Recently, I found myself putting together a presentation on BioGroovy. One of the key features that I’ve been taking advantage of is the ability to use BioGroovy models as Grails domain objects. This makes it possible to easily download and persist Genes, Proteins, and PubMed articles into a relational database. However, I always ask myself […]
BioGroovy and the Semantic Web Read More »
Several years ago a friend of mine introduced me to mindmaps as a tool for helping people visualize and link concepts (see below). The Online Mendelian Inheritance In Man (OMIM) database, created by Johns Hopkins University contains information on the genetic origins of diseases. It gives scientists a good overview of a disease and often
MindMapping OMIM Files with BioGroovy Read More »
As many Perl programmers know CPAN (the Comprehensive Perl Archive Network) is an invaluable repository for Perl modules. You can easily download and install a module and add its functionality to your script. In order for scripting languages like Groovy to gain some traction with the bioinformatics crowd there needs to be a similar repository
BioGroovy and Grapes Read More »
As part of the series of blog entries on BioGroovy, I thought I’d start with some rather simple tasks using some of the functionality found in NCBI’s eUtils API. NCBI has both RESTful and SOAP APIs that you can use. But in the interests of keeping this simple, I’m going to stick with the REST
BioGroovy: Fetching PubMed Data Read More »
Groovy is a powerful scripting language that allows you to leverage a large number of Java libraries. This series of articles describes how you can combine Groovy with bioinformatics-related libraries to solve a variety of problems. Traditionally, Perl has been seen as the language of choice for bioinformaticians. More recently, Python has been gaining ground.
I’ve blogged before about how scientists can use social media like Mendeley, Twitter and Google Reader to share information. Since social media is all about sharing, how can we make the act of sharing information easier? Recently, a colleague of mine tweeted that she wished it were easier for her to send links to useful
Social Media for Scientists: It’s All About Sharing Read More »
I’ve been a long-time user of the FireFox browser and the BioBar plugin from EBI. When I switched to Google’s Chrome browser, one of the things I immediately missed were BioBar’s search plugins.Recently I stumbled across a feature in Chrome that allows you to search sites like Wikipedia, and to add your own search plugins.
Searching PubMed, Entrez Gene & OMIM with Google Chrome Read More »
Grails’ ease-of-use makes it an ideal framework for rapid application development. In most businesses governed by the simple Time = Money equation, the ability to quickly create a fully functional web application that can be deployed on the Java platform is a no-brainer, even for the non-technical set. However, in the biotech and pharmaceutical industries
Grails In An Assay Development Setting Read More »
A few years ago, a medical writer friend of mine showed me a paper on a new tool called Cytoscape. He said, “see what you think of it, and let me know.” At the time we were both working on a project called Genome5000, to knockout the 5000 most druggable genes in the human genome. Any time
Free Software For Scientists – Cytoscape Read More »
One of the challenges of working in an industry that moves at the speed of light is keeping up with all of the changes. I mentioned to a several friends of mine that I’m a heavy user of Google Reader and we decided to form a Journal Club. A Journal Club is a way for
Creating a Journal Club With Google Reader Read More »
