Category Archives: Informatics

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

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

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Fetching Data With BioGroovy

With BioGroovy 1.1 we’ve added support for fetching data from a variety of RESTful webservices, including: EntrezGene, PubMed, UniProt and many others. Fetching Data In this example, we’ll fetch gene information from EntrezGene for 3 genes, and output the result … Continue reading

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BioGroovy and Web Service Identity

With the recent release of BioGroovy 1.1, we added support for a number of web services. Web service providers like NCBI’s eUtils, EntrezAjax and JournalTOCs have requirements for tracking usage of their services.  In some cases, a token must be … Continue reading

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Google Docs for Scientists

Science is inherently a collaborative effort, and at least once a month I encounter someone who mentions in passing some trial or tribulation they had when sharing documents.  The story usually goes like this… We were working on a presentation/paper … Continue reading

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