Benjamin Good recently asked about the existence of public repositories of predictive molecular signatures. From his description, he’s looking for platforms that are capable of deploying predictive models. The need for something like this is certainly not restricted to genomics – the QSAR field has been in need for this for many years. A few […]
Notes & thoughts from the IU semantics workshop
Over the last two days I attended a workshop titled Exploiting Big Data Semantics for Translational Medicine, held at Indiana University, organized by David Wild, Ying Ding, Katy Borner and Eric Gifford. The stated goals were to explore advances in translation medicine via data and semantic technologies, with a view towards possible fundable ideas and […]
HCSConnect, SOAP and images – the sordid details
Over the past few months I’ve been trying to work with the HCSConnect web service API that Cellomics provides as a means to programmatically access the Arrayscan image and data store. While the API works for getting things such as plate names, I was unable to retrieve images. After much poking and some suggestions from […]
Visual pairwise comparison of distributions
While analysing some data from a dose respons screen, run across multiple cell lines, I need to visualize summarize curve data in a pairwise fashion. Specifically, I wanted to compaure area under the curve (AUC) values for the curve fits for the same compound between every pair of cell line. Given that an AUC needs […]
Python, permission and forgiveness
This morning I was writing some Python code that needed to perform lookups on a very large map. 1234mapSize = 65000 amap = {} for i in range(0,mapSize): amap[’k%d’ % (i)] = i If a key did not exist in the map I needed to take some action. My initial effort performed a […]