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Re: [science-iwg] Review BoF EclipseCon
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Yes. +1 from me too.
Torkild
> Den 5. nov. 2013 kl. 21:01 skrev Stephan Druskat <stephan.druskat@xxxxxxxxxxx>:
>
> Hi All,
>
> +1 for org.eclipse.science.*, just because it's nice and generic and probably un-trademark-able.
>
> Other than that I like Matt & Philip's suggestions.
>
> Cheers,
> Stephan
> --
> Stephan Druskat
> stephan.druskat@xxxxxxxxxxx
>
>
> Zitat von UOMo <uomo@xxxxxxxxxxx>:
>
>> Just saw, Scisoft or the ESO (EU Observatory) software artifact is even
>> called "eclipse", too, http://www.eso.org/sci/software/eclipse/ for obvious
>> reasons, it deals with Solar or Lunar Eclipse observation, there is no
>> evidence of Eclipse software being used, but that makes the combination of
>> "eclipse" and "scisoft" even more irritating.
>>
>> Especiallly that looks like a very professional and well-established
>> project, even if there may not be a trademark.
>>
>> Werner
>>
>>> On Tue, Nov 5, 2013 at 6:16 PM, <science-iwg-request@xxxxxxxxxxx> wrote:
>>>
>>> Send science-iwg mailing list submissions to
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>>>
>>> Today's Topics:
>>>
>>> 1. Re: Review BoF EclipseCon (UOMo)
>>>
>>>
>>> ----------------------------------------------------------------------
>>>
>>> Message: 1
>>> Date: Tue, 5 Nov 2013 18:16:11 +0100
>>> From: UOMo <uomo@xxxxxxxxxxx>
>>> To: science-iwg@xxxxxxxxxxx
>>> Subject: Re: [science-iwg] Review BoF EclipseCon
>>> Message-ID:
>>> <CAAGawe0a_u9KMZn9prfTidYKYoFcMeURnC6V_zUn2dJ5o=
>>> Joeg@xxxxxxxxxxxxxx>
>>> Content-Type: text/plain; charset="iso-8859-1"
>>>
>>> Did I miss anything being wrong with "org.eclipse.science" or why would we
>>> prefer "scisoft"?
>>>
>>> As a matter of fact, the term "SciSoft" (maybe not so critical for a Java
>>> sub-package, but still odd) seems to be used by a product or family of
>>> Astrological products already:
>>> >Scisoft for Mac OSX Intel is a collection of astronomical software for Mac
>>> OS X Intel >10.5 and above. It is similar to the ESO Scisoft (
>>> http://www.eso.org/scisoft/) >distribution but is not an official ESO
>>> product. More information is available >at http://scisoftosx.dyndns.org.
>>>
>>> Read more: Scisoft for Mac - Free download and software reviews - CNET
>>> Download.com<
>>> http://download.cnet.com/Scisoft/3000-2053_4-41468.html#ixzz2jnAaOeLM>
>>> http://download.cnet.com/Scisoft/3000-2053_4-41468.html#ixzz2jnAaOeLM
>>>
>>>
>>> If "scisoft" was a thought, I'd like to think about "science", in the end
>>> both would work, but trying to avoid clashes with other projects or
>>> commercial products seem to be in the interest of Eclipse where possible,
>>> see "Mylar" -> "Mylyn";-)
>>>
>>> http://www.sci-soft.com/ is also a site with commercial products claiming
>>> to be around for the last 20 years.
>>>
>>> Werner
>>>
>>> On Tue, Nov 5, 2013 at 6:00 PM, <science-iwg-request@xxxxxxxxxxx> wrote:
>>>
>>> > Send science-iwg mailing list submissions to
>>> > science-iwg@xxxxxxxxxxx
>>> >
>>> > To subscribe or unsubscribe via the World Wide Web, visit
>>> > https://dev.eclipse.org/mailman/listinfo/science-iwg
>>> > or, via email, send a message with subject or body 'help' to
>>> > science-iwg-request@xxxxxxxxxxx
>>> >
>>> > You can reach the person managing the list at
>>> > science-iwg-owner@xxxxxxxxxxx
>>> >
>>> > When replying, please edit your Subject line so it is more specific
>>> > than "Re: Contents of science-iwg digest..."
>>> >
>>> >
>>> > Today's Topics:
>>> >
>>> > 1. Re: Review BoF EclipseCon (Philip Wenig)
>>> >
>>> >
>>> > ----------------------------------------------------------------------
>>> >
>>> > Message: 1
>>> > Date: Tue, 05 Nov 2013 08:35:55 +0100
>>> > From: Philip Wenig <philip.wenig@xxxxxxxxxxxxxx>
>>> > To: science-iwg@xxxxxxxxxxx
>>> > Subject: Re: [science-iwg] Review BoF EclipseCon
>>> > Message-ID: <52789FDB.4000102@xxxxxxxxxxxxxx>
>>> > Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
>>> >
>>> > Hi Matt,
>>> >
>>> > that sounds reasonable. I like the idea to have the IDN notation
>>> > "org.eclipse.scisoft.xxx" and extension points for different
>>> > implementations. We should also include a section for algorithms.
>>> > Probably an export format extension point would be also fine to create
>>> > scientific images ready for publication e.g. with R or other tools.
>>> >
>>> > org.eclipse.scisoft
>>> > org.eclipse.scisoft.1d
>>> > org.eclipse.scisoft.2d
>>> > org.eclipse.scisoft.3d
>>> >
>>> > org.eclipse.scisoft.ui
>>> > org.eclipse.scisoft.ui.1d
>>> > org.eclipse.scisoft.ui.2d
>>> > org.eclipse.scisoft.ui.3d
>>> >
>>> > Extensions:
>>> >
>>> > org.eclipse.scisoft.supplier.savitzkygolay
>>> > org.eclipse.scisoft.supplier.firstdeviation
>>> > org.eclipse.scisoft.supplier.seconddeviation
>>> > ...
>>> > org.eclipse.scisoft.ui.supplier.swtchart
>>> > org.eclipse.scisoft.ui.supplier.xygraph
>>> > org.eclipse.scisoft.ui.supplier.javafx
>>> >
>>> > That's just an idea.
>>> >
>>> >
>>> > Best Regards,
>>> > Philip
>>> >
>>> >
>>> >
>>> >
>>> > Am 04.11.2013 10:32, schrieb Matt.Gerring@xxxxxxxxxxxxx:
>>> > >
>>> > > Hi Philip,
>>> > >
>>> > > Yes I would propose something which is swappable i.e. the plotting is
>>> > > well separated from the algorithm/data. So plotting details do not
>>> > > leak into eclipse parts, instead they interact with an interface. Any
>>> > > design we choose should have to be abstract -- including from
>>> > > underlying plot objects (draw2d figures, javafx scene graphs, jogl
>>> > > objects etc. are all not in the interface!).
>>> > >
>>> > > At Diamond, we have had several plotting engines (3) in the past, so
>>> > > we have learned this over a hard earned period of time. It would mean
>>> > > that anyone could contribute a plotting system (by extension point)
>>> > > and that any user from the group can swap plotting whenever they need
>>> > > -- providing there is an implementation. I can imagine that we would
>>> > > want to swap the javafx 1D plotting into the interface fairly soon! --
>>> > > tying ourselves to any particular plotting engine would be a bad idea.
>>> > > Although I am a fan (most of the time) and would-be contributor to
>>> > > xy-graph.
>>> > >
>>> > > I would be willing to send around the interfaces with examples how to
>>> > > use them later this month if people want that. I suggest that the
>>> > > package be org.eclipse.scisoft.xxx where scisoft stands for scientific
>>> > > software.
>>> > >
>>> > > Nomenclature: Can we name the plotting type after the dimensionality
>>> > > of the data? This gives room in the nomenclature to have a name for
>>> > > images which cannot be called 3D -- so they must be 2D!
>>> > >
>>> > > *Xy-graphs, scatter, pie, area* - *1D* (e.g.
>>> > > XY-Graphs are1D data shown with two axes)
>>> > >
>>> > > *Images, surfaces, contours, vector plots* - *2D* (Note surfaces are
>>> > > 2D data shown with 3 axes and using 3D scene graph)
>>> > >
>>> > > *Iso-surface, other volume rendering* - *3D*? (They are slices
>>> > > from 3D data)
>>> > >
>>> > > Best Regards,
>>> > >
>>> > > Matt
>>> > >
>>> > > *From:*science-iwg-bounces@xxxxxxxxxxx
>>> > > [mailto:science-iwg-bounces@xxxxxxxxxxx] *On Behalf Of *Philip Wenig
>>> > > *Sent:* 02 November 2013 11:45
>>> > > *To:* science-iwg@xxxxxxxxxxx
>>> > > *Subject:* Re: [science-iwg] Review BoF EclipseCon
>>> > >
>>> > > Hi Matt,
>>> > >
>>> > > I think that's a great idea to have APIs and abstract respectively
>>> > > generalized methods and views for 2D and 3D data. Attached are two
>>> > > screenshots of DAWN and OpenChrom. Both screenshots show profiles,
>>> > > despite the fact that both have completely different data models (XRD
>>> > > and GC/MS). Hence, it would be great to have an unified and flexible
>>> > > API. Moreover, it would be great use the existing knowledge and to
>>> > > build upon the interfaces and methods that are already available in
>>> > > DAWN, Bioclipse, OpenChrom and others.
>>> > >
>>> > > ----------------------------------
>>> > > Profile Views
>>> > > ----------------------------------
>>> > > 2D / 3D
>>> > > Variable measurement units and descriptions for each Axis
>>> > > 1st Derivative
>>> > > 2nd Derivative
>>> > > ...
>>> > > Overlay
>>> > >
>>> > > ----------------------------------
>>> > > Profile Methods
>>> > > ----------------------------------
>>> > > Smoothing Algorithms (Savitzky-Golay, ...)
>>> > > Peak Detektion (1st Derivative, ..., Deconvolution, ...)
>>> > > Peak Integration (Gaussian model, ...)
>>> > > Peak Fitting (Correlation Optimized Warping, Dynamic Time Warping, ...)
>>> > > ...
>>> > >
>>> > > In my opinion, such abstract handling of profile data would make it
>>> > > much more easier for others (students, post-docs, scientists, ...) to
>>> > > implement additional algorithms. Furthermore, data from different
>>> > > detectors like XRD, NMR, GC/FID, GC/MS MS/MS could be handled in an
>>> > > unified way as long as it produces profile data. In addition, all
>>> > > specific calculations can still be executed by specialized frameworks
>>> > > for e.g. XRD (DAWN) or GC/MS (OpenChrom). Wouldn't that be great?
>>> > >
>>> > > /"As long as your going to be thinking anyway, think big."/ Donald
>>> Trump
>>> > >
>>> > >
>>> > > Cheers,
>>> > > Philip
>>> > >
>>> > > Am 01.11.2013 16:09, schrieb Matt.Gerring@xxxxxxxxxxxxx
>>> > > <mailto:Matt.Gerring@xxxxxxxxxxxxx>:
>>> > >
>>> > > Hi Philip,
>>> > >
>>> > >
>>> > >
>>> > > Yes it was a very positive step, well done in getting it organised.
>>> > I am willing to write the documents and circulate these for agreement as
>>> we
>>> > agreed.
>>> > >
>>> > >
>>> > >
>>> > > Diamond are able and, subject to review, interested in providing
>>> > interfaces and a reference implementation for all of the features
>>> mentioned
>>> > in the meeting, including everything in Jans recent email. I have a
>>> > concrete idea of how this could happen and we can detail this in the
>>> > documents. We would obviously start gradually so that the searches of
>>> > license agreement can be performed on each API provided. In fact even
>>> more
>>> > gradual than that - we should agree on interfaces of each module, I can
>>> > provide the starting point for these too including examples of how to use
>>> > the API. The APIs are elegant and powerful to use and I hope you will
>>> like
>>> > them.
>>> > >
>>> > >
>>> > >
>>> > > Since the talk I did at eclipse con was not busily attended, I am
>>> > looking forward to the video of the demonstration being available on the
>>> > youtube channel. Then people can see how cool the features the team here
>>> > has worked on are, and decide if they are interested in working with us.
>>> > >
>>> > >
>>> > >
>>> > > Best Regards,
>>> > >
>>> > >
>>> > >
>>> > > Matt
>>> > >
>>> > >
>>> > >
>>> > > -----Original Message-----
>>> > >
>>> > > From:science-iwg-bounces@xxxxxxxxxxx <mailto:
>>> > science-iwg-bounces@xxxxxxxxxxx> [mailto:
>>> science-iwg-bounces@xxxxxxxxxxx]
>>> > On Behalf Of Philip Wenig
>>> > >
>>> > > Sent: 01 November 2013 13:17
>>> > >
>>> > > To:science-iwg@xxxxxxxxxxx <mailto:science-iwg@xxxxxxxxxxx>
>>> > >
>>> > > Subject: [science-iwg] Review BoF EclipseCon
>>> > >
>>> > >
>>> > >
>>> > > Hi folks,
>>> > >
>>> > >
>>> > >
>>> > > the BoF was fantastic, wasn't it!
>>> > >
>>> > > I really feel that the time has come to bring our idea of a
>>> > scientific working group to reality :-).
>>> > >
>>> > >
>>> > >
>>> > >
>>> > >
>>> > > Best
>>> > >
>>> > > Philip
>>> > >
>>> > >
>>> > >
>>> > >
>>> > >
>>> > >
>>> > > --
>>> > > ~~~~~~~~~~~~~~~~~~~~~~~~
>>> > > Dr. Philip Wenig
>>> > >
>>> > > http://www.openchrom.net
>>> > >
>>> > > https://www.xing.com/profile/Philip_Wenig
>>> > > http://de.linkedin.com/pub/philip-wenig/2a/4a8/877
>>> > > ~~~~~~~~~~~~~~~~~~~~~~~~
>>> > >
>>> > > --
>>> > >
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>>> > >
>>> > >
>>> > >
>>> > >
>>> > > _______________________________________________
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>>> >
>>> >
>>> > --
>>> > ~~~~~~~~~~~~~~~~~~~~~~~~
>>> > Dr. Philip Wenig
>>> >
>>> > http://www.openchrom.net
>>> >
>>> > https://www.xing.com/profile/Philip_Wenig
>>> > http://de.linkedin.com/pub/philip-wenig/2a/4a8/877
>>> > ~~~~~~~~~~~~~~~~~~~~~~~~
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