Tag Archives: bioinformatics

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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Tinkering With BioGroovy 1.1

Since the initial release of BioGroovy, a lot has changed, and the library has continued to grow substantially. With the recent BioGroovy 1.1 release, I thought I would review some of the changes, and update the information on how you … Continue reading

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Network of BioThings Hackathon #2

This weekend’s Network of BioThings hackathon (#hackNoB) was a great success with some really innovative projects making great strides in a short amount of time. The event was hosted by the Jeff Grethe of the Neuroscience Information Framework group at … Continue reading

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JavaScript Libraries for Informatics

During our monthly San Diego Informatics Lunch meeting, the topic of conversation was JavaScript libraries for informatics.  Over the past few years the term “thick client application” has gradually morphed from a reference to desktop applications, to JavaScript-heavy browser-based applications.  Driven in … Continue reading

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SwissModel: It’s not what you think

One of the things that I’m always curious about, is the effect of a sequence variation on the conformation of a target.  Recently I wrote about ClinVar and SwissVar, two tools for examining variants and their associations with disease.  Since … Continue reading

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Reproducibility and Provenance

One of the key problems with reproducibility in scientific research is understanding and preserving the provenance of the data, and any digital methods used to turn raw data into actionable information. The following paper recently appeared in PLoS Computational Biology … Continue reading

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ClinVar: Clinically Relevant Gene Variations

ClinVar, NCBI’s database of clinically relevant gene variations, has continued to grow since my earlier post, so I thought I would revisit the subject and show you some of the features that it has. To get started, visit the ClinVar … Continue reading

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