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 Glassfish) gave us an update on some of the new features. You can find out […]
Java 8 New Features Read More »
During our recent San Diego Informatics Lunch program, we had a lively discussion about the possibilities that Google Glass and other wearables bring to research labs. To get the conversation started, I posted a video clip from Digital Sciences, and Imperial College London, where they had envisioned what an augmented reality might look like in
Google Glass in the Lab Read More »
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 To Export Cytoscape Sessions To HTML The new JSON export feature, looks very useful. With
Ideas from the Cytoscape Workshop Read More »
PubMed is one of those tools that everyone uses but not everyone uses it well. Usually your enthusiasm for investigating the search results will wane after the third or fourth page of results. Here are a few tips for making your searches more targeted and successful. Use MeSH Terms PubMed uses Medical Search Heading (MeSH)
Tips for Better PubMed Searches Read More »
Recently I was working on a web project, and I wanted to see how feasible it would be to build a web application that had no back end. No database, or app server, just a simple web page, some JavaScript and some data. Since I also needed to fetch data from EntrezGene, and other NCBI
Tinkering With EntrezAjax Read More »
In a previous post I wrote about how Google Docs (and the Research plugin) can be used for writing journal articles. There were two shortcomings to this approach: Google Docs doesn’t support end notes (only footnotes) The Research plugin supports only a limited number of citation styles Recently, I was contacted by the folks at
Tinkering with Paperpile Read More »
There is a belief among certain peoples in the world, that knowing the true name of a thing gives one some degree of power over it. One of the challenges for anyone writing software in a scientific setting, is figuring out the true (and sometimes unintentionally hidden) names of things. Imagine for a moment that
The Secret Names of Things Read More »
Recently, I was working on a UniProt parser for the next BioGroovy release, and while looking through the UniProt schema I started to wonder why the elements in schemas weren’t annotated with references to ontologies? Let’s take a look at an example. A typical UniProt record contains many “reference” elements like this: <reference key=”2″> <citation
Adding Semantics to XML Schemas Read More »
The advent of cloud-based office suites like Google Docs, have changed the collaborative process of research writing. Google Docs allows you and your collaborators to work on the same document at the same time. No more sending versions of a document back and forth as each person works on a particular section, followed by a
Writing Research Papers, Presentations and Blogs With Google Docs Read More »
One of the key pieces of the drug discovery puzzle involves determining the clinical relevance of the target. Over the past few years big pharma have been pulling back from this critical part of the drug discovery process and ceding this territory to biotech startups and academia. Until recently, the only major database that could
ClinVar – A database of mutations and their clinical relevance Read More »
