Archive for the ‘Systems Biology’ Category
Immunoassay analysis with Eclipse RCP
Compass is an interesting bioinformatics application developed by Cell Biosciences which is built on top of Eclipse RCP. Compass is designed to perform immunoassay analysis and it allows researchers to setup, run and analyze immunoassay experiments. It can translates data into [...]
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 [...]
Which SBML tool should I choose?
Ok this is a real pain, not because people don’t have options. SBML is painful because overabundance of choice in terms of supported tools. SBML’s software guide lists over 187 tools those support SBML one way or the other. Although [...]
Interdisciplinary scientists: Identity and market crisis
This is a topic which has always eluded me, I wrote sometime back on the fine line of multidisciplinary versus interdisciplinary scientists. Recently this question was raised again by Michael Andrec at Linkedin computational biology forum. The question he raised [...]
NodeXL for visualizing biological network data in Excel and some other serious Microsoft ventures in Bioinformatics
Lately Microsoft has released few interesting add-ins for their Office products. Yesterday I wrote about a Word add-in that enables the annotation of scientific documents using bio-ontologies and controlled vocabularies. Today I learned about their latest add-in for Excel, NodeXL, [...]
The whole is more than the sum of its parts
Systems biology is supposed to revolutionise the biology by going beyond reductionism of molecular biology which has dominated biology for decades. The reductionist approach mostly relie on breaking a larger biological system down into pieces, analysing smaller pieces seperately and [...]
Science changes the world, sometimes the world changes the science, we are overdue
Dr. Monica Anderson talks about reductionism vs holism in science. She also suggests that artificial intelligence failed because intelligence is too holistic and by its nature it always attracted the hardcore reductionists. One of my favorite quote from this talk [...]
Latest Cryptogram Challenge
4th round of Cryptogram Challenge is open now, and in the latest version of cipher-based puzzle participants have to unravel the message coded into the image of a 96-well plate from a RNAi experiment. The contest will run from January [...]
The Interactorium visualization
The Interactorium is a platform developed at University of New South Wales to visualise very large interactome datasets such as one incorporating up to 40,000 proteins or 6000 multiprotein complexes, in context of 3D virtual cell. It is built on [...]
Sherlock Holmes and Proteomics
By reading the title of the post you may be curious that what remote similarity proteomics can share with Sherlock Holmes? Well not much at this moment except the complexity of storyline. An excerpt from a bit old article, interested [...]
