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. Not only is it more easily viewable on smartphones and tablets, but you can add […]
A New Year, A New Site, A New Service Read More »
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”? I was surprised at how much that process can vary from company to company. As
Drug Target Identification: And then a miracle occurs Read More »
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 code easier. In this example, we’ll fetch data for 3 genes and write it out
Fetching Data Files With BioGroovy Read More »
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 to the console. import org.biogroovy.io.eutils.EntrezGeneSlurper; import org.biogroovy.models.Gene; @Grab(group=’org.biogroovy’, module=’biogroovy’, version=’1.1′) EntrezGeneSlurper slurper = new EntrezGeneSlurper();
Fetching Data With BioGroovy Read More »
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 passed along with each request that identifies the tool making the request, or a specific
BioGroovy and Web Service Identity Read More »
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 can get started using BioGroovy. Here’s a brief list of some of the changes: Support
Tinkering With BioGroovy 1.1 Read More »
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 UCSD, and organized by Ben Good (Su Lab @ TSRI), Dexter Pratt (NDEx project) with
Network of BioThings Hackathon #2 Read More »
In my previous post, I talked about the current state of the Grails platform and what it brings to the Research Informatics environment. In this post, I’ll discuss some of the features in the upcoming Grails 3 release, and the potential impact of those features on Research Informatics organizations.
What Grails 3 Brings To The Research Informatics Lab Read More »
During our last San Diego Informatics Forum lunch meeting, we had an interesting discussion about the JavaScript frameworks that we use. During the course of the discussion, we drifted into the topic of the development stacks that we use — these include everything from Spring Web (or Spring Roo), to Django, Torque/Turbine, Rails and Grails
Why Grails Makes Sense in Research Informatics Read More »
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 fields. The answers I get are wide and varied, but I thought I would share a
A Pocketful of Rye Read More »
