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What additional applications would you like to see?

npinhao
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zanoi wrote:I'm not familir with ELN program...do you think there is no way one can improve BasKet to work as ELN?


As I said, I'm actually testing Basket as a "kind off" ELN. However it lacks a lot of things in this respect. Some of them can be implemented - formula awareness (probably LaTeX); templates; maybe even statistical tools - but others go beyond the purpose of basket. I.e. an ELN should be a collaborative application with several users accessing if from several places (laboratories / experimental instalations). This points to a centralized database and a server-client architecture. Some ELN even have interfaces to experimental equipments allowing the direct acquisition of data. Then there are accreditation and legal issues as ELN data can be used to guaranty compliance to ISO/IEC 17025 norm (on testing and calibration laboratories) and ELN records have been used in legal disputes.

To build an ELN is a complex task but if the KDE community sets this goal I'm sure it will have a huge impact on the acceptance of KDE among scientists.

One very interesting OpenSource application that has some similar characteristics with an ELN but serves a different purpose is http://bika.sourceforge.net/, a LIMS (Laboratory Information Management System). A few years ago, when it was just starting, I lead the implementation of this application on my lab and now I see it has gain a large base of serious users. It can be an example to follow.
zanoi
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npinhao wrote:Some ELN even have interfaces to experimental equipments allowing the direct acquisition of data. Then there are accreditation and legal issues as ELN data can be used to guaranty compliance to ISO/IEC 17025 norm (on testing and calibration laboratories) and ELN records have been used in legal disputes.

Ok, that definitely sounds like it needs a dedicated application

npinhao wrote:To build an ELN is a complex task but if the KDE community sets this goal I'm sure it will have a huge impact on the acceptance of KDE among scientists.

It would be amazing to have a "scientific killer app" like that for KDE

Bika looks interesting, I'm not sure I fully understand what it does though.
ngativ
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npinhao wrote:Just one more comment on my "request" for a ELN:
I have used "Basket Note Pads" (http://basket.kde.org/) as a personal ELN and it has some interesting characteristics:
- take notes;
- Integration of text, images, worksheets and links;
- Password protection;
- Tasks.

However it lacks a lot of things (network awareness; group activities; templates; database; data treatment tools) to be a good ELN and it is too flexible for this purpose...

If someone is interested in picking this as a project I can gladly contribute to the definition of requirements and maybe some code. Unfortunately I'm not familiar with C++ and the KDE internals.


I think that this is a job for a webserver application rather than a desktop application.

TheBlackCat wrote:
The User wrote:Well, I think there are not that many people interested in Fortran…
That does not mean there is no chance (there is an Erlang-plugin, too), but somebody has to do it.

Fortran use in scientific fields is huge. It is not used in commercial software development much anymore, but it scientists still use it a lot for internal software and there is a massive amount of existing software written in it.


Fortran, like in others fields, is getting obsolete , even in science.
The User
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@Fortran-Lovers
A few examples for popular, active scientific projects would be nice.
There are also people using Cobol, but there are no people really interested in it being able to implement a language plugin.
User avatar TheBlackCat
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I still know a lab that uses fortran almost exclusively, and according to professors I talk to it is still used a huge amount. They were quick to correct my misconception that fortran is not used extensively, and insist it was still an extremely important language.


Man is the lowest-cost, 150-pound, nonlinear, all-purpose computer system which can be mass-produced by unskilled labor.
-NASA in 1965
HmpfCBR
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A Sweave application, this might also be interesting for the aforementioned ELN.

Sweave combines R and LaTeX. KDE has probably the best R (RKWard) and LaTeX (Kile) IDEs, but the combination with Sweave is missing. A syntax highlighting file for Sweave file is already available on kde-files.org and with some configuration Kile can already run Sweave files, but of course it is not an IDE designed for Sweave.
thijsdetweede
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The User wrote:@Fortran-Lovers
A few examples for popular, active scientific projects would be nice.
There are also people using Cobol, but there are no people really interested in it being able to implement a language plugin.


I'm working on atmospheric modeling, my model can be found at gitorious: gitorious.org/dales .

Using git, cmake, doxygen... I guess with good Fortran (200x) support in KDevelop, it would be a very useful IDE for me.
HmpfCBR
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The User wrote:@Fortran-Lovers
A few examples for popular, active scientific projects would be nice.

Currently a new lake ecosystem model is being written from scratch in Fortran.
cojeff
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TheBlackCat wrote:Here are some of the ideas brought up, in no particular order (see here):

  • An IDE for script (interpeted) programming languages, particularly python
  • A matlab, maple, and/or mathematica clone
  • A good reference and paper manager
  • A 2D molecular model drawer
  • A mapping/GIS tool
  • A 2D/3D design/CAD tool
  • A lexical analysis program
  • A circuit simulator
  • An economics simulation program
  • A generic simulation program
  • A sequence alignment program
  • A cladistics program
  • A generic object categorization and display program

So does anyone have an additions, or any comments on what they would like to see in any of the programs above?



As a chemist, I desperately need a good 2D molecular model drawer. There is a lot of really good 3D molecular model drawers on Linux/KDE(certainly due to the fact that most chemists using Linux are theoreticians) but almost nothing for 2D.
Tuukka
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cojeff wrote:As a chemist, I desperately need a good 2D molecular model drawer. There is a lot of really good 3D molecular model drawers on Linux/KDE(certainly due to the fact that most chemists using Linux are theoreticians) but almost nothing for 2D.


I agree, there's no good 2D molecular drawer for Linux (BKchem has the most essential features but the UI is awkward to say the least). Molecular diagrams are essentially specialized vector graphics and something that could be considered would be adding a molecule shape for KOffice (by reusing the existing vector shapes) and making an editor for it based on Karbon14.
User avatar TheBlackCat
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I'd say they are probably more like flowcharts than normal vector art. You connect objects (atoms) to each other using connectors (bonds). I think approaching it from that direction would be much easier.


Man is the lowest-cost, 150-pound, nonlinear, all-purpose computer system which can be mass-produced by unskilled labor.
-NASA in 1965
meyerm
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A good application as already described to manage your uncountable papers you read is a so much needed application (for me and my collegues) that I simply want to add a +1. There were some projects, but basically I guess all of them vanished. Gnome has some alternatives (gpapers and a good gtk-one, forgot the name).

Beeing able to index and sort your papers is of great help. Like "all from Mr XYZ", "all from this ABC conference", "all 2009 papers with Fortran" ;-) and so on. Don't forget your own notes/abstracts and keywords (perhaps just some tagging). Sounds like a Nepomuk/Akonadi/whatever ;) job, indeed.

Buuut never forget easy transportation or copying (export possibility for paper, tags and notes out of the proprietary databases when giving the paper to a collegue) from one computer to another. Sharing over the network creating a central chair-paper-database would also be interesting, but only when there is some rating, tagging etc. for multiple users possible (there are some KDE-users at the chair). Don't give up offline capabilities for that.

Thanks :)
User avatar TheBlackCat
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There is already a separate thread about managing papers, so feel free to look at the ideas floating around there and comment on them or propose your own: Proposal for a bibliographic system


Man is the lowest-cost, 150-pound, nonlinear, all-purpose computer system which can be mass-produced by unskilled labor.
-NASA in 1965
pereblay
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I definitely use Kile and Kbib a lot for paper preparation. I miss a general ploting/fiting program on the style of grace integrated in KDE.

Also a good timing/fourier analysis program would also we great.

I could extend my "wish list" but those above are surely of interest to many research areas.
User avatar einar
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For plotting you should take a look at LabPlot/SciDavis.


"Violence is the last refuge of the incompetent."
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