Tag Archives: Tools

Botcasting: Listening to your Journal Feeds

If you’ve worked at a lab before, you’ve no doubt noticed a certain rhythm to the day. People come in early, setup their experiments, and by 10 the experiments for the day are underway, and the scientists are working on … Continue reading

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A Pocketful of Rye

Unlike the Agatha Christie mystery referred to in the title of this piece, there are some mysteries that seem to defy a single answer.  One of those mysteries is how most scientists manage to keep up-to-date given the growing avalanche of developments in their … 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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SwissVar: Clinically Relevant Protein Variations

In a previous post, I described ClinVar, the NCBI’s database of clinically relevant protein variations.  Recently, I came across SwissProt’s version of this database called SwissVar. SwissVar is designed to help you answer two questions: What diseases is this protein involved … Continue reading

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Java 8 New Features

Last month’s release of Java 8 came with a slew of changes that are beginning to be picked up by the local informatics community. At this month’s San Diego Java User Group, John Clingan (Oracle Product Manager for Java EE and … Continue reading

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