Creating your own JSON Endpoints for Bio Web Services: Basics
Currently major biological databases use the SOAP/WSDL framework to provide the web-services where communication happens through exchange of XML bits. Now in most of programming language you have SOAP/WSDL clients such as SOAP4R and Savon in Ruby, SOAPy, ZSI, SUDS, and soaplib [...]
Platform for Systems Biology and Bioinformatics: NetBeans vs Eclipse
An unbiased list of systems biology, bioinformatics and chemoinformatics applications built on top of Netbeans pltform and Eclipse RCP. In all fairness, there is no clear winner. In fact with little variations both Eclipse and Netbeans can be used for [...]
The misuse of terms 'homology' in bioinformatics community
In a recent letter to the editor of journal Bioinformatics Marabotti and Facchiano have raised the concern over the misuse of term ‘homology’ in peer-reviwed bioinformatics papers. This issues is not new for the scientific community at all, in fact [...]
Mapreduce and Hadoop Algorithms in Bioinformatics Papers
Purely inspired by Atbrox’s list of academic papers for Mapreduce & Hadoop Algorithms. Unlike computer science where applications of Mapreduce/Hadoop are very much diversified, most of published implementations in bioinformatics are still focused on the analysis and/or assembly of biological [...]
Translational bioinformatics in the cloud
There is no doubt that large scale on demand computing in cloud can be highly affordable. Right now Bioinformatics and Genomics community is really enjoying this affordability. In a latest article published in Genome Medicine the leading translational bioinformatics researcher [...]
Where Does the Time Go in a Data Mining Project?
Robert Grossman is one of the prominent thinkers in the field of big data analytics. Recently I was going through his presentation about high performance and distributed data mining, where he points out one of the dirty secrets of deploying [...]
Living in the cloud with PC-over-IP
Recently I had chance to attend the latest VMware Virtualization Seminar Series in Auckland. While I liked the entire event, I was particularly excited about the PC-over-IP (PCoIP) protocol, a remote desktop solution designed and developed by Teradici. PC-over-IP protocol [...]
A typical PhD student is like the A-team so there is no plan B
If you are PhD student and you have not yet read the latest Miller Mccune cover story about degrading prospects of science as career and more specifically why having a PhD is not enough, then better do it now. A [...]
Bloom filters for bioinformatics
The Bloom filter was originally developed by Burton H. Bloom back in the seventies and for long time it was there without any major application. Google is credited for making Bloom filter popular again. Only after the Google used Bloom [...]
