bober@...,
   veleva@...
Subject: ASTM E13.15 ANIML Working Meeting

Hi Folks,

The address list for this message was gleaned from numerous lists of individuals, who at some time have expressed interest in the interchange of spectroscopy result data.  I have tried to prune the list to eliminate duplicate entries, but this has proved difficult, and there are multiple entries.  When I could not figure out which address was current, I retained the duplicates.  So, if you receive this message multiple times, I apologize.  If you wish to have an address removed from the list, please let me know.  If you know of someone whose name should be added, also let me know.

As many of you may know, ASTM Task group E13.01.03 has now be designated as ASTM Subcommittee E13.15 on Analytical Data Management.  E13.15 will be responsible for defining standards for representing, managing, and interchanging analytical chemistry data including the implementation of technique specific information and application to instrumentation data interfaces.   Furthermore, it has been proposed that ASTM Subcommittee E01.25 on Analytical Data Interchange Protocols be merged into E13.15.  At our recent PittCon meeting, E13.15 unanimously approved this proposal, and it is currently being voted on by the members of E01.25.  If this proposal is approved, the standards formerly under the jurisdiction of E01.25 (LECIS, LIMS guides, and ANDI GC & MS) would be transferred to E13.15.

The main purpose of this email is to announce a working meeting of E13.15 to continue the development of a markup language for analytical spectroscopy and chromatography result data that is now being call Analytical Information Markup Language (ANIML).  The meeting is set for Wednesday, April 23 and Thursday, April 24 at ASTM headquarters in West Conshohocken, PA. As suggested by Dave Martinsen (E13.15 Secretary), to minimize travel expenses, we will meet from 1:00 PM to 5:00 PM on Wednesday and from 9:00 AM until 2:30 PM on Thursday.  Gloria Collins (E13.15 ASTM staff liaison) has booked the ASTM Boardroom (and an LCD/computer projector) for our meeting.  Directions for getting to ASTM headquarters can be found on the ASTM web site (www.astm.org -- look under meetings and then general information). 

As we get closer to the meeting date, I'll be sending out an agenda.  In the meantime, Randy Julian (E13.15 Vice Chair) has created an ANIML SourceForge project and has put up a project web page with the presentations from the E13.15 meeting at PittCon.  The project home page is: http://animl.sourceforge.net.  There you can subscribe to the mailing lists, etc.  If you are new to XML or to the concept of using XML to represent analytical data, here are a few useful websites: http://www.w3c.org; http://www.xml.org; http://www.xml.com; http://www.xml101.com; ftp://caals.nist.gov/pub/download/; http://www.xml.org?xml registry?chemistry; http://www.gaml.org; http://www.xml.org?xml registry?chemistry.

If you have comments, agenda-item suggestions, etc., please let me know.  I hope to see you at ASTM in April.

Cheers,
Gary Kramer
Chair, ASTM E13.15



</blockquote></x-html>

Since DTDs do not follow established software engineering standards, you
would be much better off with XML Schema. The combination of XML schema and
XForms should be sufficient for handling the data and user interaction. Both
SVG and XSL can be used to present the data.
I will soon have two papers published that describe the use of DICOM
data-types in XML. For those who are interested, I will send out preprints
in PDF.
Bob Leif

-----Original Message-----
From: Sanjaya Joshi [mailto:sanjay@...]
Sent: Monday, February 24, 2003 3:29 PM
To: lecis-post@yahoogroups.com
Subject: [lecis-post] FW: ALA and XML for instruments (Structured Reporting
usign objects similar XML DOM)


Below is a link interesting paper on Structured Reporting and Event
Streams similar to the XML Document Object Model...
http://www.dclunie.com/papers/spie_mi_2001_SR_manuscript.pdf
The SR is part of the DICOM standard...
Also a book:
http://www.pixelmed.com/srbook.html

We have also been thinking of embedding conditional flow and conditional
programming into the DTD directly... This is good in an HTS scenario
(some of this grammar is already within the XSL DTD especailly for the
FO -- Formatting Objects -- area).

Another area is Aspect Oriented programming similar to Event Streams...
(More on that soon).

Another standardization area for imaging (that is gaining a big
foothold) is JPEG2000 (I think the FDA is OK with a factor of 10 or 12
for lossless compression.

Again would be good to combine the control paradigm with the data model
(process).

Sanjay

-----Original Message-----
From: James Gill [mailto:james.gill@...]
Sent: Sunday, February 23, 2003 8:51 AM
To: Gary W. Kramer; tstaab@...; Mark F Russo;
roger.mcintosh@...; bs-sc@...;
info@...
Subject: Re: ALA and XML for instruments


All,
I certainly had no intentions to dilute current efforts nor necessarily
start a new one.  Ok I'll admit the mail sounded that way - but my
intention was to offer the suggestion that ALA might have a role to
play,  and to start the discussion that if ALA does have a role - what
would that role be?  Perhaps just to make sure the ALA's efforts to
support the various efforts are continued.

I think one important question in front of us now is - Since we have a
major
vendor (certainly in the HTS area)  using   XML, and even better towards
releasing it into the public domain, how can this be leveraged to insure
better standardization? I suspect there are also numerous other in house
development efforts on going at various vendors and large industrial
sites as well.  How can we make sure that these in house developers
(especially the vendors) want to use the standards??

I should also point out that in the HTS area - I believe that standards
have been much harder to come by than in the Spectroscopy and
Chromatography areas.  I believe that the HTS area simply has not
developed a "standardization" mentality
- So please forgive my ignorance in this area and accept my suggestions
as opportunities to educate me.

Suggestions?  Is it as Torsten and Gary say - the vehicles are in place,
folks just need to start using them?  Does ALA have a role?

Jay

"Gary W. Kramer" wrote:

> Jay,
>
> There is currently an effort to develop XML data representations for
> result data from spectroscopy and chromatography instruments ongoing
> in ASTM E13. This has been in the works for about a year and a half,
> and many instrument vendors and LIMS folks are participating.  We're
> having a meeting at Pittcon, see below for the info.  We have
> preliminary indications that the IUPAC/JCAMP folks will join the ASTM
> effort so that we can develop a single standard, not multiple
> approaches like we had with the ANDI and JCAMP standards.
>
> I completely agree with you that we need to get XML standards in place
> for instrument data, but I would very much not like to see competing
> efforts evolve to do try to do this.  The ASTM effort and approach is
> not yet set in concrete, so there is plenty of opportunity for folks
> who want to see such standards to get involved and be a part of the
> solution.  Speaking for the ASTM XML Working Group, we invite all
> interested parties to work with us to develop standards that will
> benefit all of us.
>
> Cheers,
> Gary
>
> From: "Abramo, Kimberly" <KHAbramo@...>
> To: "Abramo, Kimberly" <KHAbramo@...>,
>    "'ty_abshear@...'"
>          <ty_abshear@...>,
>    "Alt, Timothy" <TMAlt@...>,
>    "'aykut.arslan@...'" <aykut.arslan@...>,
>    "'mark.f.bean@...'" <mark.f.bean@...>,
>    "'stephen.best@...'" <stephen.best@...>,
>    "'blair@...'" <blair@...>,
>    "'michael_boruta@...'" <michael_boruta@...>,
>    "'tony_brand@...'" <tony_brand@...>,
>    "'polyspec@...'" <polyspec@...>,
>    "'tony.davies@...'"
<tony.davies@...>,
>    "'dermin.fan@...'" <dermin.fan@...>,
>    "'paul.derose@...'" <paul.derose@...>,
>    "'cdollar@...'" <cdollar@...>,
>    "'james.duckworth@...'"
>          <james.duckworth@...>,
>    "'scot.ellis@...'"
>          <scot.ellis@...>,
>    "'jean-louis.excoffier@...'"
>          <jean-louis.excoffier@...>,
>    "'craig.fellows@...'"
>          <craig.fellows@...>,
>    "'thorsten.froehlich@...'"
>          <thorsten.froehlich@...>,
>    "Fugere, John \"Barry\""
>          <jbfugere@...>,
>    "'egavin@...'" <egavin@...>,
>    "'mark_harnois@...'" <mark_harnois@...>,
>    "'dheld@...'" <dheld@...>,
>    "'markus.hemmer@...'"
<markus.hemmer@...>,
>    "'sherry.hemmingsen@...'"
<sherry.hemmingsen@...>,
>    "'hooverhl@...'" <hooverhl@...>,
>    "'hughespf@...'"
>          <hughespf@...>,
>    "'tony.johnson@...'"
>          <tony.johnson@...>,
>    "'simon.kaalman@...'"
>          <simon.kaalman@...>,
>    "'pkilz@...'"
>          <pkilz@...>,
>    "'gary.kramer@...'" <gary.kramer@...>,
>    "'don_kuehl@...'" <don_kuehl@...>,
>    "'rjlanc@...'" <rjlanc@...>,
>    "'rlarsensdt@...'"
>          <rlarsensdt@...>,
>    "'dlevy@...'" <dlevy@...>,
>    "'kenlewis@...'" <kenlewis@...>,
>    "'mil55244@...'"
>          <mil55244@...>,
>    "'christopher.lynch@...'"
>          <christopher.lynch@...>,
>    "'gary.mallard@...'"
>          <gary.mallard@...>,
>    "'michael@...'" <michael@...>,
>    "'rmcdjcamp@...'" <rmcdjcamp@...>,
>    "'r_d_mcdowall@...'" <r_d_mcdowall@...>,
>    "'dave.michelsen@...'" <dave.michelsen@...>,
>    "'todd_miller@...'" <todd_miller@...>,
>    "'bryan_miller@...'" <bryan_miller@...>,
>    "'moored@...'" <moored@...>,
>    "'pm286@...'"
>          <pm286@...>,
>    "'totoole@...'" <totoole@...>,
>    "'martin.peschke@...'" <martin.peschke@...>,
>    "'jay_powell@...'" <jay_powell@...>,
>    "Richard, Shannon" <SMRichard@...>,
>    "'brian_rohrback@...'" <brian_rohrback@...>,
>    "'john.rumble@...'" <john.rumble@...>,
>    "'thomas.sauter@...'" <thomas.sauter@...>,
>    "'marie_scandone@...'" <marie_scandone@...>,
>    "'schaefer@...'"
>          <schaefer@...>,
>    "'thomas_r_sharp@...'"
<thomas_r_sharp@...>,
>    "'terry.sheehan@...'" <terry.sheehan@...>,
>    "'ssimpson@...'" <ssimpson@...>,
>    "'steve.stein@...'"
>          <steve.stein@...>,
>    "'bill.town@...'"
>          <bill.town@...>,
>    "'john.travis@...'" <john.travis@...>,
>    "'tom.tuzzeo@...'" <tom.tuzzeo@...>,
>    "'david.varley@...'" <david.varley@...>,
>    "'craig.walla@...'" <craig.walla@...>,
>    "'thomas.weber@...'"
<thomas.weber@...>,
>    "'tony@...'" <tony@...>,
>    "'debbie_zink@...'"
>          <debbie_zink@...>
> Cc: "'Paul.Fjeldsted@...'"
<Paul.Fjeldsted@...>,
>    "Wishnies, Steven" <SMWishnies@...>,
>    "Mutin, Alexander"
>          <almutin@...>,
>    "Nishimura, Masayuki" <MANishimura@...>,
>    "'frank.tontala@...'" <frank.tontala@...>,
>    "'d_martinsen@...'" <d_martinsen@...>,
>    "'peter.linstrom@...'" <peter.linstrom@...>,
>    "'aykut.arslan@...'" <aykut.arslan@...>,
>    "'anlidao.nguyen@...'" <anlidao.nguyen@...>,
>    "'rmcdjcamp@...'" <rmcdjcamp@...>,
>    "'scubbedge@...'"
>          <scubbedge@...>,
>    "'steve@...'" <steve@...>,
>    "'steve.leich@...'" <steve.leich@...>,
>    "'friedrich.brunzema@...'" <friedrich.brunzema@...>,
>    "'dave.blaha@...'" <dave.blaha@...>,
>    "'craig.walla@...'" <craig.walla@...>,
>    "'ute_bober@...'" <ute_bober@...>,
>    "'bill.town@...'" <bill.town@...>,
>    "'sgadgil@...'" <sgadgil@...>,
>    "'jerrym@...'" <jerrym@...>,
>    "'clacraver@...'"
>          <clacraver@...>,
>    "'claracraver@...'"
>          <claracraver@...>,
>    "'jay_powell@...'"
>          <jay_powell@...>,
>    "'JULIAN_RANDALL_K@...'"
>          <JULIAN_RANDALL_K@...>,
>    "'Friedrich.Brunzema@...'"
>          <Friedrich.Brunzema@...>
> Subject: RE: PITTCON SpectroML/ GAML/XML ASTM meeting
> Date: Fri, 21 Feb 2003 13:02:35 -0500
> MIME-Version: 1.0
> X-Mailer: Internet Mail Service (5.5.2653.19)
> Content-Type: text/plain;
>         charset="iso-8859-1"
>
> I apologize for the delay in sending this message.  There has been
much
> confusion  as to when the ASTM meetings where going to be held.   The
> schedule has now been finalized and the SpectroML/GAML/XML meeting
> will take place on Tuesday March 11th at 5:30PM.  I realize that this
> is late in the afternoon, but since most of the committee participants

> are vendors, it works out better that way.  We will be reviewing our
> progress in several areas.  Additionally, we hope to have attendance
> from representatives from IUPAC.  I hope that we will be able to share

> the vision and further develop plans to get the schemas finalized.
> Please let me know if you have any further questions.  I look forward
> to seeing many of you at Pittcon.
>
> > Thanks-
> > Kimberly Harris Abramo
> > Product Manager - Spectroscopy
> > Shimadzu Scientific Instruments
> > 1-800-477-1227 ext 1912
> > (Fax) 410-381-1222
> >
>
> > Guys,
> > There was a lot of talk at LA03 about xml and standards for
> > instrument data.  Roger has been working to get his format into the
> > public domain, and I had a number of discussions with folks at the
> > meeting..
> >
> > What would folks think about having the ALA sponsor a group to
> > co-ordinate the various efforts and ultimately to recommend a
> > specification which would be supported by the ALA, published in JALA

> > etc.  I think the ALA represents a unique opportunity in that there
> > is representation from the vendors, industry, consultants, academics

> > and government.  In fact, all of those constituencies are
> > represented on this mail.  In addition there has already significant

> > progress that has been made by the folks on this mail towards a
> > standard.
> >
> > I would see the next steps being
> >
> > 1) Gain agreement from you all that the ALA is the right place to
> > propose such a standard and they you would want to participate
> > 2) Propose the concept to the Board (which of course will happily
> > accept)
> > 3) Determine membership on the committee
> >
> > Finally whether or not we pursue this approach, I'm hopeful that all
> > of you keep talking.  From a personal viewpoint, I'm tired of
> > writing instrument drivers.
> >
> > Jay
> >


To view archived messages, go to:
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Your use of Yahoo! Groups is subject to http://docs.yahoo.com/info/terms/

Below is a link interesting paper on Structured Reporting and Event
Streams similar to the XML Document Object Model...
http://www.dclunie.com/papers/spie_mi_2001_SR_manuscript.pdf
The SR is part of the DICOM standard...
Also a book:
http://www.pixelmed.com/srbook.html

We have also been thinking of embedding conditional flow and conditional
programming into the DTD directly... This is good in an HTS scenario
(some of this grammar is already within the XSL DTD especailly for the
FO -- Formatting Objects -- area).

Another area is Aspect Oriented programming similar to Event Streams...
(More on that soon).

Another standardization area for imaging (that is gaining a big
foothold) is JPEG2000 (I think the FDA is OK with a factor of 10 or 12
for lossless compression.

Again would be good to combine the control paradigm with the data model
(process).

Sanjay

-----Original Message-----
From: James Gill [mailto:james.gill@...]
Sent: Sunday, February 23, 2003 8:51 AM
To: Gary W. Kramer; tstaab@...; Mark F Russo;
roger.mcintosh@...; bs-sc@...;
info@...
Subject: Re: ALA and XML for instruments


All,
I certainly had no intentions to dilute current efforts nor necessarily
start a new one.  Ok I'll admit the mail sounded that way - but my
intention was to offer the suggestion that ALA might have a role to
play,  and to start the discussion that if ALA does have a role - what
would that role be?  Perhaps just to make sure the ALA's efforts to
support the various efforts are continued.

I think one important question in front of us now is - Since we have a
major
vendor (certainly in the HTS area)  using   XML, and even better towards
releasing it into the public domain, how can this be leveraged to insure
better standardization? I suspect there are also numerous other in house
development efforts on going at various vendors and large industrial
sites as well.  How can we make sure that these in house developers
(especially the vendors) want to use the standards??

I should also point out that in the HTS area - I believe that standards
have been much harder to come by than in the Spectroscopy and
Chromatography areas.  I believe that the HTS area simply has not
developed a "standardization" mentality
- So please forgive my ignorance in this area and accept my suggestions
as opportunities to educate me.

Suggestions?  Is it as Torsten and Gary say - the vehicles are in place,
folks just need to start using them?  Does ALA have a role?

Jay

"Gary W. Kramer" wrote:

> Jay,
>
> There is currently an effort to develop XML data representations for
> result data from spectroscopy and chromatography instruments ongoing
> in ASTM E13. This has been in the works for about a year and a half,
> and many instrument vendors and LIMS folks are participating.  We're
> having a meeting at Pittcon, see below for the info.  We have
> preliminary indications that the IUPAC/JCAMP folks will join the ASTM
> effort so that we can develop a single standard, not multiple
> approaches like we had with the ANDI and JCAMP standards.
>
> I completely agree with you that we need to get XML standards in place
> for instrument data, but I would very much not like to see competing
> efforts evolve to do try to do this.  The ASTM effort and approach is
> not yet set in concrete, so there is plenty of opportunity for folks
> who want to see such standards to get involved and be a part of the
> solution.  Speaking for the ASTM XML Working Group, we invite all
> interested parties to work with us to develop standards that will
> benefit all of us.
>
> Cheers,
> Gary
>
> From: "Abramo, Kimberly" <KHAbramo@...>
> To: "Abramo, Kimberly" <KHAbramo@...>,
>    "'ty_abshear@...'"
>          <ty_abshear@...>,
>    "Alt, Timothy" <TMAlt@...>,
>    "'aykut.arslan@...'" <aykut.arslan@...>,
>    "'mark.f.bean@...'" <mark.f.bean@...>,
>    "'stephen.best@...'" <stephen.best@...>,
>    "'blair@...'" <blair@...>,
>    "'michael_boruta@...'" <michael_boruta@...>,
>    "'tony_brand@...'" <tony_brand@...>,
>    "'polyspec@...'" <polyspec@...>,
>    "'tony.davies@...'"
<tony.davies@...>,
>    "'dermin.fan@...'" <dermin.fan@...>,
>    "'paul.derose@...'" <paul.derose@...>,
>    "'cdollar@...'" <cdollar@...>,
>    "'james.duckworth@...'"
>          <james.duckworth@...>,
>    "'scot.ellis@...'"
>          <scot.ellis@...>,
>    "'jean-louis.excoffier@...'"
>          <jean-louis.excoffier@...>,
>    "'craig.fellows@...'"
>          <craig.fellows@...>,
>    "'thorsten.froehlich@...'"
>          <thorsten.froehlich@...>,
>    "Fugere, John \"Barry\""
>          <jbfugere@...>,
>    "'egavin@...'" <egavin@...>,
>    "'mark_harnois@...'" <mark_harnois@...>,
>    "'dheld@...'" <dheld@...>,
>    "'markus.hemmer@...'"
<markus.hemmer@...>,
>    "'sherry.hemmingsen@...'"
<sherry.hemmingsen@...>,
>    "'hooverhl@...'" <hooverhl@...>,
>    "'hughespf@...'"
>          <hughespf@...>,
>    "'tony.johnson@...'"
>          <tony.johnson@...>,
>    "'simon.kaalman@...'"
>          <simon.kaalman@...>,
>    "'pkilz@...'"
>          <pkilz@...>,
>    "'gary.kramer@...'" <gary.kramer@...>,
>    "'don_kuehl@...'" <don_kuehl@...>,
>    "'rjlanc@...'" <rjlanc@...>,
>    "'rlarsensdt@...'"
>          <rlarsensdt@...>,
>    "'dlevy@...'" <dlevy@...>,
>    "'kenlewis@...'" <kenlewis@...>,
>    "'mil55244@...'"
>          <mil55244@...>,
>    "'christopher.lynch@...'"
>          <christopher.lynch@...>,
>    "'gary.mallard@...'"
>          <gary.mallard@...>,
>    "'michael@...'" <michael@...>,
>    "'rmcdjcamp@...'" <rmcdjcamp@...>,
>    "'r_d_mcdowall@...'" <r_d_mcdowall@...>,
>    "'dave.michelsen@...'" <dave.michelsen@...>,
>    "'todd_miller@...'" <todd_miller@...>,
>    "'bryan_miller@...'" <bryan_miller@...>,
>    "'moored@...'" <moored@...>,
>    "'pm286@...'"
>          <pm286@...>,
>    "'totoole@...'" <totoole@...>,
>    "'martin.peschke@...'" <martin.peschke@...>,
>    "'jay_powell@...'" <jay_powell@...>,
>    "Richard, Shannon" <SMRichard@...>,
>    "'brian_rohrback@...'" <brian_rohrback@...>,
>    "'john.rumble@...'" <john.rumble@...>,
>    "'thomas.sauter@...'" <thomas.sauter@...>,
>    "'marie_scandone@...'" <marie_scandone@...>,
>    "'schaefer@...'"
>          <schaefer@...>,
>    "'thomas_r_sharp@...'"
<thomas_r_sharp@...>,
>    "'terry.sheehan@...'" <terry.sheehan@...>,
>    "'ssimpson@...'" <ssimpson@...>,
>    "'steve.stein@...'"
>          <steve.stein@...>,
>    "'bill.town@...'"
>          <bill.town@...>,
>    "'john.travis@...'" <john.travis@...>,
>    "'tom.tuzzeo@...'" <tom.tuzzeo@...>,
>    "'david.varley@...'" <david.varley@...>,
>    "'craig.walla@...'" <craig.walla@...>,
>    "'thomas.weber@...'"
<thomas.weber@...>,
>    "'tony@...'" <tony@...>,
>    "'debbie_zink@...'"
>          <debbie_zink@...>
> Cc: "'Paul.Fjeldsted@...'"
<Paul.Fjeldsted@...>,
>    "Wishnies, Steven" <SMWishnies@...>,
>    "Mutin, Alexander"
>          <almutin@...>,
>    "Nishimura, Masayuki" <MANishimura@...>,
>    "'frank.tontala@...'" <frank.tontala@...>,
>    "'d_martinsen@...'" <d_martinsen@...>,
>    "'peter.linstrom@...'" <peter.linstrom@...>,
>    "'aykut.arslan@...'" <aykut.arslan@...>,
>    "'anlidao.nguyen@...'" <anlidao.nguyen@...>,
>    "'rmcdjcamp@...'" <rmcdjcamp@...>,
>    "'scubbedge@...'"
>          <scubbedge@...>,
>    "'steve@...'" <steve@...>,
>    "'steve.leich@...'" <steve.leich@...>,
>    "'friedrich.brunzema@...'" <friedrich.brunzema@...>,
>    "'dave.blaha@...'" <dave.blaha@...>,
>    "'craig.walla@...'" <craig.walla@...>,
>    "'ute_bober@...'" <ute_bober@...>,
>    "'bill.town@...'" <bill.town@...>,
>    "'sgadgil@...'" <sgadgil@...>,
>    "'jerrym@...'" <jerrym@...>,
>    "'clacraver@...'"
>          <clacraver@...>,
>    "'claracraver@...'"
>          <claracraver@...>,
>    "'jay_powell@...'"
>          <jay_powell@...>,
>    "'JULIAN_RANDALL_K@...'"
>          <JULIAN_RANDALL_K@...>,
>    "'Friedrich.Brunzema@...'"
>          <Friedrich.Brunzema@...>
> Subject: RE: PITTCON SpectroML/ GAML/XML ASTM meeting
> Date: Fri, 21 Feb 2003 13:02:35 -0500
> MIME-Version: 1.0
> X-Mailer: Internet Mail Service (5.5.2653.19)
> Content-Type: text/plain;
>         charset="iso-8859-1"
>
> I apologize for the delay in sending this message.  There has been
much
> confusion  as to when the ASTM meetings where going to be held.   The
> schedule has now been finalized and the SpectroML/GAML/XML meeting
> will take place on Tuesday March 11th at 5:30PM.  I realize that this
> is late in the afternoon, but since most of the committee participants

> are vendors, it works out better that way.  We will be reviewing our
> progress in several areas.  Additionally, we hope to have attendance
> from representatives from IUPAC.  I hope that we will be able to share

> the vision and further develop plans to get the schemas finalized.
> Please let me know if you have any further questions.  I look forward
> to seeing many of you at Pittcon.
>
> > Thanks-
> > Kimberly Harris Abramo
> > Product Manager - Spectroscopy
> > Shimadzu Scientific Instruments
> > 1-800-477-1227 ext 1912
> > (Fax) 410-381-1222
> >
>
> > Guys,
> > There was a lot of talk at LA03 about xml and standards for
> > instrument data.  Roger has been working to get his format into the
> > public domain, and I had a number of discussions with folks at the
> > meeting..
> >
> > What would folks think about having the ALA sponsor a group to
> > co-ordinate the various efforts and ultimately to recommend a
> > specification which would be supported by the ALA, published in JALA

> > etc.  I think the ALA represents a unique opportunity in that there
> > is representation from the vendors, industry, consultants, academics

> > and government.  In fact, all of those constituencies are
> > represented on this mail.  In addition there has already significant

> > progress that has been made by the folks on this mail towards a
> > standard.
> >
> > I would see the next steps being
> >
> > 1) Gain agreement from you all that the ALA is the right place to
> > propose such a standard and they you would want to participate
> > 2) Propose the concept to the Board (which of course will happily
> > accept)
> > 3) Determine membership on the committee
> >
> > Finally whether or not we pursue this approach, I'm hopeful that all
> > of you keep talking.  From a personal viewpoint, I'm tired of
> > writing instrument drivers.
> >
> > Jay
> >

Subject: RE: ASTM is preparing for LECIS revision (with LECIS commentary attachment in PDF)
Date: Thu, 20 Feb 2003 16:14:04 -0800
Organization: Userspace Corproration

All,

(This is Sanjaya Joshi from Userspace)
SOAP (Simple Object Access Protocol) died a horrible death during our
testing...
Web services is a good marketing ploy, but the actual implementation is
not quite there yet. WSDL is CORBA-Like, but support and applications
are not industrial strength.
(our first XML project was in 1998)

What would be interesting is continuing on the path of XML-RPC (we moved
to this years ago, and based our thought process on the IML or the
Instrument Markup Language which was originally a NASA project for
Remote IR Telescopy).
There are rumbling in the process community of not sticking with RPC,
but standardization is very simple if the heart of SOAP without the fat
layers (ie XML-RPC) is retained.

Thinking of LECIS as a Process Protocol is instructive...
In my discussions with IBM and Microsoft (the benefactors of SOAP) and
the Workflow initiative, they openly admitted that SOAP was not really
meant to do very fast transactions, let alone real-time instrument
communications.
Look at the Workflow Management Coalitions eXtensible Process Definition
Language. (XPDL)
http://xml.coverpages.org/ni2002-12-10-b.html
Also NIST's process description:
http://ats.nist.gov/psl/xml/process-descriptions.html
There is also the Petri-Net Markup Language, but the node paradigm for
automation has so far been too complex a solution for automation...
(maybe a better one for data).

A rectangular LIMS model (in my opinion) should move into a dynamic
Process model...
We have looked at NetCDF and AnDI (the child of NetCDF for Analytical
Data Interchange), but there is no real threading between the major
instrument groups: LC, MS, NMR...
Also the Thermo-Galactic GAML (which needs to pass muster as a tested
DTD...)
There is SpectroML too:
http://www.mel.nist.gov/div826/msid/sima/02_instrmnt_chemrefdata.html

Our focus is on MS and NMR which are very data intensive.
Specific points from scientists is the inability of AnDI or GAML to
handle MS-MS data (and MS2+)
Separation of data from process is not going to work out, especially for
nascent protocols that keep changing till they become an "Assay"...

I would urge us to follow the route of DICOM (Digital Imaging and
Communications in Medicine) -- my previous incarnation was in Radiology
-- where the acceptance was much better with the user and vendor
community. DICOM is now an XML standard and merged with HL7 (Health
Level 7), the healthcare industry patient data standard.

My 50,000 ft 2 cent drop...

Attached is our overview (from Userspace) on LECIS (as a PDF
whitepaper)...
Note that this is not a "techie" paper, but more an "executive summary".
Also, the architecture diagram in the paper is dated...

You can contact me if you need to respond to my comments (or bash on
them!)

Best,

Sanjaya Joshi
President and CTO
Userspace Corporation

Dear LECIS subscriber,

Below you will find the latest product announcement from the e-labcompany (http://www.e-labcompany.co.uk/) regarding their LECIS Shell Suite Developer Edition software package.

Have a nice day,

Torsten Staab
LECIS Webmaster (www.lecis.org)

PS: instructions on how to post messages or how to unsubscribe yourself from this list can be found at http://www.lecis.org/contacts.htm
---------------------------------------------------------------------------------

6th November 2002

The Electric Laboratory Company Ltd is pleased to announce the release of
its LECIS Shell Suite Developer Edition. This new version integrates the OMG
LECIS COBRA standard (with DCOM) into our existing established ASTM LECIS
product set.

LECIS Shell Suite Developer Edition

The Developer Edition of the e-labcompany LECIS Shell Suite is the easiest
way to integrate LECIS compliance into your instrument systems. It allows
any of the following flavours of LECIS interface to be used. All new
versions present the same Microsoft COM/ActiveX interfaces for the SLM, TSC
and SCD modules.

The available external interfaces are:
- OMG LECIS CORBA interface (with ASTM LECIS compatibility mode)
- OMG LECIS DCOM interface (with ASTM LECIS compatibility mode)
- ASTM LECIS (incorporates compatibility with OMG LECIS)

The Developer Edition includes everything in the Run-Time version, plus:
- Run-Time Licenses for 5 concurrent SLMShell and TSCShells
- A sample SLMShell project to kick start development
- - Microsoft Visual Basic 6 source code
- - An example OMG LECIS DCD and SCD
- - Full project documentation
- A SLMShell emulator for testing TSC code, DCD's
- An easy graphical tool to view, edit or create XML DCD's and SCD's
- An graphical tool to maintain SCD's through the OMG LECIS SCD interface
- Graphical Shell Interface (GSI).
- - Provides control of LECIS SLM devices with Microsoft Visio flowcharts!

The LECIS Shell Suite software provides security and auditing to support
validation.

To view archived messages, go to:
http://groups.yahoo.com/group/lecis-post/messages


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Hello all,

Below you will find the official release announcement for e-labcompany's LECIS Shell Suite V2.0.

Have a nice day,

Torsten Staab
LECIS Webmaster (www.lecis.org)
------------------------------------------------------------------------
30th October 2002

The Electric Laboratory Company Ltd is pleased to announce the release of
version 2.0 of its LECIS Shell Suite. This new version integrates the OMG
LECIS COBRA standard (with DCOM) into our existing established ASTM LECIS
product set.
The Run-Time Edition of the e-labcompany LECIS Shell Suite applications
allows any of the four flavours of LECIS interface to be used. All new
versions present the same Microsoft COM/ActiveX interfaces for the SLM, TSC
and SCD modules.
The available external interfaces are:
- OMG LECIS CORBA interface
- OMG LECIS DCOM interface
- ASTM LECIS (Incorporates compatibility with OMG LECIS)
- ASTM LECIS (Pfizer LIG 2.05 compatible, but is not compatible with the
SCD)
Notable features include:
OMG LECIS Shell Suite V1.0 (CORBA interface)
- OMG LECIS IDL compliant.
- OMG LECIS DCD and SCD compliant.
- Ideal for controlling devices implemented on different hardware or
software platforms.
OMG LECIS Shell Suite V1.0 (DCOM interface)
- DCOM interface generated from the OMG LECIS IDL.
- OMG LECIS DCD and SCD compliant.
- Ideal for controlling devices implemented on Microsoft Windows platforms.
ASTM LECIS Shell Suite V2.0
- Improved ASTM LECIS compliance.
(See:
http://www.e-labcompany.co.uk/products/lecis.shell/LECISComplianceStatement.
2.0.0.pdf)
- OMG LECIS DCD and SCD compliant.
- Ideal for controlling devices over the internet (TCP/IP message based).
ASTM LECIS Shell Suite V1.2
- Improved ASTM LECIS and LECIS Implementers' Guide 2.05 compliance.
(See:
http://www.e-labcompany.co.uk/products/lecis.shell/LECISComplianceStatement1
.2.0.pdf)
- Support for DCD defined Events, Resources and System Variables.
- Improved session disconnect/connect handling through communications loss.
- Performance enhancements.
All products support for:
- XML DCD and SCD validation.
- Message logging to the Windows NT Event log.
The LECIS Shell Suite software provides security and auditing to support
validation.

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Hello all,

I've just added new material to the LECIS Download web page (see
http://www.lecis.org/downloads.htm). The Download section now offers the
latest versions of Pfizer's LECIS Implementer's Guide (3.0) and ReTiSoft's
Genera Integration Guide (1.1.5) for download.

Have a nice day,
Torsten
LECIS Web Admin