Author Archives: aspenbio

About aspenbio

I write software for scientists. I'm interested in Java/Groovy/Grails, the Semantic Web and Cancer Biology.

PubMed vs EuropePMC: Let’s Get Ready To Rumble

PubMed For most researchers, PubMed is the go-to resource for all biomedical literature. But from a programmatic standpoint it has some real challenges that make it difficult to integrate into many informatics applications.  Let’s take a look at a typical … Continue reading

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A New Year, A New Site, A New Service

It’s the start of a new year, and nothing says New Year like a website refresh. With the rise in the number of visitors to the site using mobile browsers, we’ve updated the site to make it more mobile friendly. … Continue reading

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Drug Target Identification: And then a miracle occurs

At the front end of most drug discovery programs lies a step called Target Identification, and a few months ago I sat down with a colleague to discuss their approach to target identification.  In particular, “how do you characterize a target”? … Continue reading

Posted in Bioinformatics, Cancer Research, Drug Development, Informatics, pancreatic cancer, Science Blogging | Leave a comment

Exchanging Drug Pipeline Data

The pharmaceutical R&D environment has always been collaborative in nature — never moreso today. Key to the success of those collaborations is the ability to share information about drug R&D programs with a wide variety of potential partners and investors. Traditionally … Continue reading

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Parsing Data Files With BioGroovy

In a previous post we showed how you can use BioGroovy to download a data file from a webservice.  In this post, we’ll show you how to parse the file that you’ve downloaded. After handling all of the imports (shown in … Continue reading

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Fetching Data Files With BioGroovy

It’s often useful to fetch data from a web service and cache it in your local directory. This cuts down on the amount of traffic between your machine and the web service you’re invoking, and it makes unit testing your … Continue reading

Posted in Bioinformatics, Informatics | Tagged | 2 Comments

Groovy vs Python

At a recent Informatics Lunch meeting, surrounded by a host of dedicated Python users I confessed to being somewhat ignorant of the business drivers behind using Python in a bioinformatics setting. Although, I have used Python on occasion, it was usually … Continue reading

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