Tom is a biomedical engineer by training, working as a back-end developer at CytoSMART and board member of CytoData. He is intrested in data science and drug discovery.
I got a helpful email from Ron van Weverwijk pointing out that constructing a Cypher query every time does not give the best performance. I didn’t know at the time that this would also solve another problem. The problem is the Neo4j desktop app crashing after approximately 1500 requests.In a... read more
PubChem is a database with millions of chemical compounds. All these can be downloaded and put into your graph database as a basis for your project.I downloaded 197M synonyms related to 57M compounds for the Open Measurement project.Open MeasurementThis project is being built as part of... read more
Combining PubChem and Neo4j even furtherIn my last blog, I downloaded 197M nodes of all the chemical synonyms out of PubChem. This number was of course too low to cover every chemical synonym ever used.I do want to connect the compounds from NCI (National Cancer Institute, USA) to the... read more
Recommendation algorithms are often written with a user-product relationship in mind. “Which user bought what product” or “Who liked this movie”. From this data, a prediction is made about an unknown user-product relation. However, this same algorithm can predict reactions... read more
The open measurement graph will be used to find connections between different measurements in different experiments and conditions. In a previous blog, we added chemical compounds — and their synonyms — from PubChem into the graph. In this blog, we are going to... read more
Do you ever wonder what licenses you need for your Python project? Me too! So I made a tool to figure it out.In short, every package has its license, but so do it’s dependencies and those dependencies’ dependencies. Creating a graph of dependencies is where Neo4j comes... read more
2:30 PM (Pacific Time) March 22, 2016. NPM packages broke for a few hours because Left-pad was unpublished. This showed us, as developers, that sometimes one person holds the power to break a lot. All because Left-pad was popular, but Left-pad was also used in other popular packages that were used... read more