Comments on: KNIME - Part I: Overview

By: Yotkes

Yotkes — Tue, 09 Feb 2010 13:34:06 +0000

I am looking for outliers detector algorithm — Java open source that run on top of DB or file (CSV)
All the parameters are strings, no numeric parameters.
I need it for high volume

Anyone can please help?
Sorry if I am not at the right forum

By: Charles Bergren

Charles Bergren — Fri, 01 Jan 2010 19:07:41 +0000

In Excel, I’ve saved xls files using ‘other’ (comma delimited) formats and then used the knime file reader to import them. Works fine on the knime version I downloaded a couple of days back

By: Frank Xavier

Frank Xavier — Mon, 30 Mar 2009 16:20:19 +0000

You can use RapidMiner ( http://www.RapidMiner.com/ ), another open source data mining tool, to convert Microsoft Excel sheets, SVM^light or LibSVM files to ARFF or CSV format or into a database of your choice and then load the data into KNIME from there.

While RapidMiner is no dedicated ETL tool (Extract, Transform, Load), you can use it for that purpose as well.

And if you install RapidMiner anyway, you can also use it as an alternative or additional data mining tool. It’s downloadable for free and well worth a try.

Have fun,
Frank

By: Anand

Anand — Tue, 10 Jun 2008 05:16:51 +0000

We use knime for chemoinformatics applications.However I am interested in using the same for QSAR predictions.I am looking for a suitable material on the same.I would be thankful if anybody could provide me some resources on it.

By: Yap Chun Wei

Yap Chun Wei — Wed, 02 Apr 2008 13:39:49 +0000

Personally, I feel that KNIME has the potential to be a very good tool for QSAR. I like the GUI and the workflow is rather intuitive. Hopefully, the next major release will bring a lot of advances to this software.

By: Profnick

Profnick — Tue, 01 Apr 2008 14:49:30 +0000

Strange indeed, I was convinced that I had used .xls files on my LINUX machine at home but when I checked on my Windows machine in the office you are quite right. Maybe I had confused the Excel-like icon associated with .csv files from Excel. I only mentioned the sdf file handling capability since KNIME enables calculation of CDK descriptors from input of sdf files followed by the CDK conversion node. Regrettably KNIME has no parameter reduction routines though, as you say.

By: Yap Chun Wei

Yap Chun Wei — Mon, 31 Mar 2008 01:41:54 +0000

That is strange. I have checked KNIME again and the File Reader node is able to read ASCII files only and not native Excel files.

For output, KNIME does have an XLS writer but input is a more important criterion than output to me personally.

Yes, the ability to read SDF files directly is definitely a distinct advantage of KNIME. However, I did not highlight this as I assumed that most QSAR modellers will use their favorite descriptor calculation software to calculate the descriptors before the modelling process. Thus they will not need to read molecular files directly.

By: Profnick

Profnick — Fri, 28 Mar 2008 12:26:06 +0000

Hi,
You say “Basically, KNIME can only read data from three sources: ARFF files (which are Weka files), text-delimited files (which include csv files), and from a database” ….”The lack of support for Microsoft Excel files is no big deal since you can easily convert them to csv format using Microsoft Excel.”

In fact you don’t need to convert from Excel since the file reader node will handle Excel files and automatically detect delimiters etc. Also as far as output is concerned their is an xls writer.
From the QSAR point of view a distinct advantage of KNIME, is that it allows direct reading of .sdf files via the SDF reader node in the Chemistry/CDK plugin.