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
______________________________________
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Laboratorio de Bioinformática
Escuela de Medicina
Tecnológico de Monterrey, Campus Monterrey
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On Fri Nov 21, 2014, at 4:11 AM, Earll Mark GBJH
<mark.ea...@syngenta.com<mailto: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<mailto:firstname.surn...@syngenta.com>
www.syngenta.com<http://www.syngenta.com/>
From: Tomas Pluskal [mailto: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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