Tag Archives: informatics

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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KNIME and Cheminformatics: A Peek Behind The Curtain

Part of what makes user group meetings so interesting is getting the opportunity to peek behind the curtains and see someone else’s operation.  In last night’s, KNIME user group meeting, Brock Luty of Dart NeuroScience gave an interesting perspective on … 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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Assessing Credibility in Scientific Research

Over the past few years, pharmaceutical companies have come to increasingly rely external research to help fill their pipelines.  This greater reliance on academic research is not without it’s risks — chief amongst these is the lack of reproducibility. Amgen … Continue reading

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Notes from San Diego KNIME User Group Meeting

This week Brock Luty of Dart Neuroscience hosted the first San Diego KNIME User Group meeting.  Michael Berthold, one of the founders of KNIME, came down from San Francisco to deliver a briefing Mark Donnelly of XIFIN demonstrated how a … Continue reading

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Ideas from the Cytoscape Workshop

During the recent Cytoscape workshop, I started out re-acquainting myself with Cytoscape and learning about some of the new features.  As I did so, I found myself accumulating a wishlist of features that I thought I would share: Using Templates … Continue reading

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