Use jupyternotebook from knime #knime #chemoinformatics #memo

Recently I posted an example to build custom knime node with python. It was a nice experience for me. And I’m still reading knime documentation. Today I tried to use jupyter notebook from knime. There is a good example to do that with workflow and dataset. The example described avobe reads dataset and do someContinue reading “Use jupyternotebook from knime #knime #chemoinformatics #memo”

Develop new knime node with python #chemoinformatics #knime

The Golden Week is a collection of four national holidays within seven days. My kid graduated the elementary school and his favorite dodgeball team and he joined vollyball team. I quit coaching the dodgeball team at same time. So I have time for coding and drinking beer again ;) I watched knime summit about newContinue reading “Develop new knime node with python #chemoinformatics #knime”

Run Knime workflow without GUI #chemoinfo #knime #RDKit

I enjoyed knime summit last week. I could learn lots of useful features of new version of Knime (ver5). Knime is useful tool for chemoinformatics but I mainly write code with python so I’m not heavy user of knime but recently I’m interested in Knime and learning to apply it in my projects. As readerContinue reading “Run Knime workflow without GUI #chemoinfo #knime #RDKit”

Make multi target predictive model for Knime #RDKit #Knime #DeepLearning

I participated my kid’s elemenary school graduation ceremony today. It was nice ceremony. …Time pasts very fast ;) In the season in Japan is very good. Beautiful cherry blossoms start to bloom. It’s good time to start anything ;-) I would like to say thank to my kid. BTW, recently chembl ver32 was released. AsContinue reading “Make multi target predictive model for Knime #RDKit #Knime #DeepLearning”

Make chemoinformatics workflow by Kinme with user defined conda envrionment #Knime #Chemoinforamtics #memo

I think workflow tool is useful for many chemoinformatician such as Knime, Pipeline Pilot(PP) and Orange. In my knowledge, it’s difficult to use user defined conda env in PP. Of course these workflow tools provides enough components to do many tasks. But I would like to have more flexibility to build chemoinformatics pipelines. Recently IContinue reading “Make chemoinformatics workflow by Kinme with user defined conda envrionment #Knime #Chemoinforamtics #memo”

Call Knime from Jupyter notebook! #Chemoinformatics #RDKit #Knime

I read exiting blog post yesterday! URL is below. developed very cool tools which can call knime from jupyter notebook and can execute jupyter notebool from knime. Details of the tool is described in the Knime blog post. I am interested the tool and I can’t wait to try it in myself. So I usedContinue reading “Call Knime from Jupyter notebook! #Chemoinformatics #RDKit #Knime”

Make interactive plot with Knime #RDKit #Chemoinformatics #Knime

Dalia Goldman provided very cool presentation in RDKit UGM 2018 about Knime. Click to access Goldmann_KNIMEandRDKit.pdf She demonstrated interactive analysis with RDKit knime node and Javascript node. I was really interested but it was difficult to build the workflow by myself at that time. BTW, I need to learn knime for data preparation in thisContinue reading “Make interactive plot with Knime #RDKit #Chemoinformatics #Knime”

Visualize chemical space using Knime rdkit node

Usually I use python for analyse, visualize chemical space. Because, I love coding. ;-) I know, work flow tool is useful solution to do that. So, I tried to plot chemical space using Knime. Knime is one of famous work flow tool and lots of nodes are developed. I made very simple work flow toContinue reading “Visualize chemical space using Knime rdkit node”


RDKitとPythonを使ってデータを加工して Rで解析するというケースを頻繁にやっていると全部つながるといいなーと思います。 RPY2を使ってうまく繋げるのもいいですがKNIMEを使うとそれぞれの連結ができて便利かも。 ということでトライしてみました。 KNIME上のRノードでは全部Rという名前のオブジェクトに対して処理をするようで それを理解するのに時間がかかりました。 例えばPLS回帰をする場合はこんな感じです。 Rノードおのおのでplsパッケージ読み込まないと、 おいおいmvrなんて扱わないぜ。とおこられます。 で作ったのはこんな感じです。 一個はモデルを作ってモデルと実測を比較するため もう一個はモデルに当てるためのフローです。 RDKITノードでディスクリプタは簡単にとれるし、そのあとのモデリングは上のようなスニペット書いとけば後はよろしくな感じでいいので、楽できそうです。 ローカルで全部やってるからパフォーマンスが悪い、、、 まあいいか。