Dear dr. Pluskal,
I think an easy linkage to R would be really useful, since I am currently
trying (and failng) to run MZmine from R, to optimize peak picking
parameters, which needs to export parameters to MZmine, run the entire
process, import the results to R, process those results, and calculate new
parameters to re-send, several (hundreds of) times. A connector library
(such as RCytoscape was for R and Cytoscape) would be immensely appreciated.
Best regards,
Carlos Rodríguez-López
On Fri, Nov 21, 2014 at 11:27 AM, Víctor Manuel Treviño Alvarado <
vtrev...@itesm.mx> wrote:
> Dear Tomas,
>
> These are good news!!!
>
> Similar to Earll, I would like that the 2D and perhaps 3D would be more
> flexible and/or powerful. Basically, ways to enhance the visualization.
>
> In the interface, as I mentioned to you time ago, the dialogs of
> parameters seems too isolated, they would need to show perhaps an overview
> of what the process do to facilitate operation for non expert users.
>
> Additionally, a "flow" diagram of the process would be fantastic (for
> example as in TOPPAS) and would probably clarify and facilitate the
> automatization of pipelines.
>
> Hope it helps.
> vt
>
> ______________________________________
> Dr. Victor Manuel Treviño Alvarado
> Profesor-Investigador, SNI - 1
> Laboratorio de Bioinformática
> Escuela de Medicina
> Tecnológico de Monterrey, Campus Monterrey
> CITES, 304, Tel. 8888 2045
> Aulas 7-421, Tel. 52-(81) 8358 2000 ext. 4536-103
> http://homepages.mty.itesm.mx/vtrevino
> http://www.itesm.mx
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> On Fri Nov 21, 2014, at 4:11 AM, Earll Mark GBJH <mark.ea...@syngenta.com>
> wrote:
>
> Hi Tomas,
>
>
>
> This is very good news, I am pleased that MZmine has a bright future.
>
>
>
> As I mentioned before I like the idea of workflow tools and have been
> involved (thanks to Stephan Beisken ex-EBI) with the open source “Mass
> Cascade” which is a KNIME based workflow tool for mass spectrometry. Just a
> crazy idea but would there be any mileage in thinking of combining the
> MZmine and Mass Cascade packages? Failing this have some linkage between
> them could be useful.
>
>
>
> I suspect you with think this is too radical a departure from the current
> stand-alone MZmine so my other suggestion is to have a wizard based
> interface which caters for different applications. (i.e. GC-MS, LC-MS,
> UPLC-MS, low res MS) possibly with typical settings from different
> manufacturers instruments. Even better if you made the wizard customizable
> then the users could write wizards for particular instruments and then
> share them! I have found that working with other people trying to show them
> the current MZmine that it is too much for them with the many menu items
> and parameters. It took me a long time to find my way through the software.
>
>
>
> It would be good to improve is the visualization of the peaks that are
> picked. The 3D plot is very good but the coloured highlight of a particular
> peak in 2D is not bright enough when you have a small peak (pale pink I
> recall). However I do think the 3D plot with the annotation is one of the
> most useful features of MZmine and a feature that is absent in nearly all
> vendor’s software. It gives you a great overview of the experiment and how
> many peaks you have picked or missed.
>
>
>
> Anything that can be done to assist with sensible peak picking/integration
> in the presence of noisy features would be welcome.
>
>
>
> Another area that I know you are thinking about is 2D chromatography. We
> would be very interested in this area. I will ask around here to see if
> there is any interest for helping provide resources for developing the 2D
> chromatography part. There might be a possibility to get a project proposal
> and hence some of Chris’s time. It’s a big “IF” but I will make enquiries.
>
>
>
> As ever I am keen to beta-test your software (time permitting) and assist
> with documentation or tutorials,
>
>
>
> Best regards,
>
>
>
> Mark
>
>
>
> -- -----------------------------------------
>
> *Mark Earll*
>
> Senior Analytical Chemist / Chemometrician
>
> GBJH Product Characterisation
>
> Office 102/168
>
>
>
> <image002.jpg>
>
>
>
> Jealott's Hill International Research Centre
> Bracknell
>
> Berkshire
>
> RG42 6EY
>
> United Kingdom
>
> Direct +44 1344 414316
>
> mark.ea...@syngenta.com <firstname.surn...@syngenta.com>
>
> www.syngenta.com
>
>
>
>
>
>
>
>
>
> *From:* Tomas Pluskal [mailto:plus...@oist.jp <plus...@oist.jp>]
> *Sent:* 21 November 2014 05:56
> *To:* Developer discussion
> *Cc:* Earll Mark GBJH; Pudney Chris (ext) GBJH; Gauthier Boaglio; Víctor
> Manuel Treviño Alvarado; Adam Tenderholt; Dan Schmidt
> *Subject:* Plans for MZmine 3
>
>
>
> Hi everyone!
>
>
>
> Following a conference call that we had with Matej and Thomas, I would
> like to announce the plans for development of the next major version of
> MZmine, that is version 3.
>
> Of course, for the time being, we will continue updating MZmine 2 with
> minor improvements and new methods. But we would like to shift our main
> effort towards developing the new generation of MZmine.
>
>
>
> *Motivation*
>
>
>
> The design of MZmine's data model is outdated and not flexible enough to
> incorporate new methods or new types of data. The GUI is using some
> obsolete libraries (e.g. Java3d, JavaHelp) and the binding between the GUI
> and the data model is far from optimal.
>
>
>
> *Plan*
>
>
>
> We want to build a new data model and GUI for MZmine using the modern
> JavaFX framework instead of (currently used) Swing framework.
>
> The main concept will be flexibility, meaning that data structures should
> be extendable with new data provided by MZmine modules. The modules will
> also be able to provide GUI components to visualize the data. Raw data and
> peak lists will be completely separated, so it will be possible to work
> with peak lists imported from another software.
>
>
>
> I already started working on the new design on a separate branch in the
> SVN: http://svn.code.sf.net/p/mzmine/code/branches/tomas_mzmine3/ (it is
> still in a very early stage)
>
>
>
> *Call for proposals*
>
>
>
> If you have any comments, suggestions, or requests for the next generation
> of MZmine, now is the best time to express them. For example, we have been
> discussing support for local databases, speeding up project opening/saving,
> simplifying the parameter settings (requested by Mark Earll), and various
> other ideas. Additional input is most welcome!
>
>
>
>
>
> Best regards,
>
>
>
> Tomas
>
>
>
>
>
> ===============================================
> Tomas Pluskal
> G0 Cell Unit, Okinawa Institute of Science and Technology Graduate
> University
> 1919-1 Tancha, Onna-son, Okinawa 904-0495, Japan
>
> WWW: https://groups.oist.jp/g0
> TEL: +81-98-966-8684
> Fax: +81-98-966-2890
>
>
>
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