Where can I find/share user-contributed nodes?

Hi there,

I am new to KNIME, but I am absolutely thrilled by its possibilities! But before I start implementing stuff myself, is there a facility where I can look if anybody has had my problem before (and hopefully solved it)?

Also, if I start producing nodes, I would like to share them... I've looked around the webpage and the forum a bit, but couldn't find any repository for user contributed code...



Hi Sebastian,

so far there is a possibility to check for KNIME user contributions under

In the next version of our website (currently in work) there might be a possiblity for the community to exchange KNIME nodes - without any warranty, of course :wink: Stay tuned 8)

Just for personal interest: what do you miss?



For instance a node that takes a table of molecules and a SMARTS pattern and creates a new column holding '1' for each molecule in which the pattern matches and '0' otherwise. This could be done using JOElib...

Also a node that loops through all sd-files in a given directory would be great.

Another great thing would be if the functionality of MATLAB could somehow be accessed.

There are many things I could think of, but these are the most urgent...

As far as I know none of these nodes are anywhere available.
But if you are used to MATLAB you may want to try our R integration (which could be downloaded under "download/extensions". As far as I remember from my studies it was not a big deal to get from MATLAB to R, regarding the syntax not the functionality, of course.



Concerning MATLAB vs. R:

It's true what you say: MATLAB and R are very similar. But I have a lot of code already implemented in MATLAB and would like to avoid having to port it all.

This has historical reasons, the group where I do my PhD is a "MATLAB-Group". When I started there, I just accepted it. At the time I wasn't really aware about the implication of using a closed language...

But it shouldn't be too difficult to get MATLAB functionality in KNIME, since MATLAB is Java based. With a little bit of help from the KNIME-developers, I would be happy to implement and contribute such nodes...

Well, this just reminds me... There is a possibility to use external tools:
which gives you the possibility to start an external tool and pass the data via a csv file to the external tool and get it back the same way. Note: use this node on your own risk :wink:
Maybe this is the fastest but certainly not best method to get your MATLAB functionality into KNIME. Nevertheless we would very much appreciate a proper KNIME-MATLAB integration.



The THINK software fingerprint node gives either a hex string or a series of columns populated by 0s or 1s depending upon the presence or absence of a set of functional groups (defined using extended SMILES). You can find a video demo of the 2D nodes at http://www.treweren.com/knime.htm

You can change the list of functional groups defined in the file key.smi - but as these are used for similarity searches as well then you would be wise not to share your edited version with any other users accessing the same installation of the software.

For academic use/evaluations there is no charge for using the software. The current release has a couple of obscure compatibility problems with 1.3.3 (works fine with 1.3.2).

I don't know if TRIPOS have exposed their fingerprinting functionality in their nodes.

In principle a SMARTS matcher node is quite easy to implement. The problem is, that SMARTS processing is only available in the latest development code of CDK. I'm pretty sure, we won't release an updated CDK plugin (including a SMARTS node) before the next version of CDK is officially released, as this will also require quite some changes in the existing KNIME nodes because of CDK API changes.


Hi Thorsten,

I have been using CDK outside KNIME quite intensively. SMARTS matching was always a problem. Back then I resorted to including the .jars of JOElib for the SMARTS matcher. Maybe this is also the most promising solution here...


Hi Sebastian,

I have been using Joelib for about 2 years before I started using KNIME last year. In order to use existing code, it was necessary for me to write my own reader nodes that utilise the new molecule type I have written which is based on the JOEMol class. This works perfectly and I have written other nodes to use the JOEMol class as normal.

I don't have any nodes that have the functionality that you require but I think it would be very easy to implement it. I am happy to share the reader nodes (mol/sdf/smi/mol2 and one for rxn/rdf). You should then be able to write your node with the SMARTS matching.

Let us know what you think about this?


Hi Hina, that sounds great!

Is there a URL where I can download your nodes? Anyway, I will send you my Email via PM, then we can get in contact.


Hi Sebastian,

I'm going to share the nodes via SourceForge using the Nodes4knime project.

I will let you know once they are on there.


Hi all,

Just tried using the Substructure Search node instead of trying a smarts matcher… I tried specifying isotopes in the substructures but these seem not to match is it a feature or am i doing something wrong.